@article{chen_genetic_2011,
	title = {Genetic influences on cortical regionalization in the human brain},
	volume = {72},
	issn = {1097-4199 (Electronic) 0896-6273 (Linking)},
	shorttitle = {Genetic influences on cortical regionalization in the human brain},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/22099457},
	doi = {10.1016/j.neuron.2011.08.021},
	abstract = {Animal data demonstrate that the development of distinct cortical areas is influenced by genes that exhibit highly regionalized expression patterns. In this paper, we show genetic patterning of cortical surface area derived from {MRI} data from 406 adult human twins. We mapped genetic correlations of areal expansion between selected seed regions and all other cortical locations, with the selection of seed points based on results from animal studies. "Marching seeds" and a data-driven, hypothesis-free, fuzzy-clustering approach provided convergent validation. The results reveal strong anterior-to-posterior graded, bilaterally symmetric patterns of regionalization, largely consistent with patterns previously reported in nonhuman mammalian models. Broad similarities in genetic patterning between rodents and humans might suggest a conservation of cortical patterning mechanisms, whereas dissimilarities might reflect the functionalities most essential to each species.},
	number = {4},
	journal = {Neuron},
	author = {Chen, C. H. and Panizzon, M. S. and Eyler, L. T. and Jernigan, T. L. and Thompson, W. and Fennema-Notestine, C. and Jak, A. J. and Neale, M. C. and Franz, C. E. and Hamza, S. and Lyons, M. J. and Grant, M. D. and Fischl, B. and Seidman, L. J. and Tsuang, M. T. and Kremen, W. S. and Dale, A. M.},
	month = nov,
	year = {2011},
	keywords = {Animals, Brain/anatomy \& histology/*physiology, Brain Mapping/methods, Cerebral Cortex/*anatomy \& histology/*physiology, Gene Expression Regulation, Developmental/*physiology, Humans, Magnetic Resonance Imaging/methods, Male, Mice, Middle Aged, Twins/*genetics},
	pages = {537--44},
	annote = {Chen, Chi-{HuaPanizzon}, Matthew {SEyler}, Lisa {TJernigan}, Terry {LThompson}, {WesFennema}-Notestine, {ChristineJak}, Amy {JNeale}, Michael {CFranz}, Carol {EHamza}, {SamarLyons}, Michael {JGrant}, Michael {DFischl}, {BruceSeidman}, Larry {JTsuang}, Ming {TKremen}, William {SDale}, Anders Meng1R01NS070963/{NS}/{NINDS} {NIH} {HHS}/1R21NS072652-01/{NS}/{NINDS} {NIH} {HHS}/{AG}018384/{AG}/{NIA} {NIH} {HHS}/{AG}018386/{AG}/{NIA} {NIH} {HHS}/{AG}022381/{AG}/{NIA} {NIH} {HHS}/{AG}022982/{AG}/{NIA} {NIH} {HHS}/{AG}031224/{AG}/{NIA} {NIH} {HHS}/{DA}029475/{DA}/{NIDA} {NIH} {HHS}/{EB}006758/{EB}/{NIBIB} {NIH} {HHS}/{NS}052585-01/{NS}/{NINDS} {NIH} {HHS}/{NS}056883/{NS}/{NINDS} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 {AG}018384-10/{AG}/{NIA} {NIH} {HHS}/R01 {AG}018386/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022381/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022381-01/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022381-10/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022982/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022982-04/{AG}/{NIA} {NIH} {HHS}/R01 {EB}006758/{EB}/{NIBIB} {NIH} {HHS}/R01 {EB}006758-01A1/{EB}/{NIBIB} {NIH} {HHS}/R01 {NS}052585-01A1/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}070963/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}070963-01A1/{NS}/{NINDS} {NIH} {HHS}/R21 {NS}072652/{NS}/{NINDS} {NIH} {HHS}/R21 {NS}072652-01/{NS}/{NINDS} {NIH} {HHS}/{RC}1 {AT}005728-01/{AT}/{NCCAM} {NIH} {HHS}/S10 {RR}019307-01/{RR}/{NCRR} {NIH} {HHS}/S10 {RR}023401/{RR}/{NCRR} {NIH} {HHS}/S10 {RR}023401-01A2/{RR}/{NCRR} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/Comparative {StudyResearch} Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov'{tResearch} Support, U.S. Gov't, Non-P.H.S.Twin Study2011/11/22 06:00Neuron. 2011 Nov 17;72(4):537-44. doi: 10.1016/j.neuron.2011.08.021.},
	file = {Chen-2011-Genetic influences on cortical regio:/autofs/cluster/freesurfer/zotero/storage/39N7GIGU/Chen-2011-Genetic influences on cortical regio.pdf:application/pdf}
}

@article{fischl_freesurfer_2012,
	title = {{FreeSurfer}},
	volume = {62},
	issn = {1095-9572 (Electronic) 1053-8119 (Linking)},
	shorttitle = {{FreeSurfer}},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3685476/},
	doi = {10.1016/j.neuroimage.2012.01.021},
	abstract = {{FreeSurfer} is a suite of tools for the analysis of neuroimaging data that provides an array of algorithms to quantify the functional, connectional and structural properties of the human brain. It has evolved from a package primarily aimed at generating surface representations of the cerebral cortex into one that automatically creates models of most macroscopically visible structures in the human brain given any reasonable T1-weighted input image. It is freely available, runs on a wide variety of hardware and software platforms, and is open source.},
	number = {2},
	journal = {Neuroimage},
	author = {Fischl, B.},
	month = aug,
	year = {2012},
	keywords = {*Algorithms, Brain/anatomy \& histology, Brain Mapping/*history/methods, History, 20th Century, History, 21st Century, Humans, Image Processing, Computer-Assisted/*history/methods, Magnetic Resonance Imaging/*history/methods, Software/*history},
	pages = {774--81},
	annote = {Fischl, Bruceeng1R01NS070963/{NS}/{NINDS} {NIH} {HHS}/1R21NS072652-01/{NS}/{NINDS} {NIH} {HHS}/1S10RR019307/{RR}/{NCRR} {NIH} {HHS}/1S10RR023043/{RR}/{NCRR} {NIH} {HHS}/1S10RR023401/{RR}/{NCRR} {NIH} {HHS}/{AG}022381/{AG}/{NIA} {NIH} {HHS}/P41 {RR}006009/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075/{RR}/{NCRR} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 {EB}006758/{EB}/{NIBIB} {NIH} {HHS}/R01 {NS}052585/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}052585-01/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}070963/{NS}/{NINDS} {NIH} {HHS}/R01 {RR}016594/{RR}/{NCRR} {NIH} {HHS}/R01EB006758/{EB}/{NIBIB} {NIH} {HHS}/R21 {NS}072652/{NS}/{NINDS} {NIH} {HHS}/{RC}1AT005728-01/{AT}/{NCCAM} {NIH} {HHS}/S10 {RR}019307/{RR}/{NCRR} {NIH} {HHS}/S10 {RR}023401/{RR}/{NCRR} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/U54 {EB}005149/{EB}/{NIBIB} {NIH} {HHS}/Historical {ArticleResearch} Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov'{tReview}2012/01/18 06:00Neuroimage. 2012 Aug 15;62(2):774-81. doi: 10.1016/j.neuroimage.2012.01.021. Epub 2012 Jan 10.},
	file = {Fischl-2012-FreeSurfer:/autofs/cluster/freesurfer/zotero/storage/EAH38REZ/Fischl-2012-FreeSurfer.pdf:application/pdf;PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/5NNVNE9M/Fischl - 2012 - FreeSurfer.pdf:application/pdf}
}

@article{van_der_kouwe_brain_2008,
	title = {Brain morphometry with multiecho {MPRAGE}},
	volume = {40},
	issn = {1053-8119 (Print) 1053-8119 (Linking)},
	shorttitle = {Brain morphometry with multiecho {MPRAGE}},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/18242102},
	doi = {10.1016/j.neuroimage.2007.12.025},
	abstract = {In brain morphometry studies using magnetic resonance imaging, several scans with a range of contrasts are often collected. The images may be locally distorted due to imperfect shimming in regions where magnetic susceptibility changes rapidly, and all scans may not be distorted in the same way. In multispectral studies it is critical that the edges of structures align precisely across all contrasts. The {MPRAGE} ({MPR}) sequence has excellent contrast properties for cortical segmentation, while multiecho {FLASH} ({MEF}) provides better contrast for segmentation of subcortical structures. Here, a multiecho version of the {MPRAGE} ({MEMPR}) is evaluated using {SIENA} and {FreeSurfer}. The higher bandwidth of the {MEMPR} results in reduced distortions that match those of the {MEF} while the {SNR} is recovered by combining the echoes. Accurate automatic identification of cortex and thickness estimation is frustrated by the presence of dura adjacent to regions such as the entorhinal cortex. In the typical {MPRAGE} protocol, dura and cortex are approximately isointense. However, dura has substantially smaller T2* than cortex. This information is represented in the multiple echoes of the {MEMPR}. An algorithm is described for correcting cortical thickness using T2*. It is shown that with {MEMPR}, {SIENA} generates more reliable percentage brain volume changes and {FreeSurfer} generates more reliable cortical models. The regions where cortical thickness is affected by dura are shown. {MEMPR} did not substantially improve subcortical segmentations. Since acquisition time is the same for {MEMPR} as for {MPRAGE}, and it has better distortion properties and additional T2* information, {MEMPR} is recommended for morphometry studies.},
	number = {2},
	journal = {Neuroimage},
	author = {van der Kouwe, A. J. and Benner, T. and Salat, D. H. and Fischl, B.},
	month = apr,
	year = {2008},
	keywords = {Adult, Brain/*anatomy \& histology, Cerebral Cortex/anatomy \& histology, Female, fs\_Misc-methodology, Humans, *Magnetic Resonance Imaging/methods, Male},
	pages = {559--69},
	annote = {van der Kouwe, Andre J {WBenner}, {ThomasSalat}, David {HFischl}, {BruceengBIRN}002/{PHS} {HHS}/P41 {RR}014075/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-075751/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-075752/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-075753/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-086765/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-086766/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-086767/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-098601/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-098602/{RR}/{NCRR} {NIH} {HHS}/P41-{RR}-14075/{RR}/{NCRR} {NIH} {HHS}/R01 {EB}001550-01/{EB}/{NIBIB} {NIH} {HHS}/R01 {EB}001550-02/{EB}/{NIBIB} {NIH} {HHS}/R01 {EB}001550-03/{EB}/{NIBIB} {NIH} {HHS}/R01 {EB}001550-04/{EB}/{NIBIB} {NIH} {HHS}/R01 {EB}006758/{EB}/{NIBIB} {NIH} {HHS}/R01 {EB}006758-01A1/{EB}/{NIBIB} {NIH} {HHS}/R01 {NS}052585/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}052585-01A1/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}052585-02/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}052585-02S1/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}052585-03/{NS}/{NINDS} {NIH} {HHS}/R01 {RR}016594/{RR}/{NCRR} {NIH} {HHS}/R01 {RR}016594-01A1/{RR}/{NCRR} {NIH} {HHS}/R01 {RR}016594-02/{RR}/{NCRR} {NIH} {HHS}/R01 {RR}016594-03/{RR}/{NCRR} {NIH} {HHS}/R01 {RR}016594-04/{RR}/{NCRR} {NIH} {HHS}/R01-{EB}001550/{EB}/{NIBIB} {NIH} {HHS}/R01-{EB}006758/{EB}/{NIBIB} {NIH} {HHS}/R01-{NS}052585-01/{NS}/{NINDS} {NIH} {HHS}/R01-{RR}16594-01A1/{RR}/{NCRR} {NIH} {HHS}/R21 {EB}002530-01/{EB}/{NIBIB} {NIH} {HHS}/R21 {EB}002530-02/{EB}/{NIBIB} {NIH} {HHS}/R21-{EB}02530/{EB}/{NIBIB} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/U24 {RR}021382-01/{RR}/{NCRR} {NIH} {HHS}/U24 {RR}021382-02/{RR}/{NCRR} {NIH} {HHS}/U24 {RR}021382-03/{RR}/{NCRR} {NIH} {HHS}/U24 {RR}021382-037970/{RR}/{NCRR} {NIH} {HHS}/U24 {RR}021382-037971/{RR}/{NCRR} {NIH} {HHS}/U24 {RR}021382-04/{RR}/{NCRR} {NIH} {HHS}/U24 {RR}021382-047975/{RR}/{NCRR} {NIH} {HHS}/U24 {RR}021382-047976/{RR}/{NCRR} {NIH} {HHS}/U24-{RR}021382/{RR}/{NCRR} {NIH} {HHS}/U54 {EB}005149/{EB}/{NIBIB} {NIH} {HHS}/U54 {EB}005149-01/{EB}/{NIBIB} {NIH} {HHS}/U54 {EB}005149-010006/{EB}/{NIBIB} {NIH} {HHS}/U54 {EB}005149-010019/{EB}/{NIBIB} {NIH} {HHS}/U54 {EB}005149-02/{EB}/{NIBIB} {NIH} {HHS}/U54 {EB}005149-020006/{EB}/{NIBIB} {NIH} {HHS}/U54 {EB}005149-029001/{EB}/{NIBIB} {NIH} {HHS}/U54 {EB}005149-03/{EB}/{NIBIB} {NIH} {HHS}/U54 {EB}005149-030006/{EB}/{NIBIB} {NIH} {HHS}/U54 {EB}005149-039001/{EB}/{NIBIB} {NIH} {HHS}/U54 {EB}005149-04/{EB}/{NIBIB} {NIH} {HHS}/U54 {EB}005149-040006/{EB}/{NIBIB} {NIH} {HHS}/U54 {EB}005149-049001/{EB}/{NIBIB} {NIH} {HHS}/U54 {EB}005149-04S1/{EB}/{NIBIB} {NIH} {HHS}/U54-{EB}005149/{EB}/{NIBIB} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov't2008/02/05 09:00Neuroimage. 2008 Apr 1;40(2):559-69. doi: 10.1016/j.neuroimage.2007.12.025. Epub 2008 Feb 1.},
	file = {van der Kouwe-2008-Brain morphometry with mult:/autofs/cluster/freesurfer/zotero/storage/4RUW4FIF/van der Kouwe-2008-Brain morphometry with mult.pdf:application/pdf}
}

@article{tertel_probing_2011,
	title = {Probing Brain Connectivity by Combined Analysis of Diffusion {MRI} Tractography and Electrocorticography},
	volume = {41},
	issn = {0010-4825},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3085041/},
	doi = {10.1016/j.compbiomed.2010.11.004},
	abstract = {Electrocorticography ({ECoG}) allows for measurement of task-related local field potentials directly from cortex in neurosurgical patients. Diffusion tensor imaging ({DTI}) tractography is an {MRI} technique that allows for reconstruction of brain white matter tracts, which can be used to infer structural connectivity. This paper reports a novel merger of these two modalities. A processing stream is described in which fiber tracts near intracranial macroelectrodes showing task-related functional responses are isolated to explore structural networks related to working memory maintenance. Results show {ECoG}-constrained tractography is useful for revealing structural connectivity patterns related to spatially- and temporally-specific functional responses.},
	number = {12},
	urldate = {2014-08-25},
	journal = {Computers in biology and medicine},
	author = {Tertel, Kathrin and Tandon, Nitin and Ellmore, Timothy M.},
	month = dec,
	year = {2011},
	pmid = {21129738},
	pmcid = {PMC3085041},
	keywords = {Adult, Brain Mapping/*methods, Brain/*physiology, Diagnostic Techniques, Neurological, Diffusion Tensor Imaging/*methods, Electrodiagnosis/*methods, Humans, Male, Neural Pathways/*physiology},
	pages = {1092--1099},
	annote = {Tertel, {KathrinTandon}, {NitinEllmore}, Timothy {MengR}01 {DA}026452-01A1/{DA}/{NIDA} {NIH} {HHS}/R01 {DA}026452-02/{DA}/{NIDA} {NIH} {HHS}/R01 {DA}026452-03/{DA}/{NIDA} {NIH} {HHS}/R01DA026452/{DA}/{NIDA} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov't2010/12/07 06:00Comput Biol Med. 2011 Dec;41(12):1092-9. doi: 10.1016/j.compbiomed.2010.11.004. Epub 2010 Dec 3.},
	file = {PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/WMUI78QZ/Tertel et al. - 2011 - Probing Brain Connectivity by Combined Analysis of.pdf:application/pdf;Tertel-2011-Probing brain connectivity by com1:/autofs/cluster/freesurfer/zotero/storage/7EXUVRKA/Tertel-2011-Probing brain connectivity by com1.pdf:application/pdf}
}

@article{juranek_anomalous_2010,
	title = {Anomalous development of brain structure and function in spina bifida myelomeningocele},
	volume = {16},
	issn = {1940-5510},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2917986/},
	doi = {10.1002/ddrr.88},
	abstract = {Spina bifida myelomeningocele ({SBM}) is a specific type of neural tube defect whereby the open neural tube at the level of the spinal cord alters brain development during early stages of gestation. Some structural anomalies are virtually unique to individuals with {SBM}, including a complex pattern of cerebellar dysplasia known as the Chiari {II} malformation. Other structural anomalies are not necessarily unique to {SBM}, including altered development of the corpus callosum and posterior fossa. Within {SBM}, tremendous heterogeneity is reflected in the degree to which brain structures are atypical in qualitative appearance and quantitative measures of morphometry. Hallmark structural features of {SBM} include overall reductions in posterior fossa and cerebellum appearance, size, and volume. Studies of the corpus callosum have shown complex patterns of agenesis or hypoplasia along its rostral-caudal axis, with rostrum and splenium regions particularly susceptible to agenesis. Studies of cortical regions have demonstrated complex patterns of thickening, thinning, and gyrification. Diffusion tensor imaging studies have reported compromised integrity of some specific white matter pathways. Given equally complex ocular motor, motor, and cognitive phenotypes consisting of relative strengths and weaknesses that seem to align with altered structural development, studies of {SBM} provide new insights to our current understanding of brain structure-function associations.},
	number = {1},
	urldate = {2014-08-24},
	journal = {Developmental disabilities research reviews},
	author = {Juranek, Jenifer and Salman, Michael S.},
	year = {2010},
	pmid = {20419768},
	pmcid = {PMC2917986},
	pages = {23--30},
	file = {PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/NWPHJN65/Juranek and Salman - 2010 - Anomalous development of brain structure and funct.pdf:application/pdf}
}

@inproceedings{reuter_placement_2013,
	title = {Placement in Scanner Causes Significant Diagnostic Errors in Brain Tumors Treatment Assessment},
	author = {Reuter, O.; Gerstner, E.; Fischl, B., M.; Rapalino},
	month = jun,
	year = {2013}
}

@article{fjell_cognitive_2007,
	title = {Cognitive function, P3a/P3b brain potentials, and cortical thickness in aging},
	volume = {28},
	issn = {10659471, 10970193},
	url = {http://onlinelibrary.wiley.com/enhanced/doi/10.1002/hbm.20335/},
	doi = {10.1002/hbm.20335},
	language = {en},
	number = {11},
	urldate = {2014-08-23},
	journal = {Human Brain Mapping},
	author = {Fjell, Anders M. and Walhovd, Kristine B. and Fischl, Bruce and Reinvang, Ivar},
	month = nov,
	year = {2007},
	pages = {1098--1116},
	file = {Cognitive function, P3a/P3b brain potentials, and cortical thickness in aging - Fjell - 2007 - Human Brain Mapping - Wiley Online Library:/autofs/cluster/freesurfer/zotero/storage/GHG7IBSH/hbm.html:text/html}
}

@article{kirk_regionally_2009,
	title = {Regionally Specific Cortical Thinning in Children with Sickle Cell Disease},
	volume = {19},
	issn = {1047-3211, 1460-2199},
	url = {http://cercor.oxfordjournals.org/content/19/7/1549},
	doi = {10.1093/cercor/bhn193},
	abstract = {Sickle cell disease ({SCD}) is a chronic disease with a significant rate of neurological complications in the first decade of life. In this retrospective study, cortical thickness was examined in children with {SCD} who had no detectable abnormalities on conventional magnetic resonance imaging/magnetic resonance angiography. Regional differences in cortical thickness from {SCD} were explored using age-matched healthy controls as comparison. A comparison analysis was done for {SCD} (n = 28) and controls (n = 29) based on age (5–11; 12–21 years), due to the age-dependent variation in cortex maturation. Distinct regions of thinning were found in {SCD} patients in both age groups. The number, spatial extent, and significance (P {\textless} 0.001) of these areas of thinning were increased in the older {SCD} group. Regions of interest ({ROIs}) were defined on the areas of highly significant thinning in the older group and then mapped onto the younger cohort; a multiparametric linear regression analysis of the {ROI} data demonstrated significant (P {\textless} 0.001) cortical thinning in {SCD} subjects, with the largest regions of thinning in the precuneus and the posterior cingulate. The regionally specific differences suggest that cortical thickness may serve as a marker for silent insults in {SCD} and hence may be a useful tool for identifying {SCD} patients at risk for neurological sequelae.},
	language = {en},
	number = {7},
	urldate = {2014-08-23},
	journal = {Cerebral Cortex},
	author = {Kirk, Gregory R. and Haynes, M. Ryan and Palasis, Susan and Brown, Clark and Burns, Thomas G. and McCormick, Megan and Jones, Richard A.},
	month = jul,
	year = {2009},
	pmid = {18996911},
	keywords = {Cortical thickness, Magnetic Resonance Imaging, sickle cell disease},
	pages = {1549--1556},
	file = {Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/CJAJZR6C/Kirk et al. - 2009 - Regionally Specific Cortical Thinning in Children .pdf:application/pdf;Snapshot:/autofs/cluster/freesurfer/zotero/storage/6EKG4U64/1549.html:text/html}
}

@article{palaniyappan_folding_2011,
	title = {Folding of the prefrontal cortex in schizophrenia: regional differences in gyrification},
	volume = {69},
	issn = {1873-2402},
	shorttitle = {Folding of the prefrontal cortex in schizophrenia},
	doi = {10.1016/j.biopsych.2010.12.012},
	abstract = {{BACKGROUND}: Anatomy of prefrontal cortex in schizophrenia has been studied previously by quantifying the degree of gyrification. Conflicting results exist, with some studies showing hypergyria and others showing hypogyria. It is likely that regional variations in cortical folding exist within the prefrontal cortex that could be explored by studying the anatomical subdivisions formed by the sulci and gyri. With surface reconstructions from magnetic resonance imaging, we studied the gyrification within anatomically meaningful subdivisions of prefrontal cortex in schizophrenia.
{METHODS}: Prefrontal cortex was studied with an automated method to obtain Local Gyrification Index, reflecting the degree of cortical folding in 57 patients with schizophrenia and 42 control subjects. Regional differences within prefrontal cortex were compared between the two groups with a sulcogyral atlas. Effects of hemisphere and age were subsequently assessed.
{RESULTS}: Patients with schizophrenia had significant hypogyria in most prefrontal regions except the frontomarginal region, which showed hypergyria. The normal left {\textgreater} right pattern of prefrontal gyrification was reversed in schizophrenia. Patients with schizophrenia also showed significant age-related reduction in gyrification at the hypogyric regions.
{CONCLUSIONS}: The differences between reported findings regarding prefrontal gyrification might reflect regional variation in the nature of the abnormal process of gyrification in schizophrenia. Prefrontal gyrification is significantly influenced by age in schizophrenia, in addition to the influence of neurodevelopmental factors.},
	language = {eng},
	number = {10},
	journal = {Biological Psychiatry},
	author = {Palaniyappan, Lena and Mallikarjun, Pavan and Joseph, Verghese and White, Thomas P. and Liddle, Peter F.},
	month = may,
	year = {2011},
	pmid = {21257157},
	keywords = {Adolescent, Adult, Age Factors, Antipsychotic Agents, Female, Functional Laterality, Humans, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Male, Middle Aged, Neuronal Plasticity, Neuropsychological Tests, Prefrontal Cortex, Psychiatric Status Rating Scales, Schizophrenia, Young Adult},
	pages = {974--979}
}

@article{desikan_development_2004,
	title = {Development of Automated Identification of Cortical Regions on {MRI} Scans in {AD} Patients},
	volume = {25},
	shorttitle = {Development of Automated Identification of Cortical Regions on {MRI} Scans in {AD} Patients},
	number = {S2S376},
	journal = {Neurobiology of Aging},
	author = {Desikan, RS and Fischl, B and Dale, AM and Salat, DH and Makris, N and Buckner, RL and Albert, MS and Killiany, RJ.},
	year = {2004}
}

@article{dickerson_detection_2008,
	title = {Detection of cortical thickness correlates of cognitive performance: Reliability across {MRI} scan sessions, scanners, and field strengths},
	volume = {39},
	issn = {1053-8119 (Print) 1053-8119 (Linking)},
	shorttitle = {Detection of cortical thickness correlates of cognitive performance: Reliability across {MRI} scan sessions, scanners, and field strengths},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/17942325},
	doi = {10.1016/j.neuroimage.2007.08.042},
	abstract = {In normal humans, relationships between cognitive test performance and cortical structure have received little study, in part, because of the paucity of tools for measuring cortical structure. Computational morphometric methods have recently been developed that enable the measurement of cortical thickness from {MRI} data, but little data exist on their reliability. We undertook this study to evaluate the reliability of an automated cortical thickness measurement method to detect correlates of interest between thickness and cognitive task performance. Fifteen healthy older participants were scanned four times at 2-week intervals on three different scanner platforms. The four {MRI} data sets were initially treated independently to investigate the reliability of the spatial localization of findings from exploratory whole-cortex analyses of cortical thickness-cognitive performance correlates. Next, the first data set was used to define cortical {ROIs} based on the exploratory results that were then applied to the remaining three data sets to determine whether the relationships between cognitive performance and regional cortical thickness were comparable across different scanner platforms and field strengths. Verbal memory performance was associated with medial temporal cortical thickness, while visuomotor speed/set shifting was associated with lateral parietal cortical thickness. These effects were highly reliable - in terms of both spatial localization and magnitude of absolute cortical thickness measurements - across the four scan sessions. Brain-behavior relationships between regional cortical thickness and cognitive task performance can be reliably identified using an automated data analysis system, suggesting that these measures may be useful as imaging biomarkers of disease or performance ability in multicenter studies in which {MRI} data are pooled.},
	number = {1},
	journal = {Neuroimage},
	author = {Dickerson, B. C. and Fenstermacher, E. and Salat, D. H. and Wolk, D. A. and Maguire, R. P. and Desikan, R. and Pacheco, J. and Quinn, B. T. and Van der Kouwe, A. and Greve, D. N. and Blacker, D. and Albert, M. S. and Killiany, R. J. and Fischl, B.},
	month = jan,
	year = {2008},
	keywords = {Aged, Aged, 80 and over, Cerebral Cortex/*anatomy \& histology/*physiology, Cognition/*physiology, Equipment Design, Equipment Failure Analysis, Female, Humans, Imaging, Three-Dimensional/*instrumentation/methods, Magnetic Resonance Imaging/*instrumentation/*methods, Male, Organ Size/physiology, Radiation Dosage, Reproducibility of Results, Sensitivity and Specificity, Statistics as Topic, *Task Performance and Analysis},
	pages = {10--8},
	annote = {Dickerson, B {CFenstermacher}, {ESalat}, D {HWolk}, D {AMaguire}, R {PDesikan}, {RPacheco}, {JQuinn}, B {TVan} der Kouwe, {AGreve}, D {NBlacker}, {DAlbert}, M {SKilliany}, R {JFischl}, {BengBIRN}002/{PHS} {HHS}/K23 {AG}022509-04/{AG}/{NIA} {NIH} {HHS}/K23-{AG}22509/{AG}/{NIA} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 {EB}001550/{EB}/{NIBIB} {NIH} {HHS}/R01 {NS}052585/{NS}/{NINDS} {NIH} {HHS}/R01 {RR}16594-01A1/{RR}/{NCRR} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/U24-{RR}021382/{RR}/{NCRR} {NIH} {HHS}/U54 {EB}005149/{EB}/{NIBIB} {NIH} {HHS}/Comparative {StudyEvaluation} {StudiesResearch} Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov't2007/10/19 09:00Neuroimage. 2008 Jan 1;39(1):10-8. Epub 2007 Sep 5.},
	file = {Dickerson-2008-Detection of cortical thickness:/autofs/cluster/freesurfer/zotero/storage/7WM6PQMH/Dickerson-2008-Detection of cortical thickness.pdf:application/pdf;PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/FWHV8KC9/Dickerson et al. - 2008 - Detection of cortical thickness correlates of cogn.pdf:application/pdf}
}

@article{smith_correlations_2011,
	title = {Correlations between {MRI} white matter lesion location and executive function and episodic memory},
	volume = {76},
	issn = {0028-3878},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3087468/},
	doi = {10.1212/WNL.0b013e318217e7c8},
	abstract = {Objectives:
{MRI} white matter hyperintensity ({WMH}) volume is associated with cognitive impairment. We hypothesized that specific loci of {WMH} would correlate with cognition even after accounting for total {WMH} volume.

Methods:
Subjects were identified from a prospective community-based study: 40 had normal cognition, 94 had mild impairment (defined here as a Clinical Dementia Rating [{CDR}] score of 0.5 without dementia), and 11 had mild Alzheimer's dementia. Factor analysis of a 22-item neuropsychological battery yielded 4 factors (episodic memory, executive function, spatial skills, and general knowledge). {MRI} {WMH} segmentation and analysis was performed using {FreeSurfer} software.

Results:
Higher {WMH} volume was independently associated with lower executive function and episodic memory factor scores. Voxel-based general linear models showed loci where {WMH} was strongly inversely associated with specific cognitive factor scores (p {\textless} 0.001), controlling for age, education, sex, {APOE} genotype, and total {WMH} volume. For episodic memory, clusters were observed in bilateral temporal-occipital and right parietal periventricular white matter, and the left anterior limb of the internal capsule. For executive function, clusters were observed in bilateral inferior frontal white matter, bilateral temporal-occipital and right parietal periventricular white matter, and the anterior limb of the internal capsule bilaterally.

Conclusions:
Specific {WMH} loci are closely associated with executive function and episodic memory, independent of total {WMH} volume. The anatomic locations suggest that {WMH} may cause cognitive impairment by affecting connections between cortex and subcortical structures, including the thalamus and striatum, or connections between the occipital lobe and frontal or parietal lobes.},
	number = {17},
	urldate = {2014-08-25},
	journal = {Neurology},
	author = {Smith, E.E. and Salat, D.H. and Jeng, J. and McCreary, C.R. and Fischl, B. and Schmahmann, J.D. and Dickerson, B.C. and Viswanathan, A. and Albert, M.S. and Blacker, D. and Greenberg, S.M.},
	month = apr,
	year = {2011},
	pmid = {21518999},
	pmcid = {PMC3087468},
	keywords = {Aged, Aged, 80 and over, Brain Mapping, Brain/*pathology, Cognition Disorders/*pathology, Executive Function/*physiology, Female, Humans, Longitudinal Studies, Magnetic Resonance Imaging/methods, Male, Memory Disorders/*pathology, Mental Recall/*physiology, Nerve Fibers, Myelinated/*pathology, Neuropsychological Tests, Residence Characteristics, *Statistics as Topic},
	pages = {1492--1499},
	annote = {Smith, E {ESalat}, D {HJeng}, {JMcCreary}, C {RFischl}, {BSchmahmann}, J {DDickerson}, B {CViswanathan}, {AAlbert}, M {SBlacker}, {DGreenberg}, S {MengP}01 {AG}04953/{AG}/{NIA} {NIH} {HHS}/R01 {AG}026484-07/{AG}/{NIA} {NIH} {HHS}/R01 {AG}26484/{AG}/{NIA} {NIH} {HHS}/R01 {NS}062028/{NS}/{NINDS} {NIH} {HHS}/Research Support, N.I.H., Extramural2011/04/27 06:00Neurology. 2011 Apr 26;76(17):1492-9. doi: 10.1212/{WNL}.0b013e318217e7c8.},
	file = {PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/7WB4MANW/Smith et al. - 2011 - Correlations between MRI white matter lesion locat.pdf:application/pdf;PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/AUTSVFUS/Smith et al. - 2011 - Correlations between MRI white matter lesion locat.pdf:application/pdf;Smith-2011-Correlations between MRI white matt:/autofs/cluster/freesurfer/zotero/storage/WJ8DT5DQ/Smith-2011-Correlations between MRI white matt.pdf:application/pdf}
}

@article{wisco_abnormal_2007,
	title = {Abnormal cortical folding patterns within Broca's area in schizophrenia: Evidence from structural {MRI}},
	volume = {94},
	issn = {0920-9964},
	shorttitle = {Abnormal cortical folding patterns within Broca's area in schizophrenia},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2034662/},
	doi = {10.1016/j.schres.2007.03.031},
	abstract = {We compared cortical folding patterns between patients with schizophrenia and demographically-matched healthy controls in prefrontal and temporal regions of interest. Using the Freesurfer (http://surfer.nmr.mgh.harvard.edu) cortical surface-based reconstruction methodology, we indirectly ascertained cortical displacement and convolution, together, by measuring the degree of metric distortion required to optimally register cortical folding patterns to an average template. An area within the pars triangularis of the left inferior frontal gyrus (Broca's area) showed significantly reduced metric distortion in the patient group relative to the control group (p = 0.0352). We discuss these findings in relation to the neurodevelopmental hypothesis and language dysfunction in schizophrenia.},
	number = {1-3},
	urldate = {2014-08-25},
	journal = {Schizophrenia research},
	author = {Wisco, Jonathan J. and Kuperberg, Gina and Manoach, Dara and Quinn, Brian T. and Busa, Evelina and Fischl, Bruce and Heckers, Stephan and Sorensen, A. Gregory},
	month = aug,
	year = {2007},
	pmid = {17490861},
	pmcid = {PMC2034662},
	pages = {317--327},
	file = {PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/TVMZ9HMA/Wisco et al. - 2007 - Abnormal cortical folding patterns within Broca's .pdf:application/pdf}
}

@article{jovicich_brain_2013,
	title = {Brain morphometry reproducibility in multi-center 3T {MRI} studies: a comparison of cross-sectional and longitudinal segmentations},
	volume = {83},
	issn = {1095-9572},
	shorttitle = {Brain morphometry reproducibility in multi-center 3T {MRI} studies},
	doi = {10.1016/j.neuroimage.2013.05.007},
	abstract = {Large-scale longitudinal multi-site {MRI} brain morphometry studies are becoming increasingly crucial to characterize both normal and clinical population groups using fully automated segmentation tools. The test-retest reproducibility of morphometry data acquired across multiple scanning sessions, and for different {MR} vendors, is an important reliability indicator since it defines the sensitivity of a protocol to detect longitudinal effects in a consortium. There is very limited knowledge about how across-session reliability of morphometry estimates might be affected by different 3T {MRI} systems. Moreover, there is a need for optimal acquisition and analysis protocols in order to reduce sample sizes. A recent study has shown that the longitudinal {FreeSurfer} segmentation offers improved within session test-retest reproducibility relative to the cross-sectional segmentation at one 3T site using a nonstandard multi-echo {MPRAGE} sequence. In this study we implement a multi-site 3T {MRI} morphometry protocol based on vendor provided T1 structural sequences from different vendors (3D {MPRAGE} on Siemens and Philips, 3D {IR}-{SPGR} on {GE}) implemented in 8 sites located in 4 European countries. The protocols used mild acceleration factors (1.5-2) when possible. We acquired across-session test-retest structural data of a group of healthy elderly subjects (5 subjects per site) and compared the across-session reproducibility of two full-brain automated segmentation methods based on either longitudinal or cross-sectional {FreeSurfer} processing. The segmentations include cortical thickness, intracranial, ventricle and subcortical volumes. Reproducibility is evaluated as absolute changes relative to the mean (\%), Dice coefficient for volume overlap and intraclass correlation coefficients across two sessions. We found that this acquisition and analysis protocol gives comparable reproducibility results to previous studies that used longer acquisitions without acceleration. We also show that the longitudinal processing is systematically more reliable across sites regardless of {MRI} system differences. The reproducibility errors of the longitudinal segmentations are on average approximately half of those obtained with the cross sectional analysis for all volume segmentations and for entorhinal cortical thickness. No significant differences in reliability are found between the segmentation methods for the other cortical thickness estimates. The average of two {MPRAGE} volumes acquired within each test-retest session did not systematically improve the across-session reproducibility of morphometry estimates. Our results extend those from previous studies that showed improved reliability of the longitudinal analysis at single sites and/or with non-standard acquisition methods. The multi-site acquisition and analysis protocol presented here is promising for clinical applications since it allows for smaller sample sizes per {MRI} site or shorter trials in studies evaluating the role of potential biomarkers to predict disease progression or treatment effects.},
	language = {eng},
	journal = {{NeuroImage}},
	author = {Jovicich, Jorge and Marizzoni, Moira and Sala-Llonch, Roser and Bosch, Beatriz and Bartrés-Faz, David and Arnold, Jennifer and Benninghoff, Jens and Wiltfang, Jens and Roccatagliata, Luca and Nobili, Flavio and Hensch, Tilman and Tränkner, Anja and Schönknecht, Peter and Leroy, Melanie and Lopes, Renaud and Bordet, Régis and Chanoine, Valérie and Ranjeva, Jean-Philippe and Didic, Mira and Gros-Dagnac, Hélène and Payoux, Pierre and Zoccatelli, Giada and Alessandrini, Franco and Beltramello, Alberto and Bargalló, Núria and Blin, Olivier and Frisoni, Giovanni B. and {PharmaCog Consortium}},
	month = dec,
	year = {2013},
	pmid = {23668971},
	pages = {472--484},
	annote = {Jovicich, {JorgeMarizzoni}, {MoiraSala}-Llonch, {RoserBosch}, {BeatrizBartres}-Faz, {DavidArnold}, {JenniferBenninghoff}, {JensWiltfang}, {JensRoccatagliata}, {LucaNobili}, {FlavioHensch}, {TilmanTrankner}, {AnjaSchonknecht}, {PeterLeroy}, {MelanieLopes}, {RenaudBordet}, {RegisChanoine}, {ValerieRanjeva}, Jean-{PhilippeDidic}, {MiraGros}-Dagnac, {HelenePayoux}, {PierreZoccatelli}, {GiadaAlessandrini}, {FrancoBeltramello}, {AlbertoBargallo}, {NuriaBlin}, {OlivierFrisoni}, Giovanni {BengResearch} Support, Non-U.S. Gov't2013/05/15 06:00Neuroimage. 2013 Dec;83:472-84. doi: 10.1016/j.neuroimage.2013.05.007. Epub 2013 May 11.}
}

@article{wang_cross-validation_2014,
	title = {Cross-validation of serial optical coherence scanning and diffusion tensor imaging: A study on neural fiber maps in human medulla oblongata},
	volume = {100},
	issn = {1095-9572 (Electronic) 1053-8119 (Linking)},
	shorttitle = {Cross-validation of serial optical coherence scanning and diffusion tensor imaging},
	url = {https://surfer.nmr.mgh.harvard.edu/pub/articles/2014/Wang.2014.NeuroImage.SOCS.pdf},
	doi = {10.1016/j.neuroimage.2014.06.032},
	abstract = {We established a strategy to perform cross-validation of serial optical coherence scanner imaging ({SOCS}) and diffusion tensor imaging ({DTI}) on a postmortem human medulla. Following {DTI}, the sample was serially scanned by {SOCS}, which integrates a vibratome slicer and a multi-contrast optical coherence tomography rig for large-scale three-dimensional imaging at microscopic resolution. The {DTI} dataset was registered to the {SOCS} space. An average correlation coefficient of 0.9 was found between the co-registered fiber maps constructed by fractional anisotropy and retardance contrasts. Pixelwise comparison of fiber orientations demonstrated good agreement between the {DTI} and {SOCS} measures. Details of the comparison were studied in regions exhibiting a variety of fiber organizations. {DTI} estimated the preferential orientation of small fiber tracts; however, it didn't capture their complex patterns as {SOCS} did. In terms of resolution and imaging depth, {SOCS} and {DTI} complement each other, and open new avenues for cross-modality investigations of the brain.},
	language = {en},
	urldate = {2014-08-21},
	journal = {Neuroimage},
	author = {Wang, H. and Zhu, J. and Reuter, M. and Vinke, L. N. and Yendiki, A. and Boas, D. A. and Fischl, B. and Akkin, T.},
	month = oct,
	year = {2014},
	keywords = {fs\_OCT},
	pages = {395--404},
	annote = {Wang, {HuiZhu}, {JunfengReuter}, {MartinVinke}, Louis {NYendiki}, {AnastasiaBoas}, David {AFischl}, {BruceAkkin}, {TanerengP}41 {EB}015896/{EB}/{NIBIB} {NIH} {HHS}/R01 {AG}008122/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022381/{AG}/{NIA} {NIH} {HHS}/R01 {EB}006758/{EB}/{NIBIB} {NIH} {HHS}/R01 {EB}012538/{EB}/{NIBIB} {NIH} {HHS}/R01 {NS}052585/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}070963/{NS}/{NINDS} {NIH} {HHS}/R21 {NS}072652/{NS}/{NINDS} {NIH} {HHS}/S10 {RR}019307/{RR}/{NCRR} {NIH} {HHS}/S10 {RR}023043/{RR}/{NCRR} {NIH} {HHS}/S10 {RR}023401/{RR}/{NCRR} {NIH} {HHS}/U01 {MH}093765/{MH}/{NIMH} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/2014/06/24 06:00Neuroimage. 2014 Oct;100:395-404. doi: 10.1016/j.neuroimage.2014.06.032. Epub 2014 Jun 20.}
}

@inproceedings{polimeni_laminar-specific_2010,
	title = {Laminar-specific output- to input-layer connections between cortical areas V1 and {MT} observed with high-resolution resting-state {fMRI}},
	volume = {18},
	shorttitle = {Laminar-specific output- to input-layer connections between cortical areas V1 and {MT} observed with high-resolution resting-state {fMRI}},
	author = {Polimeni, J. R. and Fischl, B. and Greve, D. N. and Wald, L. L.},
	year = {2010},
	pages = {3471}
}

@article{kremen_heritability_2012,
	title = {Heritability of brain ventricle volume: converging evidence from inconsistent results},
	volume = {33},
	issn = {1558-1497 (Electronic) 0197-4580 (Linking)},
	shorttitle = {Heritability of brain ventricle volume: converging evidence from inconsistent results},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/20363053},
	doi = {10.1016/j.neurobiolaging.2010.02.007},
	abstract = {Twin studies generally show great consistency for the heritability of brain structures. Ironically, the lateral ventricles--perhaps the most reliably measured brain regions of interest--are the most inconsistent when it comes to estimating genetic influences on their volume. Heritability estimates in twin studies have ranged from zero to almost 0.80. Here we aggregate heritability estimates from extant twin studies, and we review and reinterpret some of the findings. Based on our revised estimates, we conclude that lateral ventricular volume is indeed heritable. The weighted average heritability of the revised estimates was 0.54. Although accumulated environmental insults might seem most logical as the predominant cause of age-related ventricular expansion, the data strongly suggest that genetic influences on lateral ventricular volume are increasing with age. Genetic influences accounted for 32-35\% of the variance in lateral ventricular volume in childhood, but about 75\% of the variance in late middle and older age. These conclusions have implications for the basic understanding of the genetic and environmental underpinnings of normative and pathological brain aging.},
	number = {1},
	journal = {Neurobiol Aging},
	author = {Kremen, W. S. and Panizzon, M. S. and Neale, M. C. and Fennema-Notestine, C. and Prom-Wormley, E. and Eyler, L. T. and Stevens, A. and Franz, C. E. and Lyons, M. J. and Grant, M. D. and Jak, A. J. and Jernigan, T. L. and Xian, H. and Fischl, B. and Thermenos, H. W. and Seidman, L. J. and Tsuang, M. T. and Dale, A. M.},
	month = jan,
	year = {2012},
	keywords = {Adolescent, Adult, Aged, Aged, 80 and over, Aging/pathology, Cerebral Ventricles/*anatomy \& histology/*pathology, Child, *Gene-Environment Interaction, Humans, Middle Aged, Organ Size/*genetics, Sample Size, Twin Studies as Topic, Young Adult},
	pages = {1--8},
	annote = {Kremen, William {SPanizzon}, Matthew {SNeale}, Michael {CFennema}-Notestine, {ChristineProm}-Wormley, {ElizabethEyler}, Lisa {TStevens}, {AllisonFranz}, Carol {ELyons}, Michael {JGrant}, Michael {DJak}, Amy {JJernigan}, Terry {LXian}, {HongFischl}, {BruceThermenos}, Heidi {WSeidman}, Larry {JTsuang}, Ming {TDale}, Anders {MengAG}018384/{AG}/{NIA} {NIH} {HHS}/{AG}018386/{AG}/{NIA} {NIH} {HHS}/{AG}022381/{AG}/{NIA} {NIH} {HHS}/{AG}022982/{AG}/{NIA} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 {AG}018384-10/{AG}/{NIA} {NIH} {HHS}/R01 {AG}018386-09/{AG}/{NIA} {NIH} {HHS}/R01 {AG}018386-10/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022381-09/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022381-10/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022982/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022982-04/{AG}/{NIA} {NIH} {HHS}/R01 {NS}052585-01/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}052585-05/{NS}/{NINDS} {NIH} {HHS}/R01 {RR}016594-01A1/{RR}/{NCRR} {NIH} {HHS}/R01EB006758/{EB}/{NIBIB} {NIH} {HHS}/R21 {NS}072652-01/{NS}/{NINDS} {NIH} {HHS}/U54 {EB}005149/{EB}/{NIBIB} {NIH} {HHS}/Meta-{AnalysisResearch} Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov'{tResearch} Support, U.S. Gov't, Non-P.H.S.2010/04/07 06:00Neurobiol Aging. 2012 Jan;33(1):1-8. doi: 10.1016/j.neurobiolaging.2010.02.007. Epub 2010 Apr 3.},
	file = {Kremen-2012-Heritability of brain ventricle vo:/autofs/cluster/freesurfer/zotero/storage/JX4D4VVW/Kremen-2012-Heritability of brain ventricle vo.pdf:application/pdf}
}

@article{cerasa_dysbindin_2011,
	title = {Dysbindin C-A-T haplotype is associated with thicker medial orbitofrontal cortex in healthy population},
	volume = {55},
	issn = {1095-9572},
	url = {https://surfer.nmr.mgh.harvard.edu/pub/articles/Dysbindin_Neuroimage_2011.pdf},
	doi = {10.1016/j.neuroimage.2010.12.042},
	abstract = {The dysbindin (dystrobrevin-binding protein 1) gene has been indicated as one of the most important schizophrenia susceptibility genes. Several genetic variations of this gene have been investigated by using an "intermediate phenotype" approach showing a particular detrimental effect on the prefrontal function in schizophrenic patients. However, the nature of dysbindin function within the brains of healthy individuals is poorly understood, in particular as concerns brain anatomy. We examine relationships between a previously implicated three marker C-A-T dysbindin haplotype and regional cortical thickness in a wide population genotyped for risk carriers (n=14) and non-risk carriers (n=93). Surface-based analysis of the cortical mantle showed that the dysbindin haplotype was associated with structural differences in the medial orbitofrontal cortex, where the risk carriers showed the highest cortical thickness values and the non-risk carriers the lowest. Our study extends previous evidence found on schizophrenic patients to the healthy population, demonstrating the influence of dysbindin risk variants on the neuronal architecture of a specific brain region relevant to the neuropathology of schizophrenia.},
	language = {eng},
	number = {2},
	journal = {{NeuroImage}},
	author = {Cerasa, Antonio and Quattrone, Aldo and Gioia, Maria C. and Tarantino, Patrizia and Annesi, Grazia and Assogna, Francesca and Caltagirone, Carlo and De Luca, Vincenzo and Spalletta, Gianfranco},
	month = mar,
	year = {2011},
	pmid = {21184829},
	keywords = {Adolescent, Adolescent, Adult, Adult, Aged, Aged, Carrier Proteins, Carrier Proteins/*genetics, Cerebral Cortex, Cerebral Cortex/*anatomy \& histology, Female, Female, Genetic Predisposition to Disease, Genetic Predisposition to Disease, Haplotypes, Haplotypes, Humans, Humans, Magnetic Resonance Imaging, Magnetic Resonance Imaging, Male, Male, Middle Aged, Middle Aged, Risk Factors, Risk Factors, Schizophrenia, Schizophrenia/genetics, Young Adult, Young Adult},
	pages = {508--513},
	annote = {Cerasa, {AntonioQuattrone}, {AldoGioia}, Maria {CTarantino}, {PatriziaAnnesi}, {GraziaAssogna}, {FrancescaCaltagirone}, {CarloDe} Luca, {VincenzoSpalletta}, Gianfrancoeng2010/12/28 06:00Neuroimage. 2011 Mar 15;55(2):508-13. doi: 10.1016/j.neuroimage.2010.12.042. Epub 2010 Dec 22.}
}

@article{walhovd_size_2004,
	title = {Size does matter in the long run: hippocampal and cortical volume predict recall across weeks},
	volume = {63},
	issn = {1526-632X (Electronic) 0028-3878 (Linking)},
	shorttitle = {Size does matter in the long run: hippocampal and cortical volume predict recall across weeks},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/15477537},
	abstract = {{OBJECTIVE}: To study the morphometric determinants of recall of verbal material for an extended period in an adult lifespan sample. {METHODS}: Healthy adults of varying ages were studied using automated segmentation of {MRI} scans with volumes of hippocampus, cortex, and white matter, and verbal memory tests assessing recall after 5 minutes, 30 minutes, and a mean period of 11 weeks. Stepwise regression analyses were performed with 5 minutes, 30 minutes, and 11-week recall as the dependent variables. Hippocampal, cortical, and white matter volumes were included in the initial set of predictor variables in each case, and the analyses were repeated with age as an additional predictor variable. {RESULTS}: When age was not included, cortical volume was the only variable predicting recall after 5 and 30 minutes, whereas hippocampal and cortical volumes predicted recall after 11 weeks. When age was included in the model, this was the only variable predicting recall after 5 and 30 minutes, whereas age and hippocampus gave contributions in prediction of recall after several weeks. {CONCLUSION}: This study supports a critical role of cortical and hippocampal size in recall. Hippocampal size seems more important in recall after 11 weeks than after a shorter time interval.},
	language = {eng},
	number = {7},
	journal = {Neurology},
	author = {Walhovd, K. B. and Fjell, A. M. and Reinvang, I. and Lundervold, A. and Fischl, B. and Quinn, B. T. and Dale, A. M.},
	month = oct,
	year = {2004},
	keywords = {Adult, Aged, Aged, 80 and over, Aging/pathology, Cerebral Cortex/*anatomy \& histology, Female, Hippocampus/*anatomy \& histology, Humans, Magnetic Resonance Imaging, Male, Mental Recall/*physiology, Middle Aged, Organ Size/physiology, Regression Analysis, Time Factors},
	pages = {1193--7},
	annote = {Walhovd, K {BFjell}, A {MReinvang}, {ILundervold}, {AFischl}, {BQuinn}, B {TDale}, A {MengP}41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01-{NS}39581/{NS}/{NINDS} {NIH} {HHS}/R01-{RR}13609/{RR}/{NCRR} {NIH} {HHS}/R01-{RR}16594/{RR}/{NCRR} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, U.S. Gov't, P.H.S.2004/10/13 09:00Neurology. 2004 Oct 12;63(7):1193-7.},
	file = {Walhovd-2004-Size does matter in the long run_:/autofs/cluster/freesurfer/zotero/storage/VEZMB3JW/Walhovd-2004-Size does matter in the long run_.pdf:application/pdf}
}

@article{carlson_influence_2013,
	title = {Influence of the {BDNF} Genotype on Amygdalo-Prefrontal White Matter Microstructure is Linked to Nonconscious Attention Bias to Threat},
	issn = {1047-3211, 1460-2199},
	url = {http://cercor.oxfordjournals.org/content/early/2013/04/12/cercor.bht089},
	doi = {10.1093/cercor/bht089},
	abstract = {Cognitive processing biases, such as increased attention to threat, are gaining recognition as causal factors in anxiety. Yet, little is known about the anatomical pathway by which threat biases cognition and how genetic factors might influence the integrity of this pathway, and thus, behavior. For 40 normative adults, we reconstructed the entire amygdalo-prefrontal white matter tract (uncinate fasciculus) using diffusion tensor weighted {MRI} and probabilistic tractography to test the hypothesis that greater fiber integrity correlates with greater nonconscious attention bias to threat as measured by a backward masked dot-probe task. We used path analysis to investigate the relationship between brain-derived nerve growth factor genotype, uncinate fasciculus integrity, and attention bias behavior. Greater structural integrity of the amygdalo-prefrontal tract correlates with facilitated attention bias to nonconscious threat. Genetic variability associated with brain-derived nerve growth factor appears to influence the microstructure of this pathway and, in turn, attention bias to nonconscious threat. These results suggest that the integrity of amygdalo-prefrontal projections underlie nonconscious attention bias to threat and mediate genetic influence on attention bias behavior. Prefrontal cognition and attentional processing in high bias individuals appear to be heavily influenced by nonconscious threat signals relayed via the uncinate fasciculus.},
	language = {en},
	urldate = {2014-08-25},
	journal = {Cerebral Cortex},
	author = {Carlson, Joshua M. and Cha, Jiook and Harmon-Jones, Eddie and Mujica-Parodi, Lilianne R. and Hajcak, Greg},
	month = apr,
	year = {2013},
	pmid = {23585520},
	keywords = {Amygdala, anterior cingulate, dot-probe, {DTI}, uncinate fasciculus},
	pages = {bht089},
	file = {Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/7IW5TVP6/Carlson et al. - 2013 - Influence of the BDNF Genotype on Amygdalo-Prefron.pdf:application/pdf;Snapshot:/autofs/cluster/freesurfer/zotero/storage/A94FZHFI/cercor.html:text/html}
}

@article{walhovd_effects_2005,
	title = {Effects of age on volumes of cortex, white matter and subcortical structures},
	volume = {26},
	issn = {0197-4580},
	url = {https://surfer.nmr.mgh.harvard.edu/pub/articles/walhovd2005a.pdf},
	doi = {10.1016/j.neurobiolaging.2005.05.020},
	abstract = {The effect of age was investigated in and compared across 16 automatically segmented brain measures: cortical gray matter, cerebral white matter, hippocampus, amygdala, thalamus, the accumbens area, caudate, putamen, pallidum, brainstem, cerebellar cortex, cerebellar white matter, the lateral ventricle, the inferior lateral ventricle, and the 3rd and 4th ventricle. Significant age effects were found for all volumes except pallidum and the 4th ventricle. Heterogeneous age responses were seen in that age relationships for cortex, amygdala, thalamus, the accumbens area, and caudate were linear, while cerebral white matter, hippocampus, brainstem, cerebellar white, and gray matter, as well as volume of the lateral, inferior lateral, and 3rd ventricles showed curvilinear relationships with age. In general, the findings point to global and large effects of age across brain volumes.},
	language = {eng},
	number = {9},
	journal = {Neurobiology of Aging},
	author = {Walhovd, Kristine B. and Fjell, Anders M. and Reinvang, Ivar and Lundervold, Arvid and Dale, Anders M. and Eilertsen, Dag E. and Quinn, Brian T. and Salat, David and Makris, Nikos and Fischl, Bruce},
	month = oct,
	year = {2005},
	pmid = {16005549},
	keywords = {Adult, Adult, Aged, Aged, Aged, 80 and over, Aged, 80 and over, Age Factors, Age Factors, Aging, Aging/*pathology/physiology, Brain Mapping, Brain Mapping, Cerebral Cortex, Cerebral Cortex/*pathology/physiology, Female, Female, Functional Laterality, Functional Laterality/physiology, Humans, Humans, Image Processing, Computer-Assisted, Image Processing, Computer-Assisted/methods, Lateral Ventricles, Lateral Ventricles, Magnetic Resonance Imaging, Magnetic Resonance Imaging/methods, Male, Male, Middle Aged, Middle Aged, Neural Pathways, Neural Pathways, Regression Analysis, Regression Analysis, Statistics, Nonparametric, Statistics, Nonparametric},
	pages = {1261--1270; discussion 1275--1278},
	annote = {Walhovd, Kristine {BFjell}, Anders {MReinvang}, {IvarLundervold}, {ArvidDale}, Anders {MEilertsen}, Dag {EQuinn}, Brian {TSalat}, {DavidMakris}, {NikosFischl}, {BruceengP}41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01-{NS}39581/{NS}/{NINDS} {NIH} {HHS}/R01-{RR}13609/{RR}/{NCRR} {NIH} {HHS}/R01-{RR}16594/{RR}/{NCRR} {NIH} {HHS}/Comparative {StudyResearch} Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov'{tResearch} Support, U.S. Gov't, P.H.S.2005/07/12 09:00Neurobiol Aging. 2005 Oct;26(9):1261-70; discussion 1275-8.}
}

@article{desbordes_effects_2012,
	title = {Effects of mindful-attention and compassion meditation training on amygdala response to emotional stimuli in an ordinary, non-meditative state},
	volume = {6},
	issn = {1662-5161},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3485650/},
	doi = {10.3389/fnhum.2012.00292},
	abstract = {The amygdala has been repeatedly implicated in emotional processing of both positive and negative-valence stimuli. Previous studies suggest that the amygdala response to emotional stimuli is lower when the subject is in a meditative state of mindful-attention, both in beginner meditators after an 8-week meditation intervention and in expert meditators. However, the longitudinal effects of meditation training on amygdala responses have not been reported when participants are in an ordinary, non-meditative state. In this study, we investigated how 8 weeks of training in meditation affects amygdala responses to emotional stimuli in subjects when in a non-meditative state. Healthy adults with no prior meditation experience took part in 8 weeks of either Mindful Attention Training ({MAT}), Cognitively-Based Compassion Training ({CBCT}; a program based on Tibetan Buddhist compassion meditation practices), or an active control intervention. Before and after the intervention, participants underwent an {fMRI} experiment during which they were presented images with positive, negative, and neutral emotional valences from the {IAPS} database while remaining in an ordinary, non-meditative state. Using a region-of-interest analysis, we found a longitudinal decrease in right amygdala activation in the Mindful Attention group in response to positive images, and in response to images of all valences overall. In the {CBCT} group, we found a trend increase in right amygdala response to negative images, which was significantly correlated with a decrease in depression score. No effects or trends were observed in the control group. This finding suggests that the effects of meditation training on emotional processing might transfer to non-meditative states. This is consistent with the hypothesis that meditation training may induce learning that is not stimulus- or task-specific, but process-specific, and thereby may result in enduring changes in mental function.},
	urldate = {2014-08-25},
	journal = {Frontiers in Human Neuroscience},
	author = {Desbordes, Gaelle and Negi, Lobsang T. and Pace, Thaddeus W. W. and Wallace, B. Alan and Raison, Charles L. and Schwartz, Eric L.},
	month = nov,
	year = {2012},
	pmid = {23125828},
	pmcid = {PMC3485650},
	annote = {Desbordes, {GaelleNegi}, Lobsang {TPace}, Thaddeus W {WWallace}, B {AlanRaison}, Charles {LSchwartz}, Eric {LengSwitzerland}2012/11/06 06:00Front Hum Neurosci. 2012 Nov 1;6:292. doi: 10.3389/fnhum.2012.00292. {eCollection} 2012.},
	file = {Desbordes-2012-Effects of mindful-attention a1:/autofs/cluster/freesurfer/zotero/storage/QAJK95FF/Desbordes-2012-Effects of mindful-attention a1.pdf:application/pdf;PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/QIPZXQQC/Desbordes et al. - 2012 - Effects of mindful-attention and compassion medita.pdf:application/pdf}
}

@article{rosas_regional_2002,
	title = {Regional and progressive thinning of the cortical ribbon in Huntington's disease},
	volume = {58},
	issn = {0028-3878 (Print) 0028-3878 (Linking)},
	shorttitle = {Regional and progressive thinning of the cortical ribbon in Huntington's disease},
	url = {http://www.nmr.mgh.harvard.edu/~fischl/reprints/hd_neurology_reprint.pdf},
	abstract = {{BACKGROUND}: Huntington's disease ({HD}) is a fatal and progressive neurodegenerative disease that is accompanied by involuntary movements, cognitive dysfunction, and psychiatric symptoms. Although progressive striatal degeneration is known to occur, little is known about how the disease affects the cortex, including which cortical regions are affected, how degeneration proceeds, and the relationship of the cortical degeneration to clinical symptoms. The cortex has been difficult to study in neurodegenerative diseases primarily because of its complex folding patterns and regional variability; however, an understanding of how the cortex is affected by the disease may provide important new insights into it. {METHODS}: Novel automated surface reconstruction and high-resolution {MR} images of 11 patients with {HD} and 13 age-matched subjects were used to obtain cortical thickness measurements. The same analyses were performed on two postmortem brains to validate these methods. {RESULTS}: Regionally specific heterogeneous thinning of the cortical ribbon was found in subjects with {HD}. Thinning occurred early, differed among patients in different clinical stages of disease, and appeared to proceed from posterior to anterior cortical regions with disease progression. The sensorimotor region was statistically most affected. Measurements performed on {MR} images of autopsy brains analyzed similarly were within 0.25 mm of those obtained using traditional neuropathologic methods and were statistically indistinguishable. {CONCLUSIONS}: The authors propose that the cortex degenerates early in disease and that regionally selective cortical degeneration may explain the heterogeneity of clinical expression in {HD}. These measures might provide a sensitive prospective surrogate marker for clinical trials of neuroprotective medications.},
	number = {5},
	journal = {Neurology},
	author = {Rosas, H. D. and Liu, A. K. and Hersch, S. and Glessner, M. and Ferrante, R. J. and Salat, D. H. and van der Kouwe, A. and Jenkins, B. G. and Dale, A. M. and Fischl, B.},
	month = mar,
	year = {2002},
	keywords = {Adult, Cerebral Cortex/*pathology, Cortical thickness, Female, Humans, Huntington Disease/*pathology/physiopathology, Magnetic Resonance Imaging/*methods, Male, Middle Aged},
	pages = {695--701},
	annote = {Rosas, H {DLiu}, A {KHersch}, {SGlessner}, {MFerrante}, R {JSalat}, D Hvan der Kouwe, {AJenkins}, B {GDale}, A {MFischl}, {BengAG}05886/{AG}/{NIA} {NIH} {HHS}/{AT}00613/{AT}/{NCCAM} {NIH} {HHS}/{NS}02060/{NS}/{NINDS} {NIH} {HHS}/{NS}35255/{NS}/{NINDS} {NIH} {HHS}/{NS}37102/{NS}/{NINDS} {NIH} {HHS}/{NS}39581/{NS}/{NINDS} {NIH} {HHS}/Research Support, Non-U.S. Gov'{tResearch} Support, U.S. Gov't, Non-P.H.S.Research Support, U.S. Gov't, P.H.S.2002/03/13 10:00Neurology. 2002 Mar 12;58(5):695-701.},
	file = {Rosas-2002-Regional and progressive thinning o:/autofs/cluster/freesurfer/zotero/storage/JZG6QMNR/Rosas-2002-Regional and progressive thinning o.pdf:application/pdf}
}

@article{fischl_whole_2002,
	title = {Whole brain segmentation: automated labeling of neuroanatomical structures in the human brain},
	volume = {33},
	issn = {0896-6273 (Print) 0896-6273 (Linking)},
	shorttitle = {Whole brain segmentation: automated labeling of neuroanatomical structures in the human brain},
	url = {https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl02-labeling.pdf},
	abstract = {We present a technique for automatically assigning a neuroanatomical label to each voxel in an {MRI} volume based on probabilistic information automatically estimated from a manually labeled training set. In contrast to existing segmentation procedures that only label a small number of tissue classes, the current method assigns one of 37 labels to each voxel, including left and right caudate, putamen, pallidum, thalamus, lateral ventricles, hippocampus, and amygdala. The classification technique employs a registration procedure that is robust to anatomical variability, including the ventricular enlargement typically associated with neurological diseases and aging. The technique is shown to be comparable in accuracy to manual labeling, and of sufficient sensitivity to robustly detect changes in the volume of noncortical structures that presage the onset of probable Alzheimer's disease.},
	number = {3},
	journal = {Neuron},
	author = {Fischl, B. and Salat, D. H. and Busa, E. and Albert, M. and Dieterich, M. and Haselgrove, C. and van der Kouwe, A. and Killiany, R. and Kennedy, D. and Klaveness, S. and Montillo, A. and Makris, N. and Rosen, B. and Dale, A. M.},
	month = jan,
	year = {2002},
	keywords = {Aged, Alzheimer Disease/diagnosis/pathology, Brain/*anatomy \& histology/pathology, Brain Mapping, Female, fs\_Subcortical-segmentation, Humans, Magnetic Resonance Imaging/*methods, Male, Reproducibility of Results},
	pages = {341--55},
	annote = {Fischl, {BruceSalat}, David {HBusa}, {EvelinaAlbert}, {MarilynDieterich}, {MeganHaselgrove}, Christianvan der Kouwe, {AndreKilliany}, {RonKennedy}, {DavidKlaveness}, {ShunaMontillo}, {AlbertMakris}, {NikosRosen}, {BruceDale}, Anders {MengP}41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01-{NS}34189/{NS}/{NINDS} {NIH} {HHS}/R01-{NS}39581/{NS}/{NINDS} {NIH} {HHS}/R01-{RR}13609/{RR}/{NCRR} {NIH} {HHS}/Comparative {StudyResearch} Support, U.S. Gov't, P.H.S.2002/02/08 10:00Neuron. 2002 Jan 31;33(3):341-55.},
	file = {Fischl-2002-Whole brain segmentation_ automate:/autofs/cluster/freesurfer/zotero/storage/M3U6SAKW/Fischl-2002-Whole brain segmentation_ automate.pdf:application/pdf}
}

@inproceedings{rosen_human_2010,
	title = {The Human Connectome Project},
	author = {Rosen, B. and Wedee, V. and Van Horn, J.D. and Fischl, B. and Buckner, R. and Wald, L. and Hamalainen, M and Stufflebeam, S. and Roffman, J. and Shattuck, D. W. and Thompson, P.M. and Woods, R. P. and Freimer, N. and Bilder, R.M. and Toga, A.W.},
	month = jun,
	year = {2010}
}

@article{cerasa_cerebellar_2009,
	title = {Cerebellar Atrophy in Essential Tremor Using an Automated Segmentation Method},
	volume = {30},
	issn = {0195-6108, 1936-959X},
	url = {http://www.ajnr.org/content/30/6/1240},
	doi = {10.3174/ajnr.A1544},
	abstract = {{BACKGROUND} {AND} {PURPOSE}: Essential tremor ({ET}) is a slowly progressive disorder characterized by postural and kinetic tremors most commonly affecting the forearms and hands. Several lines of evidence from physiologic and neuroimaging studies point toward a major role of the cerebellum in this disease. Recently, voxel-based morphometry ({VBM}) has been proposed to quantify cerebellar atrophy in {ET}. However, {VBM} was not originally designed to study subcortical structures, and the complicated anatomy of the cerebellum may hamper the automatic processing of {VBM}. The aim of this study was to determine the efficacy and utility of using automated subcortical segmentation to identify atrophy of the cerebellum and other subcortical structures in patients with {ET}.
{MATERIALS} {AND} {METHODS}: We used a recently developed automated volumetric method ({FreeSurfer}) to quantify subcortical atrophy in {ET} by comparing results obtained with this method with those provided by previous evidence. The study included T1-weighted {MR} images of 46 patients with {ET} grouped into those having arm {ET} (n = 27, a-{ET}) or head {ET} (n = 19, h-{ET}) and 28 healthy controls.
{RESULTS}: Results revealed the expected reduction of cerebellar volume in patients with h-{ET} with respect to healthy controls after controlling for intracranial volume. No significant difference was detected in any other subcortical area.
{CONCLUSIONS}: Volumetric data obtained with automated segmentation of subcortical and cerebellar structures approximate data from a previous study based on {VBM}. The current findings extend the literature by providing initial validation for using fully automated segmentation to derive cerebellar volumetric information from patients with {ET}.},
	language = {en},
	number = {6},
	urldate = {2014-08-25},
	journal = {American Journal of Neuroradiology},
	author = {Cerasa, A. and Messina, D. and Nicoletti, G. and Novellino, F. and Lanza, P. and Condino, F. and Arabia, G. and Salsone, M. and Quattrone, A.},
	month = jun,
	year = {2009},
	pmid = {19342539},
	pages = {1240--1243},
	file = {Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/SBPMCC7J/Cerasa et al. - 2009 - Cerebellar Atrophy in Essential Tremor Using an Au.pdf:application/pdf;Snapshot:/autofs/cluster/freesurfer/zotero/storage/NUNKHZSF/1240.html:text/html}
}

@article{greve_accurate_2009,
	title = {Accurate and robust brain image alignment using boundary-based registration},
	volume = {48},
	shorttitle = {Accurate and robust brain image alignment using boundary-based registration},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2733527/pdf/nihms129229.pdf},
	number = {1},
	journal = {{NeuroImage}},
	author = {Greve, D. and Fischl, B.},
	year = {2009},
	keywords = {fs\_BBR},
	pages = {63--72},
	file = {Greve-2009-Accurate and robust brain image ali:/autofs/cluster/freesurfer/zotero/storage/8XANKW7G/Greve-2009-Accurate and robust brain image ali.pdf:application/pdf}
}

@article{fjell_age_2005,
	title = {Age does not increase rate of forgetting over weeks--neuroanatomical volumes and visual memory across the adult life-span},
	volume = {11},
	issn = {1355-6177},
	url = {https://surfer.nmr.mgh.harvard.edu/ftp/articles/fjell2005.pdf},
	doi = {10.1017/S1355617705050046},
	abstract = {The aim of the study was to investigate whether age affects visual memory retention across extended time intervals. In addition, we wanted to study how memory capabilities across different time intervals are related to the volume of different neuroanatomical structures (right hippocampus, right cortex, right white matter). One test of recognition ({CVMT}) and one test of recall (Rey-Osterrieth Complex Figure Test) were administered, giving measures of immediate recognition/recall, 20-30 min recognition/recall, and recognition/recall at a mean of 75 days. Volumetric measures of right hemisphere hippocampus, cortex, and white matter were obtained through an automated labelling procedure of {MRI} recordings. Results did not demonstrate a steeper rate of forgetting for older participants when the retention intervals were increased, indicating that older people have spared ability to retain information in the long-term store. Differences in neuroanatomical volumes could explain up to 36\% of the variance in memory performance, but were not significantly related to rates of forgetting. Cortical volume and hippocampal volume were in some cases independent as predictors of memory function. Generally, cortical volume was a better predictor of recognition memory than hippocampal volume, while the 2 structures did not differ in their predictive power of recall abilities. While neuroanatomical volumetric differences can explain some of the differences in memory functioning between younger and older persons, the hippocampus does not seem to be unique in this respect.},
	language = {eng},
	number = {1},
	journal = {Journal of the International Neuropsychological Society: {JINS}},
	author = {Fjell, Anders M. and Walhovd, Kristine B. and Reinvang, Ivar and Lundervold, Arvid and Dale, Anders M. and Quinn, Brian T. and Makris, Nikos and Fischl, Bruce},
	month = jan,
	year = {2005},
	pmid = {15686603},
	keywords = {Adult, Adult, Aged, Aged, Aged, 80 and over, Aged, 80 and over, Aging, Aging/*psychology, Brain, Brain/*anatomy \& histology/physiology, Cerebral Cortex, Cerebral Cortex/anatomy \& histology/physiology, Female, Female, Hippocampus, Hippocampus/anatomy \& histology/physiology, Humans, Humans, Image Processing, Computer-Assisted, Image Processing, Computer-Assisted, Learning, Learning/physiology, Magnetic Resonance Imaging, Magnetic Resonance Imaging, Male, Male, Memory, Memory/*physiology, Mental Recall, Mental Recall/physiology, Middle Aged, Middle Aged, Psychomotor Performance, Psychomotor Performance/physiology, Visual Perception, Visual Perception/*physiology},
	pages = {2--15},
	annote = {Fjell, Anders {MWalhovd}, Kristine {BReinvang}, {IvarLundervold}, {ArvidDale}, Anders {MQuinn}, Brian {TMakris}, {NikosFischl}, {BruceengP}01-{RR}13609/{RR}/{NCRR} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01-{NS}39581/{NS}/{NINDS} {NIH} {HHS}/R01-{RR}16594/{RR}/{NCRR} {NIH} {HHS}/Clinical {TrialResearch} Support, Non-U.S. Gov'{tResearch} Support, U.S. Gov't, P.H.S.England2005/02/03 09:00J Int Neuropsychol Soc. 2005 Jan;11(1):2-15.}
}

@article{cerasa_morphological_2010,
	title = {Morphological correlates of {MAO} A {VNTR} polymorphism: new evidence from cortical thickness measurement},
	volume = {211},
	issn = {1872-7549},
	shorttitle = {Morphological correlates of {MAO} A {VNTR} polymorphism},
	doi = {10.1016/j.bbr.2010.03.021},
	abstract = {A functional variant in the mono-amine oxidase A ({MAO} A) gene has been shown to impact neural function related to cognitive and affective processing and increase risk for conduct disorders. However, whether {MAO} A could be a candidate gene for structural variation in the human brain remains to be clarified. This study is the first to investigate the effect of this genotype on brain morphology by measuring cortical thickness. We genotyped 59 healthy male subjects (36 carrying the {MAO} A High-activity allele and 23 the {MAO} A Low-activity allele) who underwent structural {MRI} at 3T. Models of the grey-white and pial surfaces were generated for each individual's cortices, and the distance between these two surfaces was used to compute cortical thickness within a priori regions of interest of the orbitofrontal and cingulate cortices. Surface-based analysis of the cortical mantle showed that the {MAO} A genotype was associated with structural differences in the orbitofrontal cortex bilaterally, where the {MAO} A High-activity group showed the highest cortical thickness value and the {MAO} A Low-activity group the lowest. Otherwise, no significant difference was detected within the cingulate cortex. Thus, we confirm the hypothesis that the {MAO} A genotype has a specific impact on human brain morphology. In particular, thickness measurement of the orbitofrontal cortex provides new evidence about the biological impact of the {MAO} A genotype on neural systems relevant to the pathophysiology of behavioural disorders.},
	language = {eng},
	number = {1},
	journal = {Behavioural Brain Research},
	author = {Cerasa, Antonio and Cherubini, Andrea and Quattrone, Aldo and Gioia, Maria C. and Magariello, Angela and Muglia, Maria and Manna, Ida and Assogna, Francesca and Caltagirone, Carlo and Spalletta, Gianfranco},
	month = jul,
	year = {2010},
	pmid = {20303364},
	keywords = {Adolescent, Adult, Aged, Cerebral Cortex, Genetic Variation, Humans, Imaging, Three-Dimensional, Isoenzymes, Magnetic Resonance Imaging, Male, Middle Aged, Minisatellite Repeats, Monoamine Oxidase, Organ Size, Reference Values},
	pages = {118--124}
}

@article{dziobek_role_2010,
	title = {The role of the fusiform-amygdala system in the pathophysiology of autism},
	volume = {67},
	issn = {1538-3636},
	doi = {10.1001/archgenpsychiatry.2010.31},
	abstract = {{CONTEXT}: Autism is a condition of unknown origin with well-documented impairments in social perception and cognition.
{OBJECTIVE}: To assess the relevance of the fusiform-amygdala system to the pathophysiology of autism spectrum conditions.
{DESIGN}: Cross-sectional case-control study.
{SETTING}: University hospital.
{PARTICIPANTS}: A total of 27 adults with autism spectrum conditions and 29 age-, sex-, and intelligence quotient-matched typically developed healthy controls. Patients were assessed according to {DSM}-{IV} criteria using the Autism Diagnostic Interview-Revised.
{INTERVENTIONS}: We applied an automated measurement to estimate fusiform gyrus cortical thickness and a manual tracing method to obtain amygdala volumes. We analyzed volumetric covariance among these brain regions and assessed the functional relevance of anatomical findings by analyzing correlations with emotional face-processing performance.
{MAIN} {OUTCOME} {MEASURES}: Fusiform gyrus cortical thickness, amygdala volume, emotional face processing.
{RESULTS}: We found a specific local increase in cortical thickness of the fusiform gyrus and associated impairments in face processing in individuals with autism. Anatomical covariance between amygdala volume and the increase in fusiform gyrus local thickness was significantly smaller in the group with autism spectrum conditions.
{CONCLUSIONS}: Our data provide the first anatomical evidence of an abnormal amygdala-fusiform system and its behavioral relevance to face-processing deficits in autism spectrum conditions. In light of recent evidence of the involvement of the fusiform gyrus and amygdala in social perception as well as the areas of social cognition and emotional awareness, all of which are relevant to autism, our findings might represent a core pathophysiological mechanism of autism.},
	language = {eng},
	number = {4},
	journal = {Archives of General Psychiatry},
	author = {Dziobek, Isabel and Bahnemann, Markus and Convit, Antonio and Heekeren, Hauke R.},
	month = apr,
	year = {2010},
	pmid = {20368515},
	keywords = {Adult, Amygdala, Autistic Disorder, Case-Control Studies, Cross-Sectional Studies, Female, Humans, Magnetic Resonance Imaging, Male, Neuropsychological Tests, Organ Size, Temporal Lobe},
	pages = {397--405}
}

@article{yeo_spherical_2010,
	title = {Spherical demons: fast diffeomorphic landmark-free surface registration},
	volume = {29},
	issn = {1558-254X (Electronic) 0278-0062 (Linking)},
	shorttitle = {Spherical demons: fast diffeomorphic landmark-free surface registration},
	url = {https://surfer.nmr.mgh.harvard.edu/pub/articles/2010SphericalDemons-TMI.pdf},
	doi = {10.1109/TMI.2009.2030797},
	abstract = {We present the Spherical Demons algorithm for registering two spherical images. By exploiting spherical vector spline interpolation theory, we show that a large class of regularizors for the modified Demons objective function can be efficiently approximated on the sphere using iterative smoothing. Based on one parameter subgroups of diffeomorphisms, the resulting registration is diffeomorphic and fast. The Spherical Demons algorithm can also be modified to register a given spherical image to a probabilistic atlas. We demonstrate two variants of the algorithm corresponding to warping the atlas or warping the subject. Registration of a cortical surface mesh to an atlas mesh, both with more than 160 k nodes requires less than 5 min when warping the atlas and less than 3 min when warping the subject on a Xeon 3.2 {GHz} single processor machine. This is comparable to the fastest nondiffeomorphic landmark-free surface registration algorithms. Furthermore, the accuracy of our method compares favorably to the popular {FreeSurfer} registration algorithm. We validate the technique in two different applications that use registration to transfer segmentation labels onto a new image 1) parcellation of in vivo cortical surfaces and 2) Brodmann area localization in ex vivo cortical surfaces.},
	number = {3},
	journal = {{IEEE} Trans Med Imaging},
	author = {Yeo, B. T. and Sabuncu, M. R. and Vercauteren, T. and Ayache, N. and Fischl, B. and Golland, P.},
	month = mar,
	year = {2010},
	keywords = {*Algorithms, Cerebral Cortex/*anatomy \& histology, fs\_Intersubject-averaging, Humans, *Image Processing, Computer-Assisted, Least-Squares Analysis, Magnetic Resonance Imaging/*methods, Models, Biological, Reproducibility of Results, Time Factors},
	pages = {650--68},
	annote = {Yeo, B T {ThomasSabuncu}, Mert {RVercauteren}, {TomAyache}, {NicholasFischl}, {BruceGolland}, {PolinaengAG}02238/{AG}/{NIA} {NIH} {HHS}/P41-{RR}13218/{RR}/{NCRR} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 {EB}001550/{EB}/{NIBIB} {NIH} {HHS}/R01 {NS}052585-01/{NS}/{NINDS} {NIH} {HHS}/R01 {RR}16594-01A1/{RR}/{NCRR} {NIH} {HHS}/R01-{NS}051826/{NS}/{NINDS} {NIH} {HHS}/R01EB006758/{EB}/{NIBIB} {NIH} {HHS}/U24-{RR}021382/{RR}/{NCRR} {NIH} {HHS}/U54 {EB}005149-050001/{EB}/{NIBIB} {NIH} {HHS}/U54-{EB}005149/{EB}/{NIBIB} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov'{tResearch} Support, U.S. Gov't, Non-P.H.S.2009/08/28 09:00IEEE Trans Med Imaging. 2010 Mar;29(3):650-68. doi: 10.1109/{TMI}.2009.2030797. Epub 2009 Aug 25.},
	file = {Yeo-2010-Spherical demons_ fast diffeomorphic:/autofs/cluster/freesurfer/zotero/storage/V2F3E48E/Yeo-2010-Spherical demons_ fast diffeomorphic.pdf:application/pdf}
}

@article{eyler_genetic_2011,
	title = {Genetic and environmental contributions to regional cortical surface area in humans: a magnetic resonance imaging twin study},
	volume = {21},
	issn = {1460-2199 (Electronic) 1047-3211 (Linking)},
	shorttitle = {Genetic and environmental contributions to regional cortical surface area in humans: a magnetic resonance imaging twin study},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/21378112},
	doi = {10.1093/cercor/bhr013},
	abstract = {Cortical surface area measures appear to be functionally relevant and distinct in etiology, development, and behavioral correlates compared with other size characteristics, such as cortical thickness. Little is known about genetic and environmental influences on individual differences in regional surface area in humans. Using a large sample of adult twins, we determined relative contributions of genes and environment on variations in regional cortical surface area as measured by magnetic resonance imaging before and after adjustment for genetic and environmental influences shared with total cortical surface area. We found high heritability for total surface area and, before adjustment, moderate heritability for regional surface areas. Compared with other lobes, heritability was higher for frontal lobe and lower for medial temporal lobe. After adjustment for total surface area, regionally specific genetic influences were substantially reduced, although still significant in most regions. Unlike other lobes, left frontal heritability remained high after adjustment. Thus, global and regionally specific genetic factors both influence cortical surface areas. These findings are broadly consistent with results from animal studies regarding the evolution and development of cortical patterning and may guide future research into specific environmental and genetic determinants of variation among humans in the surface area of particular regions.},
	number = {10},
	journal = {Cereb Cortex},
	author = {Eyler, L. T. and Prom-Wormley, E. and Panizzon, M. S. and Kaup, A. R. and Fennema-Notestine, C. and Neale, M. C. and Jernigan, T. L. and Fischl, B. and Franz, C. E. and Lyons, M. J. and Grant, M. and Stevens, A. and Pacheco, J. and Perry, M. E. and Schmitt, J. E. and Seidman, L. J. and Thermenos, H. W. and Tsuang, M. T. and Chen, C. H. and Thompson, W. K. and Jak, A. and Dale, A. M. and Kremen, W. S.},
	month = oct,
	year = {2011},
	keywords = {Animals, Brain Mapping/*methods, Cerebral Cortex/*physiology, Humans, Magnetic Resonance Imaging/*methods, Male, Middle Aged, *Quantitative Trait, Heritable, *Social Environment},
	pages = {2313--21},
	annote = {Eyler, Lisa {TProm}-Wormley, {ElizabethPanizzon}, Matthew {SKaup}, Allison {RFennema}-Notestine, {ChristineNeale}, Michael {CJernigan}, Terry {LFischl}, {BruceFranz}, Carol {ELyons}, Michael {JGrant}, {MichaelStevens}, {AllisonPacheco}, {JenniferPerry}, Michele {ESchmitt}, J {EricSeidman}, Larry {JThermenos}, Heidi {WTsuang}, Ming {TChen}, Chi-{HuaThompson}, Wesley {KJak}, {AmyDale}, Anders {MKremen}, William {SengP}41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 {AG} 22982/{AG}/{NIA} {NIH} {HHS}/R01 {AG}018386-09/{AG}/{NIA} {NIH} {HHS}/R01 {AG}18384/{AG}/{NIA} {NIH} {HHS}/R01 {AG}18386/{AG}/{NIA} {NIH} {HHS}/R01 {AG}22381/{AG}/{NIA} {NIH} {HHS}/R01 {DA}18673/{DA}/{NIDA} {NIH} {HHS}/R01 {EB}006758/{EB}/{NIBIB} {NIH} {HHS}/R01 {MH}083968-03/{MH}/{NIMH} {NIH} {HHS}/R01 {NS}052585-01/{NS}/{NINDS} {NIH} {HHS}/T32 {MH}20030/{MH}/{NIMH} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/Comparative {StudyResearch} Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov'{tResearch} Support, U.S. Gov't, Non-P.H.S.Twin {StudyNew} York, N.Y. : 19912011/03/08 06:00Cereb Cortex. 2011 Oct;21(10):2313-21. doi: 10.1093/cercor/bhr013. Epub 2011 Mar 4.},
	file = {Eyler-2011-Genetic and environmental contribut:/autofs/cluster/freesurfer/zotero/storage/DXX2FIFX/Eyler-2011-Genetic and environmental contribut.pdf:application/pdf}
}

@article{walhovd_cortical_2005,
	title = {Cortical volume and speed-of-processing are complementary in prediction of performance intelligence},
	volume = {43},
	issn = {0028-3932},
	url = {https://surfer.nmr.mgh.harvard.edu/ftp/articles/walhovd2005.pdf},
	doi = {10.1016/j.neuropsychologia.2004.08.006},
	abstract = {The rationale for the present study was to investigate the relationship between cortical volume, the latency of the {ERP} component P3a (as a measure of speed-of-processing), and performance intelligence (not adjusted for age differences). Seventy-one participants aged 20-88 years underwent a visual 3-stimuli oddball {ERP} task, an {MRI}-scan, and intelligence testing. P3a latency and cortical volume shared 9\% variance (p{\textless}.05) and both were significantly related to performance intelligence (R2=.26 and .40, respectively). The amount of explained variance increased significantly (to R2=.51) when both measures were used as simultaneous predictors. When a path diagram was constructed including age as an exogenous variable, P3a latency and cortical volume both significantly predicted performance intelligence, but were no longer related to one another. The main conclusion from the study is that speed and size are complementary in prediction of performance intelligence, and the theoretical implications are discussed.},
	language = {eng},
	number = {5},
	journal = {Neuropsychologia},
	author = {Walhovd, Kristine B. and Fjell, Anders M. and Reinvang, Ivar and Lundervold, Arvid and Fischl, Bruce and Salat, David and Quinn, Brian T. and Makris, Nikos and Dale, Anders M.},
	year = {2005},
	pmid = {15721183},
	keywords = {Adult, Adult, Aged, Aged, Aged, 80 and over, Aged, 80 and over, Brain Mapping, Brain Mapping, Cerebral Cortex, Cerebral Cortex/*anatomy \& histology/*physiology, Electroencephalography, Electroencephalography/methods, Evoked Potentials, Visual, Evoked Potentials, Visual/*physiology, Female, Female, Humans, Humans, Intelligence, Intelligence/*physiology, Intelligence Tests, Intelligence Tests, Male, Male, Middle Aged, Middle Aged, Models, Psychological, Models, Psychological, Neuropsychological Tests, Neuropsychological Tests, Photic Stimulation, Photic Stimulation/methods, Psychomotor Performance, Psychomotor Performance/physiology, Reaction Time, Reaction Time/*physiology, Verbal Behavior, Verbal Behavior/physiology},
	pages = {704--713},
	annote = {Walhovd, Kristine {BFjell}, Anders {MReinvang}, {IvarLundervold}, {ArvidFischl}, {BruceSalat}, {DavidQuinn}, Brian {TMakris}, {NikosDale}, Anders {MengP}41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01-{NS}39581/{NS}/{NINDS} {NIH} {HHS}/R01-{RR}13609/{RR}/{NCRR} {NIH} {HHS}/R01-{RR}16594/{RR}/{NCRR} {NIH} {HHS}/Comparative {StudyResearch} Support, Non-U.S. Gov'{tResearch} Support, U.S. Gov't, P.H.S.England2005/02/22 09:00Neuropsychologia. 2005;43(5):704-13.}
}

@article{rippon_multicenter_2010,
	title = {A Multicenter, Randomized, Double-Blind, Placebo-Controlled {fMRI} Study of the Effect of Armodafinil on Prefrontal Cortical Activation in Patients with Residual Excessive Sleepiness Associated with {CPAP}-Treated {OSA}},
	volume = {74},
	issn = {0028-3878},
	shorttitle = {A Multicenter, Randomized, Double-Blind, Placebo-Controlled {fMRI} Study of the Effect of Armodafinil on Prefrontal Cortical Activation in Patients with Residual Excessive Sleepiness Associated with {CPAP}-Treated {OSA}},
	url = {://WOS:000275274001337},
	number = {9},
	journal = {Neurology},
	author = {Rippon, G. and Greve, D. N. and Duntley, S. and Larson-Prior, L. and Krystal, A. and Fischl, B. and Thein, S. and Yang, R. H. and Dayno, J. and Kushida, C. and Thomas, R.},
	month = mar,
	year = {2010},
	pages = {A276--A277},
	annote = {Times Cited: 0Rippon, Gregory Greve, Douglas N. Duntley, Stephen Larson-Prior, Linda Krystal, Andrew Fischl, Bruce Thein, Stephen Yang, Ronghua Dayno, Jeffrey Kushida, Clete Thomas, Robert62nd Annual Meeting of the American-Academy-of-{NeurologyApr} 10-17, 2010Toronto, {CANADA}2}
}

@article{rauch_orbitofrontal_2005,
	title = {Orbitofrontal thickness, retention of fear extinction, and extraversion},
	volume = {16},
	issn = {0959-4965 (Print) 0959-4965 (Linking)},
	shorttitle = {Orbitofrontal thickness, retention of fear extinction, and extraversion},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/16272877},
	abstract = {People differ in their personality traits and in their ability to modulate fear. Does our personality determine how well we extinguish conditioned fear responses? Or is the opposite true? Herein, we examine the relationships between personality traits, memory for fear extinction, and cortical thickness as a measure of brain structure. We found that in healthy humans, extinction retention and thickness of the medial orbitofrontal cortex are positively correlated with extraversion. Path analysis indicates that extinction retention mediates the relationship between the medial orbitofrontal cortex thickness and extraversion, thereby illustrating one path through which brain structure influences personality.},
	number = {17},
	journal = {Neuroreport},
	author = {Rauch, S. L. and Milad, M. R. and Orr, S. P. and Quinn, B. T. and Fischl, B. and Pitman, R. K.},
	month = nov,
	year = {2005},
	keywords = {Conditioning (Psychology)/physiology, Extinction, Psychological/*physiology, *Extraversion (Psychology), Fear/*physiology, Female, Humans, Male, Prefrontal Cortex/*anatomy \& histology/*physiology},
	pages = {1909--12},
	annote = {Rauch, Scott {LMilad}, Mohammed {ROrr}, Scott {PQuinn}, Brian {TFischl}, {BrucePitman}, Roger {KengResearch} Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov'{tEngland}2005/11/08 09:00Neuroreport. 2005 Nov 28;16(17):1909-12.},
	file = {Rauch-2005-Orbitofrontal thickness, retention:/autofs/cluster/freesurfer/zotero/storage/CDSXI2UM/Rauch-2005-Orbitofrontal thickness, retention.pdf:application/pdf}
}

@article{schwartz_structural_2010,
	title = {Structural differences in adult orbital and ventromedial prefrontal cortex are predicted by 4-month infant temperament},
	volume = {67},
	issn = {0003-990X},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2811077/},
	doi = {10.1001/archgenpsychiatry.2009.171},
	abstract = {Context
The term temperament refers to a biologically based predilection for a distinctive pattern of emotions, cognitions, and behaviours first observed in infancy or early childhood. High reactive infants are characterized at 4 months by vigorous motor activity and crying in response to unfamiliar visual, auditory, and olfactory stimuli, whereas low reactive infants show low motor activity and low vocal distress to the same stimuli. High reactive infants are biased to become behaviorally inhibited in the second year of life, defined by timidity with unfamiliar people, objects and situations. In contrast, low reactive infants are biased to develop into uninhibited children who spontaneously approach novel situations.

Objective
To examine whether differences in the structure of ventromedial or orbitofrontal cerebral cortex at age 18 years are associated with high or low reactivity at 4 months of age.

Design
Structural {MRI} in a cohort of 18-year olds enrolled in a longitudinal study. Temperament was determined at 4 months of age by direct observation in the laboratory.

Setting
Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital

Participants
76 subjects who were high reactive or low reactive infants at 4 months of age.

Main Outcome Measures
Cortical thickness

Results
Adults with a low reactive infant temperament, compared with those categorized as high reactive, showed greater thickness in left orbitofrontal cortex. Subjects categorized as high reactive in infancy, compared with those previously categorized as low reactive, showed greater thickness in right ventromedial prefrontal cortex. This is the first demonstration that temperamental differences measured at 4 months of age have implications for the architecture of human cerebral cortex lasting into adulthood. Understanding the developmental mechanisms that shape these differences may offer new ways to understand mood and anxiety disorders as well as the formation of adult personality.},
	number = {1},
	urldate = {2014-08-23},
	journal = {Archives of general psychiatry},
	author = {Schwartz, Carl E. and Kunwar, Pratap S. and Greve, Douglas N. and Moran, Lyndsey R. and Viner, Jane C. and Covino, Jennifer M. and Kagan, Jerome and Stewart, S. Evelyn and Snidman, Nancy C. and Vangel, Mark G. and Wallace, Stuart R.},
	month = jan,
	year = {2010},
	pmid = {20048225},
	pmcid = {PMC2811077},
	pages = {78--84},
	file = {PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/7UWAAQZ2/Schwartz et al. - 2010 - Structural differences in adult orbital and ventro.pdf:application/pdf}
}

@article{salat_white_2010,
	title = {White Matter Pathology Isolates the Hippocampal Formation in Alzheimer's Disease},
	volume = {31},
	issn = {0197-4580},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3038572/},
	doi = {10.1016/j.neurobiolaging.2008.03.013},
	abstract = {Prior work has demonstrated that the memory dysfunction of Alzheimer’s disease ({AD}) is accompanied by marked cortical pathology in medial temporal lobe ({MTL}) gray matter. In contrast, changes in white matter ({WM}) of pathways associated with the {MTL} have rarely been studied. We used diffusion tensor imaging ({DTI}) to examine regional patterns of {WM} tissue changes in individuals with {AD}. Alterations of diffusion properties with {AD} were found in several regions including parahippocampal {WM}, and in regions with direct and secondary connections to the {MTL}. A portion of the changes measured, including effects in the parahippocampal {WM}, were independent of gray matter degeneration as measured by hippocampal volume. Examination of regional changes in unique diffusion parameters including anisotropy and axial and radial diffusivity demonstrated distinct zones of alterations, potentially stemming from differences in underlying pathology, with a potential myelin specific pathology in the parahippocampal {WM}. These results demonstrate that deterioration of neocortical connections to the hippocampal formation results in part from the degeneration of critical {MTL} and associated fiber pathways.},
	number = {2},
	urldate = {2014-08-25},
	journal = {Neurobiology of aging},
	author = {Salat, DH and Tuch, DS and van der Kouwe, AJW and Greve, DN and Pappu, V and Lee, SY and Hevelone, ND and Zaleta, AK and Growdon, JH and Corkin, S and Fischl, B and Rosas, HD},
	month = feb,
	year = {2010},
	pmid = {18455835},
	pmcid = {PMC3038572},
	keywords = {Aged, Alzheimer Disease/*pathology, Anisotropy, Brain/pathology, Diffusion Tensor Imaging, Female, Hippocampus/*pathology, Humans, Image Processing, Computer-Assisted, Male, Nerve Fibers, Myelinated/*pathology, Nerve Fibers, Unmyelinated/pathology, Neural Pathways/pathology, Organ Size, Parahippocampal Gyrus/pathology},
	pages = {244--256},
	annote = {Salat, D {HTuch}, D Svan der Kouwe, A J {WGreve}, D {NPappu}, {VLee}, S {YHevelone}, N {DZaleta}, A {KGrowdon}, J {HCorkin}, {SFischl}, {BRosas}, H {DengAG}05886/{AG}/{NIA} {NIH} {HHS}/K01 {AG}024898-01A1/{AG}/{NIA} {NIH} {HHS}/K01 {AG}024898-02/{AG}/{NIA} {NIH} {HHS}/K01 {AG}024898-03/{AG}/{NIA} {NIH} {HHS}/K01 {AG}024898-04/{AG}/{NIA} {NIH} {HHS}/K01AG024898/{AG}/{NIA} {NIH} {HHS}/P41 {RR}014075/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-01A1/{RR}/{NCRR} {NIH} {HHS}/P41RR14075/{RR}/{NCRR} {NIH} {HHS}/R01 {NR}010827-05/{NR}/{NINR} {NIH} {HHS}/U54 {EB}005149-01/{EB}/{NIBIB} {NIH} {HHS}/U54 {EB}05149/{EB}/{NIBIB} {NIH} {HHS}/Research Support, N.I.H., Extramural2008/05/06 09:00Neurobiol Aging. 2010 Feb;31(2):244-56. doi: 10.1016/j.neurobiolaging.2008.03.013. Epub .},
	file = {PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/UK2Q8F3Q/Salat et al. - 2010 - White Matter Pathology Isolates the Hippocampal Fo.pdf:application/pdf;Salat-2010-White matter pathology isolates the:/autofs/cluster/freesurfer/zotero/storage/5MXR92GB/Salat-2010-White matter pathology isolates the.pdf:application/pdf}
}

@article{sasaki_local_2001,
	title = {Local and global attention are mapped retinotopically in human occipital cortex},
	volume = {98},
	issn = {0027-8424 (Print) 0027-8424 (Linking)},
	shorttitle = {Local and global attention are mapped retinotopically in human occipital cortex},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/11172078},
	doi = {10.1073/pnas.98.4.2077},
	abstract = {Clinical evidence suggests that control mechanisms for local and global attention are lateralized in the temporal-parietal cortex. However, in the human occipital (visual) cortex, the evidence for lateralized local/global attention is controversial. To clarify this matter, we used functional {MRI} to map activity in the human occipital cortex, during local and global attention, with sustained visual fixation. Data were analyzed in a flattened cortical format, relative to maps of retinotopy and spatial frequency peak tuning. Neither local nor global attention was lateralized in the occipital cortex. Instead, local attention and global attention appear to be special cases of visual spatial attention, which are mapped consistently with the maps of retinotopy and spatial frequency tuning, in multiple visual cortical areas.},
	number = {4},
	journal = {Proc Natl Acad Sci U S A},
	author = {Sasaki, Y. and Hadjikhani, N. and Fischl, B. and Liu, A. K. and Marrett, S. and Dale, A. M. and Tootell, R. B.},
	month = feb,
	year = {2001},
	keywords = {Attention/*physiology, *Brain Mapping/methods, Humans, Photic Stimulation, Tomography, Emission-Computed, Visual Cortex/*physiology},
	pages = {2077--82},
	annote = {Sasaki, {YHadjikhani}, {NFischl}, {BLiu}, A {KMarrett}, {SDale}, A {MTootell}, R {BengEY}07980/{EY}/{NEI} {NIH} {HHS}/R01 {NS}39581/{NS}/{NINDS} {NIH} {HHS}/Research Support, Non-U.S. Gov'{tResearch} Support, U.S. Gov't, P.H.S.2001/02/15 11:00Proc Natl Acad Sci U S A. 2001 Feb 13;98(4):2077-82.},
	file = {Sasaki-2001-Local and global attention are map:/autofs/cluster/freesurfer/zotero/storage/B6P72I32/Sasaki-2001-Local and global attention are map.pdf:application/pdf}
}

@article{nesvag_regional_2008,
	title = {Regional thinning of the cerebral cortex in schizophrenia: effects of diagnosis, age and antipsychotic medication},
	volume = {98},
	issn = {0920-9964},
	shorttitle = {Regional thinning of the cerebral cortex in schizophrenia},
	doi = {10.1016/j.schres.2007.09.015},
	abstract = {Morphological abnormalities of the cerebral cortex have been reported in a number of {MRI}-studies in schizophrenia. Uncertainty remains regarding cause, mechanism and progression of the alterations. It has been suggested that antipsychotic medication reduces total gray matter volumes, but results are inconsistent. In the present study differences in regional cortical thickness between 96 patients with a {DSM}-{IV} diagnosis of schizophrenia (n=81) or schizoaffective disorder (n=15) and 107 healthy subjects (mean age 42 years, range 17-57 years) were investigated using {MRI} and computer image analysis. Cortical thickness was estimated as the shortest distance between the gray/white matter border and the pial surface at numerous points across the entire cortical mantle. The influence of age and antipsychotic medication on variation in global and regional cortical thickness was explored. Thinner cortex among patients than controls was found in prefrontal and temporal regions of both hemispheres, while parietal and occipital regions were relatively spared. Some hemispheric specificity was noted, as regions of the prefrontal cortex were more affected in the right hemisphere, and regions of the temporal cortex in the left hemisphere. No significant interaction effect of age and diagnostic group on variation in cortical thickness was demonstrated. Among patients, dose or type of antipsychotic medication did not affect variation in cortical thickness. The results from this hitherto largest study on the topic show that prefrontal and temporal cortical thinning in patients with schizophrenia compared to controls is as pronounced in older as in younger subjects. The lack of significant influence from antipsychotic medication supports that regional cortical thinning is an inherent feature of the neurobiological disease process in schizophrenia.},
	language = {eng},
	number = {1-3},
	journal = {Schizophrenia Research},
	author = {Nesvåg, Ragnar and Lawyer, Glenn and Varnäs, Katarina and Fjell, Anders M. and Walhovd, Kristine B. and Frigessi, Arnoldo and Jönsson, Erik G. and Agartz, Ingrid},
	month = jan,
	year = {2008},
	pmid = {17933495},
	keywords = {Adult, Age Factors, Age of Onset, Antipsychotic Agents, Atrophy, Brain Mapping, Cerebral Cortex, Diagnostic and Statistical Manual of Mental Disorders, Female, Functional Laterality, Humans, Magnetic Resonance Imaging, Male, Middle Aged, Psychiatric Status Rating Scales, Schizophrenia, Sweden, Wechsler Scales},
	pages = {16--28}
}

@article{desikan_mri_2008,
	title = {{MRI} measures of temporoparietal regions show differential rates of atrophy during prodromal {AD}},
	volume = {71},
	issn = {0028-3878},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2577003/},
	doi = {10.1212/01.wnl.0000320055.57329.34},
	abstract = {Background:
{MRI} studies have demonstrated differential rates of atrophy in the entorhinal cortex and hippocampus during the prodromal phase of Alzheimer disease ({AD}). The current study was designed to determine whether a broader set of temporoparietal regions show differential rates of atrophy during the evolution of {AD}.

Methods:
Sixteen regions of interest ({ROIs}) were analyzed on {MRI} scans obtained at baseline and follow-up in 66 subjects comprising three groups: controls = individuals who were cognitively normal at both baseline and follow-up; nonconverters = subjects with mild cognitive impairment ({MCI}) at both baseline and follow-up; converters had {MCI} at baseline but had progressed to {AD} at follow-up.

Results:
Annualized percent change was analyzed with multivariate analysis of variance ({MANOVA}), covaried for age. The {MANOVA} demonstrated an effect of group (p = 0.004). Post hoc comparisons demonstrated greater rates of atrophy for converters vs nonconverters for six {ROIs}: hippocampus, entorhinal cortex, temporal pole, middle temporal gyrus, fusiform gyrus, and inferior temporal gyrus. Converters showed differentially greater rates of atrophy than controls in five of the same {ROIs} (and inferior parietal lobule). Rates of change in clinical status were correlated with the atrophy rates in these regions. Comparisons between controls and nonconverters demonstrated no differences.

Conclusion:
These results demonstrate that temporoparietal regions show differential rates of atrophy on {MRI} during prodromal Alzheimer disease ({AD}). {MRI} data correlate with measures of clinical severity and cognitive decline, suggesting the potential of these regions of interest as antemortem markers of prodromal {AD}.

{GLOSSARY}
null},
	number = {11},
	urldate = {2014-08-25},
	journal = {Neurology},
	author = {Desikan, R S. and Fischl, B and Cabral, H J. and Kemper, T L. and Guttmann, C R.G. and Blacker, D and Hyman, B T. and Albert, M S. and Killiany, R J.},
	month = sep,
	year = {2008},
	pmid = {18672473},
	pmcid = {PMC2577003},
	keywords = {Aged, Alzheimer Disease/metabolism/*pathology, Atrophy, Female, Follow-Up Studies, Humans, Magnetic Resonance Imaging/*methods/standards, Male, Parietal Lobe/metabolism/*pathology, Research Design/standards, Temporal Lobe/metabolism/*pathology, Time Factors},
	pages = {819--825},
	annote = {Desikan, R {SFischl}, {BCabral}, H {JKemper}, T {LGuttmann}, C R {GBlacker}, {DHyman}, B {TAlbert}, M {SKilliany}, R {JengP}01 {AG}004953/{AG}/{NIA} {NIH} {HHS}/P01 {AG}004953-230001/{AG}/{NIA} {NIH} {HHS}/P01 {AG}004953-230006/{AG}/{NIA} {NIH} {HHS}/P01-{AG}04953/{AG}/{NIA} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 {NS}052585/{NS}/{NINDS} {NIH} {HHS}/R01-{EB}001550/{EB}/{NIBIB} {NIH} {HHS}/R01-{RR}16594/{RR}/{NCRR} {NIH} {HHS}/U24-{RR}021382/{RR}/{NCRR} {NIH} {HHS}/Comparative {StudyResearch} Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov't2008/08/02 09:00Neurology. 2008 Sep 9;71(11):819-25. doi: 10.1212/01.wnl.0000320055.57329.34. Epub 2008 Jul 30.},
	file = {Desikan-2008-MRI measures of temporoparietal r:/autofs/cluster/freesurfer/zotero/storage/33FTVEHP/Desikan-2008-MRI measures of temporoparietal r.pdf:application/pdf;PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/97WX3GWN/Desikan et al. - 2008 - MRI measures of temporoparietal regions show diffe.pdf:application/pdf}
}

@article{yendiki_automated_2011,
	title = {Automated probabilistic reconstruction of white-matter pathways in health and disease using an atlas of the underlying anatomy},
	volume = {5},
	issn = {1662-5196 (Electronic) 1662-5196 (Linking)},
	shorttitle = {Automated probabilistic reconstruction of white-matter pathways in health and disease using an atlas of the underlying anatomy},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/22016733},
	doi = {10.3389/fninf.2011.00023},
	abstract = {We have developed a method for automated probabilistic reconstruction of a set of major white-matter pathways from diffusion-weighted {MR} images. Our method is called {TRACULA} ({TRActs} Constrained by {UnderLying} Anatomy) and utilizes prior information on the anatomy of the pathways from a set of training subjects. By incorporating this prior knowledge in the reconstruction procedure, our method obviates the need for manual interaction with the tract solutions at a later stage and thus facilitates the application of tractography to large studies. In this paper we illustrate the application of the method on data from a schizophrenia study and investigate whether the inclusion of both patients and healthy subjects in the training set affects our ability to reconstruct the pathways reliably. We show that, since our method does not constrain the exact spatial location or shape of the pathways but only their trajectory relative to the surrounding anatomical structures, a set a of healthy training subjects can be used to reconstruct the pathways accurately in patients as well as in controls.},
	urldate = {2014-08-21},
	journal = {Front Neuroinform},
	author = {Yendiki, A. and Panneck, P. and Srinivasan, P. and Stevens, A. and Zollei, L. and Augustinack, J. and Wang, R. and Salat, D. and Ehrlich, S. and Behrens, T. and Jbabdi, S. and Gollub, R. and Fischl, B.},
	year = {2011},
	keywords = {fs\_TRACULA},
	pages = {23},
	annote = {Yendiki, {AnastasiaPanneck}, {PatriciaSrinivasan}, {PritiStevens}, {AllisonZollei}, {LillaAugustinack}, {JeanWang}, {RuopengSalat}, {DavidEhrlich}, {StefanBehrens}, {TimJbabdi}, {SaadGollub}, {RandyFischl}, {BruceengG}0800578/Medical Research Council/United {KingdomR}00 {EB}008129/{EB}/{NIBIB} {NIH} {HHS}/Switzerland2011/10/22 06:00Front Neuroinform. 2011 Oct 14;5:23. doi: 10.3389/fninf.2011.00023. {eCollection} 2011.},
	file = {Yendiki-2011-Automated probabilistic reconstru:/autofs/cluster/freesurfer/zotero/storage/9H9G56CP/Yendiki-2011-Automated probabilistic reconstru.pdf:application/pdf}
}

@article{destrieux_automatic_2010,
	title = {Automatic parcellation of human cortical gyri and sulci using standard anatomical nomenclature},
	volume = {53},
	issn = {1095-9572 (Electronic) 1053-8119 (Linking)},
	shorttitle = {Automatic parcellation of human cortical gyri and sulci using standard anatomical nomenclature},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2937159/pdf/nihms213933.pdf},
	doi = {10.1016/j.neuroimage.2010.06.010},
	abstract = {Precise localization of sulco-gyral structures of the human cerebral cortex is important for the interpretation of morpho-functional data, but requires anatomical expertise and is time consuming because of the brain's geometric complexity. Software developed to automatically identify sulco-gyral structures has improved substantially as a result of techniques providing topologically correct reconstructions permitting inflated views of the human brain. Here we describe a complete parcellation of the cortical surface using standard internationally accepted nomenclature and criteria. This parcellation is available in the {FreeSurfer} package. First, a computer-assisted hand parcellation classified each vertex as sulcal or gyral, and these were then subparcellated into 74 labels per hemisphere. Twelve datasets were used to develop rules and algorithms (reported here) that produced labels consistent with anatomical rules as well as automated computational parcellation. The final parcellation was used to build an atlas for automatically labeling the whole cerebral cortex. This atlas was used to label an additional 12 datasets, which were found to have good concordance with manual labels. This paper presents a precisely defined method for automatically labeling the cortical surface in standard terminology.},
	number = {1},
	journal = {Neuroimage},
	author = {Destrieux, C. and Fischl, B. and Dale, A. and Halgren, E.},
	month = oct,
	year = {2010},
	keywords = {Adolescent, Adult, *Algorithms, Brain/*anatomy \& histology, Computer Simulation, Female, fs\_Cortical-parcellation, Humans, Image Enhancement/methods, Image Interpretation, Computer-Assisted/*methods, Imaging, Three-Dimensional/*methods, Magnetic Resonance Imaging/*methods, Male, Models, Anatomic, Pattern Recognition, Automated/*methods, Reproducibility of Results, Sensitivity and Specificity, *Terminology as Topic, Young Adult},
	pages = {1--15},
	annote = {Destrieux, {ChristopheFischl}, {BruceDale}, {AndersHalgren}, {EricengP}41 {RR}014075/{RR}/{NCRR} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 {AG}018386-09/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022381-01/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022381-09/{AG}/{NIA} {NIH} {HHS}/R01 {EB}001550/{EB}/{NIBIB} {NIH} {HHS}/R01 {EB}006758-01A1/{EB}/{NIBIB} {NIH} {HHS}/R01 {EB}009282/{EB}/{NIBIB} {NIH} {HHS}/R01 {EB}009282-01/{EB}/{NIBIB} {NIH} {HHS}/R01 {NS}018741/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}052585-01A1/{NS}/{NINDS} {NIH} {HHS}/R01EB006758/{EB}/{NIBIB} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/U54 {EB}005149-01/{EB}/{NIBIB} {NIH} {HHS}/Research Support, N.I.H., Extramural2010/06/16 06:00Neuroimage. 2010 Oct 15;53(1):1-15. doi: 10.1016/j.neuroimage.2010.06.010. Epub 2010 Jun 12.},
	file = {Destrieux-2010-Automatic parcellation of human:/autofs/cluster/freesurfer/zotero/storage/ARZ3SE4C/Destrieux-2010-Automatic parcellation of human.pdf:application/pdf}
}

@article{desikan_automated_2006,
	title = {An automated labeling system for subdividing the human cerebral cortex on {MRI} scans into gyral based regions of interest},
	volume = {31},
	issn = {1053-8119 (Print) 1053-8119 (Linking)},
	shorttitle = {An automated labeling system for subdividing the human cerebral cortex on {MRI} scans into gyral based regions of interest},
	url = {https://surfer.nmr.mgh.harvard.edu/ftp/articles/desikan06-parcellation.pdf},
	doi = {10.1016/j.neuroimage.2006.01.021},
	abstract = {In this study, we have assessed the validity and reliability of an automated labeling system that we have developed for subdividing the human cerebral cortex on magnetic resonance images into gyral based regions of interest ({ROIs}). Using a dataset of 40 {MRI} scans we manually identified 34 cortical {ROIs} in each of the individual hemispheres. This information was then encoded in the form of an atlas that was utilized to automatically label {ROIs}. To examine the validity, as well as the intra- and inter-rater reliability of the automated system, we used both intraclass correlation coefficients ({ICC}), and a new method known as mean distance maps, to assess the degree of mismatch between the manual and the automated sets of {ROIs}. When compared with the manual {ROIs}, the automated {ROIs} were highly accurate, with an average {ICC} of 0.835 across all of the {ROIs}, and a mean distance error of less than 1 mm. Intra- and inter-rater comparisons yielded little to no difference between the sets of {ROIs}. These findings suggest that the automated method we have developed for subdividing the human cerebral cortex into standard gyral-based neuroanatomical regions is both anatomically valid and reliable. This method may be useful for both morphometric and functional studies of the cerebral cortex as well as for clinical investigations aimed at tracking the evolution of disease-induced changes over time, including clinical trials in which {MRI}-based measures are used to examine response to treatment.},
	number = {3},
	journal = {Neuroimage},
	author = {Desikan, R. S. and Segonne, F. and Fischl, B. and Quinn, B. T. and Dickerson, B. C. and Blacker, D. and Buckner, R. L. and Dale, A. M. and Maguire, R. P. and Hyman, B. T. and Albert, M. S. and Killiany, R. J.},
	month = jul,
	year = {2006},
	keywords = {Adult, Aged, Aged, 80 and over, Aging/*physiology, Algorithms, Alzheimer Disease/*pathology, Atrophy, Brain Mapping/*methods, Cerebral Cortex/*pathology, Corpus Callosum/pathology, Dominance, Cerebral/physiology, Female, fs\_Cortical-parcellation, Humans, Image Processing, Computer-Assisted/*methods, Imaging, Three-Dimensional/*methods, Magnetic Resonance Imaging/*methods, Male, Middle Aged, Observer Variation, Reproducibility of Results, Software, Statistics as Topic},
	pages = {968--80},
	annote = {Desikan, Rahul {SSegonne}, {FlorentFischl}, {BruceQuinn}, Brian {TDickerson}, Bradford {CBlacker}, {DeborahBuckner}, Randy {LDale}, Anders {MMaguire}, R {PaulHyman}, Bradley {TAlbert}, Marilyn {SKilliany}, Ronald {JengP}01-{AG}04953/{AG}/{NIA} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 {RR} 06594-01A1/{RR}/{NCRR} {NIH} {HHS}/R01 {EB}001550/{EB}/{NIBIB} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov't2006/03/15 09:00Neuroimage. 2006 Jul 1;31(3):968-80. Epub 2006 Mar 10.}
}

@article{klein_evaluation_2010,
	title = {Evaluation of volume-based and surface-based brain image registration methods},
	volume = {51},
	issn = {1095-9572 (Electronic) 1053-8119 (Linking)},
	shorttitle = {Evaluation of volume-based and surface-based brain image registration methods},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/20123029},
	doi = {10.1016/j.neuroimage.2010.01.091},
	abstract = {Establishing correspondences across brains for the purposes of comparison and group analysis is almost universally done by registering images to one another either directly or via a template. However, there are many registration algorithms to choose from. A recent evaluation of fully automated nonlinear deformation methods applied to brain image registration was restricted to volume-based methods. The present study is the first that directly compares some of the most accurate of these volume registration methods with surface registration methods, as well as the first study to compare registrations of whole-head and brain-only (de-skulled) images. We used permutation tests to compare the overlap or Hausdorff distance performance for more than 16,000 registrations between 80 manually labeled brain images. We compared every combination of volume-based and surface-based labels, registration, and evaluation. Our primary findings are the following: 1. de-skulling aids volume registration methods; 2. custom-made optimal average templates improve registration over direct pairwise registration; and 3. resampling volume labels on surfaces or converting surface labels to volumes introduces distortions that preclude a fair comparison between the highest ranking volume and surface registration methods using present resampling methods. From the results of this study, we recommend constructing a custom template from a limited sample drawn from the same or a similar representative population, using the same algorithm used for registering brains to the template.},
	language = {en},
	number = {1},
	urldate = {2014-08-21},
	journal = {Neuroimage},
	author = {Klein, A. and Ghosh, S. S. and Avants, B. and Yeo, B. T. and Fischl, B. and Ardekani, B. and Gee, J. C. and Mann, J. J. and Parsey, R. V.},
	month = may,
	year = {2010},
	keywords = {Adult, *Algorithms, Brain/*anatomy \& histology, Female, fs\_Validation-Evaluations, Head/anatomy \& histology, Humans, Image Processing, Computer-Assisted/*methods, Imaging, Three-Dimensional/methods, Magnetic Resonance Imaging/*methods, Male, Organ Size, Software, Young Adult},
	pages = {214--20},
	annote = {Klein, {ArnoGhosh}, Satrajit {SAvants}, {BrianYeo}, B T {TFischl}, {BruceArdekani}, {BabakGee}, James {CMann}, J {JParsey}, Ramin {VengAG}02238/{AG}/{NIA} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 {EB}006758/{EB}/{NIBIB} {NIH} {HHS}/R01 {MH}084029/{MH}/{NIMH} {NIH} {HHS}/R01 {MH}084029-01A1/{MH}/{NIMH} {NIH} {HHS}/R01 {MH}084029-03/{MH}/{NIMH} {NIH} {HHS}/R01 {NS}052585-01/{NS}/{NINDS} {NIH} {HHS}/R03 {EB}008201/{EB}/{NIBIB} {NIH} {HHS}/R03 {EB}008673/{EB}/{NIBIB} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/U54 {EB}005149/{EB}/{NIBIB} {NIH} {HHS}/Comparative {StudyEvaluation} {StudiesResearch} Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov't2010/02/04 06:00Neuroimage. 2010 May 15;51(1):214-20. doi: 10.1016/j.neuroimage.2010.01.091. Epub 2010 Feb 1.},
	file = {Klein-2010-Evaluation of volume-based and surf:/autofs/cluster/freesurfer/zotero/storage/9K8G8JSZ/Klein-2010-Evaluation of volume-based and surf.pdf:application/pdf}
}

@article{milad_thickness_2005,
	title = {Thickness of ventromedial prefrontal cortex in humans is correlated with extinction memory},
	volume = {102},
	shorttitle = {Thickness of ventromedial prefrontal cortex in humans is correlated with extinction memory},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1180773/pdf/pnas-0502441102.pdf},
	journal = {Proc.Natl.Acad.Sci.U.S.A},
	author = {Milad, M. R. and Quinn, B. T. and Pitman, R. K. and Orr, S. P. and Fischl, B. and Rauch, S. L.},
	year = {2005},
	keywords = {cortex, human, Humans, memory, prefrontal cortex},
	pages = {10706--10711},
	annote = {{DA} - 20050727NOT {IN} {FILE}},
	file = {Milad-2005-Thickness of ventromedial prefronta:/autofs/cluster/freesurfer/zotero/storage/MSI6D59T/Milad-2005-Thickness of ventromedial prefronta.pdf:application/pdf}
}

@article{chee_cognitive_2009,
	title = {Cognitive function and brain structure correlations in healthy elderly East Asians},
	volume = {46},
	issn = {1095-9572},
	doi = {10.1016/j.neuroimage.2009.01.036},
	abstract = {We investigated the effect of age and health variables known to modulate cognitive aging on several measures of cognitive performance and brain volume in a cohort of healthy, non-demented persons of Chinese descent aged between 55 and 86 years. 248 subjects contributed combined neuropsychological, {MR} imaging, health and socio-demographic information. Speed of processing showed the largest age-related decline. Education and plasma homocysteine levels modulated age-related decline in cognitive performance. Total cerebral volume declined at an annual rate of 0.4\%/yr. Gray and white matter volume loss was comparable in magnitude. Regionally, there was relatively greater volume loss in the lateral prefrontal cortex bilaterally, around the primary visual cortex as well as bilateral superior parietal cortices. Speed of processing showed significant positive correlation with gray matter volume in several frontal, parietal and midline occipital regions bilaterally. In spite of differences in diet, lifestyle and culture, these findings are broadly comparable to studies conducted in Caucasian populations and suggest generalizability of processes involved in age-related decline in cognition and brain volume.},
	language = {eng},
	number = {1},
	journal = {{NeuroImage}},
	author = {Chee, Michael W. L. and Chen, Karren H. M. and Zheng, Hui and Chan, Karen P. L. and Isaac, Vivian and Sim, Sam K. Y. and Chuah, Lisa Y. M. and Schuchinsky, Maria and Fischl, Bruce and Ng, Tze Pin},
	month = may,
	year = {2009},
	pmid = {19457386},
	keywords = {Aged, Aged, 80 and over, Aging, Asian Continental Ancestry Group, Brain, Brain Mapping, Cognition, Female, Humans, Image Interpretation, Computer-Assisted, Magnetic Resonance Imaging, Male, Middle Aged, Neuropsychological Tests},
	pages = {257--269}
}

@article{segonne_hybrid_2004,
	title = {A hybrid approach to the skull stripping problem in {MRI}},
	volume = {22},
	issn = {1053-8119 (Print) 1053-8119 (Linking)},
	shorttitle = {A hybrid approach to the skull stripping problem in {MRI}},
	url = {http://www.nmr.mgh.harvard.edu/~fischl/reprints/Neuroimage_Segonne_watershed.pdf},
	doi = {10.1016/j.neuroimage.2004.03.032},
	abstract = {We present a novel skull-stripping algorithm based on a hybrid approach that combines watershed algorithms and deformable surface models. Our method takes advantage of the robustness of the former as well as the surface information available to the latter. The algorithm first localizes a single white matter voxel in a T1-weighted {MRI} image, and uses it to create a global minimum in the white matter before applying a watershed algorithm with a preflooding height. The watershed algorithm builds an initial estimate of the brain volume based on the three-dimensional connectivity of the white matter. This first step is robust, and performs well in the presence of intensity nonuniformities and noise, but may erode parts of the cortex that abut bright nonbrain structures such as the eye sockets, or may remove parts of the cerebellum. To correct these inaccuracies, a surface deformation process fits a smooth surface to the masked volume, allowing the incorporation of geometric constraints into the skull-stripping procedure. A statistical atlas, generated from a set of accurately segmented brains, is used to validate and potentially correct the segmentation, and the {MRI} intensity values are locally re-estimated at the boundary of the brain. Finally, a high-resolution surface deformation is performed that accurately matches the outer boundary of the brain, resulting in a robust and automated procedure. Studies by our group and others outperform other publicly available skull-stripping tools.},
	language = {eng},
	number = {3},
	journal = {Neuroimage},
	author = {Segonne, F. and Dale, A. M. and Busa, E. and Glessner, M. and Salat, D. and Hahn, H. K. and Fischl, B.},
	month = jul,
	year = {2004},
	keywords = {*Algorithms, Brain/*anatomy \& histology, Data Interpretation, Statistical, fs\_Surface-reconstruction, Humans, Image Processing, Computer-Assisted/*methods, Magnetic Resonance Imaging/*methods, Models, Neurological},
	pages = {1060--75},
	annote = {Segonne, {FDale}, A {MBusa}, {EGlessner}, {MSalat}, {DHahn}, H {KFischl}, {BengP}41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 {RR}16594-01A1/{RR}/{NCRR} {NIH} {HHS}/Research Support, Non-U.S. Gov'{tResearch} Support, U.S. Gov't, P.H.S.2004/06/29 05:00Neuroimage. 2004 Jul;22(3):1060-75.}
}

@article{espeseth_interactive_2006,
	title = {Interactive effects of {APOE} and {CHRNA}4 on attention and white matter volume in healthy middle-aged and older adults},
	volume = {6},
	issn = {1530-7026},
	url = {https://surfer.nmr.mgh.harvard.edu/pub/articles/CognAffBehNeurosci%20(2006).pdf},
	abstract = {In the present study, we investigated age-related changes in interactions between efficiency of neuronal repair mechanisms and efficiency of cholinergic neurotransmission in the context of attentional orienting. In addition, we explored white matter volume changes as possible neuronal underpinnings. A sample of 230 healthy middle-aged (53-64 years) and older (65-75 years) adults was genotyped for polymorphisms of {APOE} and {CHRNA}4, a nicotinic receptor subunit gene. Participants were administered a visuospatial attention task involving letter discrimination with location cues of varying validity. Genotype effects on white matter volume were also investigated in a subset of participants who received {MRI} scans. {APOE} interacted with {CHRNA}4, such that {APOE}-epsilon4 carriers who were also {CHRNA}4 {TT} homozygotes showed disproportionately slowed reaction time ({RT}) following invalid location cues. The interaction was stronger in the middle-aged participants than in the older participants. There was also a trend for individuals with combined {APOE}-epsilon4/{CHRNA}4 {TT} genotypes to show both lower white matter volume and slower overall {RT} on the attention task The interaction of a neurotransmission gene ({CHRNA}4) and a susceptibility gene ({APOE}) suggests that the efficiency of neuronal repair mechanisms may modulate the cholinergic system to influence attentional function.},
	language = {eng},
	number = {1},
	journal = {Cognitive, Affective \& Behavioral Neuroscience},
	author = {Espeseth, Thomas and Greenwood, Pamela M. and Reinvang, Ivar and Fjell, Anders M. and Walhovd, Kristine B. and Westlye, Lars T. and Wehling, Eike and Lundervold, Astri and Rootwelt, Helge and Parasuraman, Raja},
	month = mar,
	year = {2006},
	pmid = {16869227},
	keywords = {Aged, Aging, Analysis of Variance, Apolipoprotein E4, Apolipoproteins E, Attention, Brain, Cues, Discrimination (Psychology), Female, Genotype, Humans, Male, Middle Aged, Neuropsychological Tests, Pattern Recognition, Visual, Photic Stimulation, Polymorphism, Genetic, Reaction Time, Receptors, Nicotinic},
	pages = {31--43}
}

@inproceedings{greve_automatic_2011,
	title = {Automatic Surface-based Interhemispheric Registration with {FreeSurfer}},
	shorttitle = {Automatic Surface-based Interhemispheric Registration with {FreeSurfer}},
	author = {Greve, D.N. and Sabuncu, M.R. and Shafee, R and Schmansky, N and Buckner, R.L. and Fischl, B},
	year = {2011}
}

@article{janssen_gyral_2009,
	title = {Gyral and sulcal cortical thinning in adolescents with first episode early-onset psychosis},
	volume = {66},
	issn = {1873-2402},
	doi = {10.1016/j.biopsych.2009.07.021},
	abstract = {{BACKGROUND}: Psychosis is associated with volumetric decreases of cortical structures. Whether these volumetric decreases imply abnormalities in cortical thickness, surface, or cortical folding is not clear. Due to differences in cytoarchitecture, cortical gyri and sulci might be differentially affected by psychosis. Therefore, we examined differences in gyral and sulcal cortical thickness, surface, folding, and volume between a minimally treated male adolescent population with early-onset first-episode psychosis ({EOP}) and a healthy control group, with surface-based morphometry.
{METHODS}: Magnetic resonance imaging brain scans were obtained from 49 adolescent {EOP} patients and 34 healthy control subjects. Subjects were younger than 18 years (age range 12 years-18 years), and {EOP} patients had a duration of positive symptoms of {\textless}6 months.
{RESULTS}: Early-onset first-episode psychosis was associated with local bilateral cortical thinning and volume deficits in both the gyri and sulci of the superior temporal cortex and the inferior, middle, medial, and superior prefrontal cortex. In the pars triangularis and opercularis cortex of patients, gyral cortical thickness was thinner, whereas sulcal thickness was not. Patients exhibited cortical thinning together with a decreased degree of cortical folding in the right superior frontal cortex.
{CONCLUSIONS}: Cortical thinning of both gyri and sulci seem to underlie most cortical volume deficits in adolescent patients with {EOP}. Except for the right superior frontal region, the degree of cortical folding was normal in regions showing decreased cortical thickness, suggesting that the process of cortical thinning in adolescent patients with {EOP} primarily takes place after the formation of cortical folds.},
	language = {eng},
	number = {11},
	journal = {Biological Psychiatry},
	author = {Janssen, Joost and Reig, Santiago and Alemán, Yasser and Schnack, Hugo and Udias, J. M. and Parellada, Mara and Graell, Montserrat and Moreno, Dolores and Zabala, Arantzazu and Balaban, Evan and Desco, Manuel and Arango, Celso},
	month = dec,
	year = {2009},
	pmid = {19717139},
	keywords = {Adolescent, Age of Onset, Antipsychotic Agents, Cerebral Cortex, Child, Humans, Intelligence, Magnetic Resonance Imaging, Male, Organ Size, Psychotic Disorders},
	pages = {1047--1054}
}

@article{zollei_improved_2010,
	title = {Improved tractography alignment using combined volumetric and surface registration},
	volume = {51},
	issn = {1095-9572 (Electronic) 1053-8119 (Linking)},
	shorttitle = {Improved tractography alignment using combined volumetric and surface registration},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/20153833},
	doi = {10.1016/j.neuroimage.2010.01.101},
	abstract = {Previously we introduced an automated high-dimensional non-linear registration framework, {CVS}, that combines volumetric and surface-based alignment to achieve robust and accurate correspondence in both cortical and sub-cortical regions (Postelnicu et al., 2009). In this paper we show that using {CVS} to compute cross-subject alignment from anatomical images, then applying the previously computed alignment to diffusion weighted {MRI} images, outperforms state-of-the-art techniques for computing cross-subject alignment directly from the {DWI} data itself. Specifically, we show that {CVS} outperforms the alignment component of {TBSS} in terms of degree-of-alignment of manually labeled tract models for the uncinate fasciculus, the inferior longitudinal fasciculus and the corticospinal tract. In addition, we compare linear alignment using {FLIRT} based on either fractional anisotropy or anatomical volumes across-subjects, and find a comparable effect. Together these results imply a clear advantage to aligning anatomy as opposed to lower resolution {DWI} data even when the final goal is diffusion analysis.},
	language = {en},
	number = {1},
	urldate = {2014-08-21},
	journal = {Neuroimage},
	author = {Zollei, L. and Stevens, A. and Huber, K. and Kakunoori, S. and Fischl, B.},
	month = may,
	year = {2010},
	keywords = {Anisotropy, Aurovertins, Brain/*anatomy \& histology, Diffusion, Diffusion Magnetic Resonance Imaging/*methods, fs\_CVS, Humans, Image Processing, Computer-Assisted/*methods, Linear Models, Neural Pathways/anatomy \& histology, Nonlinear Dynamics, Organ Size, Pyramidal Tracts/anatomy \& histology, Reproducibility of Results},
	pages = {206--13},
	annote = {Zollei, {LillaStevens}, {AllisonHuber}, {KristenKakunoori}, {SitaFischl}, {BruceengBIRN}002/{PHS} {HHS}/P41 {RR}013642/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}013642-070054/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-117867/{RR}/{NCRR} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 {EB}001550/{EB}/{NIBIB} {NIH} {HHS}/R01 {EB}001550-01/{EB}/{NIBIB} {NIH} {HHS}/R01 {EB}006758-01A1/{EB}/{NIBIB} {NIH} {HHS}/R01 {NS}052585-01/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}052585-01A1/{NS}/{NINDS} {NIH} {HHS}/R01 {RR}016594-01A1/{RR}/{NCRR} {NIH} {HHS}/R01 {RR}16594-01A1/{RR}/{NCRR} {NIH} {HHS}/R01EB006758/{EB}/{NIBIB} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/U24 {RR}021382-01/{RR}/{NCRR} {NIH} {HHS}/U54 {EB}005149/{EB}/{NIBIB} {NIH} {HHS}/U54 {EB}005149-050002/{EB}/{NIBIB} {NIH} {HHS}/Comparative {StudyEvaluation} {StudiesResearch} Support, N.I.H., Extramural2010/02/16 06:00Neuroimage. 2010 May 15;51(1):206-13. doi: 10.1016/j.neuroimage.2010.01.101. Epub 2010 Feb 12.},
	file = {PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/IK4UQPHN/Zollei et al. - 2010 - Improved Tractography Alignment Using Combined Vol.pdf:application/pdf;Zollei-2010-Improved tractography alignment us:/autofs/cluster/freesurfer/zotero/storage/G54ASA9X/Zollei-2010-Improved tractography alignment us.pdf:application/pdf}
}

@article{blackmon_phonetically_2010,
	title = {Phonetically Irregular Word Pronunciation and Cortical Thickness in the Adult Brain},
	volume = {51},
	issn = {1053-8119},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2873116/},
	doi = {10.1016/j.neuroimage.2010.03.028},
	abstract = {Accurate pronunciation of phonetically irregular words (exception words) requires prior exposure to unique relationships between orthographic and phonemic features. Whether such word knowledge is accompanied by structural variation in areas associated with orthographic-to-phonemic transformations has not been investigated. We used high resolution {MRI} to determine whether performance on a visual word-reading test composed of phonetically irregular words, the Wechsler Test of Adult Reading ({WTAR}), is associated with regional variations in cortical structure. A sample of 60 right-handed, neurologically intact individuals were administered the {WTAR} and underwent 3T volumetric {MRI}. Using quantitative, surface-based image analysis, cortical thickness was estimated at each vertex on the cortical mantle and correlated with {WTAR} scores while controlling for age. Higher scores on the {WTAR} were associated with thicker cortex in bilateral anterior superior temporal gyrus, bilateral angular gyrus/posterior superior temporal gyrus, and left hemisphere intraparietal sulcus. Higher scores were also associated with thinner cortex in left hemisphere posterior fusiform gyrus and central sulcus, bilateral inferior frontal gyrus, and right hemisphere lingual gyrus and supramarginal gyrus. These results suggest that the ability to correctly pronounce phonetically irregular words is associated with structural variations in cortical areas that are commonly activated in functional neuroimaging studies of word reading, including areas associated with grapheme-to–phonemic conversion.},
	number = {4},
	urldate = {2014-08-23},
	journal = {{NeuroImage}},
	author = {Blackmon, Karen and Barr, William B. and Kuzniecky, Ruben and DuBois, Jonathan and Carlson, Chad and Quinn, Brian T. and Blumberg, Mark and Halgren, Eric and Hagler, Donald J. and Mikhly, Mark and Devinsky, Orrin and McDonald, Carrie R. and Dale, Anders M. and Thesen, Thomas},
	month = jul,
	year = {2010},
	pmid = {20302944},
	pmcid = {PMC2873116},
	pages = {1453--1458},
	file = {PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/48KNP7ZP/Blackmon et al. - 2010 - Phonetically Irregular Word Pronunciation and Cort.pdf:application/pdf}
}

@article{winkler_cortical_2010,
	title = {Cortical Thickness or Grey Matter Volume? The Importance of Selecting the Phenotype for Imaging Genetics Studies},
	volume = {53},
	issn = {1053-8119},
	shorttitle = {Cortical Thickness or Grey Matter Volume?},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2891595/},
	doi = {10.1016/j.neuroimage.2009.12.028},
	abstract = {Choosing the appropriate neuroimaging phenotype is critical to successfully identify genes that influence brain structure or function. While neuroimaging methods provide numerous potential phenotypes, their role for imaging genetics studies are unclear. Here we examine the relationship between brain volume, grey matter volume, cortical thickness and surface area, from a genetic standpoint. Four hundred and eighty-six individuals from randomly ascertained extended pedigrees with high-quality T1-weighted neuroanatomic {MRI} images participated in the study. Surface-based and voxel-based representations of brain structure were derived, using automated methods, and these measurements were analysed using a variance-components method to identify the heritability of these traits and their genetic correlations. All neuroanatomic traits were significantly influenced by genetic factors. Cortical thickness and surface area measurements were found to be genetically and phenotypically independent. While both thickness and area influenced volume measurements of cortical grey matter, volume was more closely related to surface area than cortical thickness. This trend was observed for both the volume-based and surface-based techniques. The results suggest that surface area and cortical thickness measurements should be considered separately and preferred over gray matter volumes for imaging genetic studies.},
	number = {3},
	urldate = {2014-08-25},
	journal = {{NeuroImage}},
	author = {Winkler, Anderson M. and Kochunov, Peter and Blangero, John and Almasy, Laura and Zilles, Karl and Fox, Peter T. and Duggirala, Ravindranath and Glahn, David C.},
	month = nov,
	year = {2010},
	pmid = {20006715},
	pmcid = {PMC2891595},
	keywords = {Adult, Aged, Aged, 80 and over, Brain/*anatomy \& histology, Brain Mapping/*methods, Female, Humans, Image Interpretation, Computer-Assisted, Magnetic Resonance Imaging, Male, Middle Aged, Pedigree, *Phenotype, *Quantitative Trait, Heritable},
	pages = {1135--1146},
	annote = {Winkler, Anderson {MKochunov}, {PeterBlangero}, {JohnAlmasy}, {LauraZilles}, {KarlFox}, Peter {TDuggirala}, {RavindranathGlahn}, David {CengEB}006395/{EB}/{NIBIB} {NIH} {HHS}/K01 {EB}006395/{EB}/{NIBIB} {NIH} {HHS}/K01 {EB}006395-01A1/{EB}/{NIBIB} {NIH} {HHS}/{MH}0708143/{MH}/{NIMH} {NIH} {HHS}/{MH}078111/{MH}/{NIMH} {NIH} {HHS}/{MH}083824/{MH}/{NIMH} {NIH} {HHS}/{MH}59490/{MH}/{NIMH} {NIH} {HHS}/R01 {MH}078111-01/{MH}/{NIMH} {NIH} {HHS}/R01 {MH}078143/{MH}/{NIMH} {NIH} {HHS}/R01 {MH}078143-01/{MH}/{NIMH} {NIH} {HHS}/R01 {MH}083824-01/{MH}/{NIMH} {NIH} {HHS}/R01 {MH}083824-04/{MH}/{NIMH} {NIH} {HHS}/R01 {MH}083824-05/{MH}/{NIMH} {NIH} {HHS}/R37 {MH}059490-04/{MH}/{NIMH} {NIH} {HHS}/Research Support, N.I.H., Extramural2009/12/17 06:00Neuroimage. 2010 Nov 15;53(3):1135-46. doi: 10.1016/j.neuroimage.2009.12.028. Epub 2009 Dec 16.},
	file = {PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/ADBHPEJ9/Winkler et al. - 2010 - Cortical Thickness or Grey Matter Volume The Impo.pdf:application/pdf;PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/Q8X69MD8/Winkler et al. - 2010 - Cortical Thickness or Grey Matter Volume The Impo.pdf:application/pdf;Winkler-2010-Cortical thickness or grey matte1:/autofs/cluster/freesurfer/zotero/storage/E92PABC5/Winkler-2010-Cortical thickness or grey matte1.pdf:application/pdf}
}

@inproceedings{yendiki_fully_2009,
	title = {Fully Automated Probabilistic White-Matter Tractography with Anatomical Priors: Application to Huntington's Disease,},
	shorttitle = {Fully Automated Probabilistic White-Matter Tractography with Anatomical Priors: Application to Huntington's Disease,},
	author = {Yendiki, A. and Stevens, A. and Augustinack, J. and Salat, D. and Zollei, L. and Wang, R. and Rosas, D. and Fischl, B.},
	year = {2009},
	keywords = {fs\_TRACULA},
	pages = {860}
}

@article{cuingnet_automatic_2011,
	title = {Automatic classification of patients with Alzheimer's disease from structural {MRI}: a comparison of ten methods using the {ADNI} database},
	volume = {56},
	issn = {1095-9572},
	shorttitle = {Automatic classification of patients with Alzheimer's disease from structural {MRI}},
	url = {http://cogimage.dsi.cnrs.fr/perso/colliot/files/neuroimage2010_Remi_Comparaison.pdf},
	doi = {10.1016/j.neuroimage.2010.06.013},
	abstract = {Recently, several high dimensional classification methods have been proposed to automatically discriminate between patients with Alzheimer's disease ({AD}) or mild cognitive impairment ({MCI}) and elderly controls ({CN}) based on T1-weighted {MRI}. However, these methods were assessed on different populations, making it difficult to compare their performance. In this paper, we evaluated the performance of ten approaches (five voxel-based methods, three methods based on cortical thickness and two methods based on the hippocampus) using 509 subjects from the {ADNI} database. Three classification experiments were performed: {CN} vs {AD}, {CN} vs {MCIc} ({MCI} who had converted to {AD} within 18 months, {MCI} converters - {MCIc}) and {MCIc} vs {MCInc} ({MCI} who had not converted to {AD} within 18 months, {MCI} non-converters - {MCInc}). Data from 81 {CN}, 67 {MCInc}, 39 {MCIc} and 69 {AD} were used for training and hyperparameters optimization. The remaining independent samples of 81 {CN}, 67 {MCInc}, 37 {MCIc} and 68 {AD} were used to obtain an unbiased estimate of the performance of the methods. For {AD} vs {CN}, whole-brain methods (voxel-based or cortical thickness-based) achieved high accuracies (up to 81\% sensitivity and 95\% specificity). For the detection of prodromal {AD} ({CN} vs {MCIc}), the sensitivity was substantially lower. For the prediction of conversion, no classifier obtained significantly better results than chance. We also compared the results obtained using the {DARTEL} registration to that using {SPM}5 unified segmentation. {DARTEL} significantly improved six out of 20 classification experiments and led to lower results in only two cases. Overall, the use of feature selection did not improve the performance but substantially increased the computation times.},
	language = {eng},
	number = {2},
	journal = {{NeuroImage}},
	author = {Cuingnet, Rémi and Gerardin, Emilie and Tessieras, Jérôme and Auzias, Guillaume and Lehéricy, Stéphane and Habert, Marie-Odile and Chupin, Marie and Benali, Habib and Colliot, Olivier and {Alzheimer's Disease Neuroimaging Initiative}},
	month = may,
	year = {2011},
	pmid = {20542124},
	keywords = {Aged, Aged, 80 and over, Alzheimer Disease, Brain, Cognition Disorders, Databases, Factual, Female, fs\_Validation-Evaluations, Humans, Image Interpretation, Computer-Assisted, Magnetic Resonance Imaging, Male, Middle Aged, Sensitivity and Specificity},
	pages = {766--781}
}

@article{sabuncu_relevance_2012,
	title = {The relevance voxel machine ({RVoxM}): a self-tuning Bayesian model for informative image-based prediction.},
	volume = {31},
	url = {https://surfer.nmr.mgh.harvard.edu/pub/articles/SabuncuTMI2012.pdf},
	doi = {10.1109/TMI.2012.2216543},
	abstract = {This paper presents the relevance voxel machine ({RVoxM}), a dedicated Bayesian model for making predictions based on medical imaging data. In contrast to the generic machine learning algorithms that have often been used for this purpose, the method is designed to utilize a small number of spatially clustered sets of voxels that are particularly suited for clinical interpretation. {RVoxM} automatically tunes all its free parameters during the training phase, and offers the additional advantage of producing probabilistic prediction outcomes. We demonstrate {RVoxM} as a regression model by predicting age from volumetric gray matter segmentations, and as a classification model by distinguishing patients with Alzheimer's disease from healthy controls using surface-based cortical thickness data. Our results indicate that {RVoxM} yields biologically meaningful models, while providing state-of-the-art predictive accuracy.},
	language = {eng},
	number = {12},
	journal = {{IEEE} transactions on medical imaging},
	author = {Sabuncu, Mert R. and Van Leemput, Koen},
	month = dec,
	year = {2012},
	pmid = {23008245},
	pmcid = {PMC3623564},
	keywords = {Adolescent, Adult, Aged, Aged, 80 and over, Age Factors, Algorithms, Alzheimer Disease/pathology, *Artificial Intelligence, *Bayes Theorem, Case-Control Studies, Cerebral Cortex/anatomy \& histology/pathology, Databases, Factual, Female, fs\_Misc-methodology, Humans, Image Processing, Computer-Assisted/*methods, Magnetic Resonance Imaging, Male, Middle Aged, Pattern Recognition, Automated/*methods, Regression Analysis, Reproducibility of Results, {ROC} Curve},
	pages = {2290--2306}
}

@inproceedings{han_cnr_2005,
	title = {{CNR} comparison of three pulse sequences for structural {MR} brain imaging},
	shorttitle = {{CNR} comparison of three pulse sequences for structural {MR} brain imaging},
	author = {Han, Jovicich, J., Salat, D.H., van der Kouwe, A.J.W., Dickerson, B., Rosas, D., Makris, N., Dale, A., Fischl, B., X.},
	year = {2005},
	pages = {847}
}

@article{han_atlas_2007,
	title = {Atlas renormalization for improved brain {MR} image segmentation across scanner platforms},
	volume = {26},
	issn = {0278-0062 (Print) 0278-0062 (Linking)},
	shorttitle = {Atlas renormalization for improved brain {MR} image segmentation across scanner platforms},
	url = {https://surfer.nmr.mgh.harvard.edu/ftp/articles/AtlasSeg_TMI2007April.pdf},
	doi = {10.1109/TMI.2007.893282},
	abstract = {Atlas-based approaches have demonstrated the ability to automatically identify detailed brain structures from 3-D magnetic resonance ({MR}) brain images. Unfortunately, the accuracy of this type of method often degrades when processing data acquired on a different scanner platform or pulse sequence than the data used for the atlas training. In this paper, we improve the performance of an atlas-based whole brain segmentation method by introducing an intensity renormalization procedure that automatically adjusts the prior atlas intensity model to new input data. Validation using manually labeled test datasets has shown that the new procedure improves the segmentation accuracy (as measured by the Dice coefficient) by 10\% or more for several structures including hippocampus, amygdala, caudate, and pallidum. The results verify that this new procedure reduces the sensitivity of the whole brain segmentation method to changes in scanner platforms and improves its accuracy and robustness, which can thus facilitate multicenter or multisite neuroanatomical imaging studies.},
	number = {4},
	journal = {{IEEE} Trans Med Imaging},
	author = {Han, X. and Fischl, B.},
	month = apr,
	year = {2007},
	keywords = {Algorithms, Anatomy, Artistic/methods, *Artificial Intelligence, Brain/*anatomy \& histology, fs\_Subcortical-segmentation, Humans, Image Enhancement/*methods, Image Interpretation, Computer-Assisted/*methods, Imaging, Three-Dimensional/methods, Magnetic Resonance Imaging/instrumentation/*methods, Medical Illustration, Pattern Recognition, Automated/*methods, Reproducibility of Results, Sensitivity and Specificity, *Subtraction Technique},
	pages = {479--86},
	annote = {Han, {XiaoFischl}, {BruceengP}41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 {EB}001550/{EB}/{NIBIB} {NIH} {HHS}/R01 {RR}16594-01A1/{RR}/{NCRR} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/U54 {EB}005149/{EB}/{NIBIB} {NIH} {HHS}/Evaluation {StudiesResearch} Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov'{tValidation} Studies2007/04/13 09:00IEEE Trans Med Imaging. 2007 Apr;26(4):479-86.}
}

@article{voets_evidence_2008,
	title = {Evidence for abnormalities of cortical development in adolescent-onset schizophrenia},
	volume = {43},
	issn = {1095-9572},
	url = {https://surfer.nmr.mgh.harvard.edu/pub/articles/Voets-HoughNI2008.pdf},
	doi = {10.1016/j.neuroimage.2008.08.013},
	abstract = {Voxel-Based Morphometry ({VBM}) identifies differences in grey matter brain structure in patients with schizophrenia relative to healthy controls, with particularly prominent differences found in patients with the more severe, adolescent-onset form of the disease. However, as {VBM} is sensitive to a combination of changes in grey matter thickness, intensity and folding, specific neuropathological interpretations are not possible. Here, we attempt to more precisely define cortical changes in 25 adolescent-onset schizophrenic patients and 25 age- and sex-matched healthy volunteers using Surface-Based Morphometry ({SBM}) to disambiguate the relative contributions of cortical thickness and surface area differences to changes in regional grey matter ({GM}) density measured with {VBM}. Cortical changes in schizophrenia were widespread, including particularly the prefrontal cortex and superior temporal gyrus. Nine regions of apparent reduction in {GM} density in patients relative to healthy matched controls were found using {VBM} that were not found with {SBM}-derived cortical thickness measures. In Regions of Interest ({ROIs}) derived from the {VBM} group results, we confirmed that local surface area differences accounted for these {VBM} changes. Our results emphasize widespread, but focally distinct cortical pathology in adolescent-onset schizophrenia. Evidence for changes in local surface area (as opposed to simply cortical thinning) is consistent with a neurodevelopmental contribution to the underlying neuropathology of the disease.},
	language = {eng},
	number = {4},
	journal = {{NeuroImage}},
	author = {Voets, Natalie L. and Hough, Morgan G. and Douaud, Gwenaelle and Matthews, Paul M. and James, Anthony and Winmill, Louise and Webster, Paula and Smith, Stephen},
	month = dec,
	year = {2008},
	pmid = {18793730},
	keywords = {Adolescent, Adolescent, Cerebral Cortex, Cerebral Cortex/*pathology, Evidence-Based Medicine, Evidence-Based Medicine, Female, Female, Humans, Humans, Image Interpretation, Computer-Assisted, Image Interpretation, Computer-Assisted/*methods, Imaging, Three-Dimensional, Imaging, Three-Dimensional/*methods, Magnetic Resonance Imaging, Magnetic Resonance Imaging/*methods, Male, Male, Neurons, Neurons/*pathology, Schizophrenia, Schizophrenia/*pathology},
	pages = {665--675},
	annote = {Voets, Natalie {LHough}, Morgan {GDouaud}, {GwenaelleMatthews}, Paul {MJames}, {AnthonyWinmill}, {LouiseWebster}, {PaulaSmith}, {StephenengG}0500092/Medical Research Council/United {KingdomG}9409634/Medical Research Council/United {KingdomMedical} Research Council/United {KingdomResearch} Support, Non-U.S. Gov't2008/09/17 09:00Neuroimage. 2008 Dec;43(4):665-75. doi: 10.1016/j.neuroimage.2008.08.013. Epub 2008 Aug 26.}
}

@article{thesen_detection_2011,
	title = {Detection of Epileptogenic Cortical Malformations with Surface-Based {MRI} Morphometry},
	volume = {6},
	issn = {1932-6203},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3033882/},
	doi = {10.1371/journal.pone.0016430},
	abstract = {Magnetic resonance imaging has revolutionized the detection of structural abnormalities in patients with epilepsy. However, many focal abnormalities remain undetected in routine visual inspection. Here we use an automated, surface-based method for quantifying morphometric features related to epileptogenic cortical malformations to detect abnormal cortical thickness and blurred gray-white matter boundaries. Using {MRI} morphometry at 3T with surface-based spherical averaging techniques that precisely align anatomical structures between individual brains, we compared single patients with known lesions to a large normal control group to detect clusters of abnormal cortical thickness, gray-white matter contrast, local gyrification, sulcal depth, jacobian distance and curvature. To assess the effects of threshold and smoothing on detection sensitivity and specificity, we systematically varied these parameters with different thresholds and smoothing levels. To test the effectiveness of the technique to detect lesions of epileptogenic character, we compared the detected structural abnormalities to expert-tracings, intracranial {EEG}, pathology and surgical outcome in a homogeneous patient sample. With optimal parameters and by combining thickness and {GWC}, the surface-based detection method identified 92\% of cortical lesions (sensitivity) with few false positives (96\% specificity), successfully discriminating patients from controls 94\% of the time. The detected structural abnormalities were related to the seizure onset zones, abnormal histology and positive outcome in all surgical patients. However, the method failed to adequately describe lesion extent in most cases. Automated surface-based {MRI} morphometry, if used with optimized parameters, may be a valuable additional clinical tool to improve the detection of subtle or previously occult malformations and therefore could improve identification of patients with intractable focal epilepsy who may benefit from surgery.},
	number = {2},
	urldate = {2014-08-24},
	journal = {{PLoS} {ONE}},
	author = {Thesen, Thomas and Quinn, Brian T. and Carlson, Chad and Devinsky, Orrin and DuBois, Jonathan and McDonald, Carrie R. and French, Jacqueline and Leventer, Richard and Felsovalyi, Olga and Wang, Xiuyuan and Halgren, Eric and Kuzniecky, Ruben},
	month = feb,
	year = {2011},
	pmid = {21326599},
	pmcid = {PMC3033882},
	file = {PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/AGJ58STB/Thesen et al. - 2011 - Detection of Epileptogenic Cortical Malformations .pdf:application/pdf}
}

@article{crosson_semantic_2002,
	title = {Semantic monitoring of words with emotional connotation during {fMRI}: contribution of anterior left frontal cortex},
	volume = {8},
	shorttitle = {Semantic monitoring of words with emotional connotation during {fMRI}: contribution of anterior left frontal cortex},
	journal = {J.Int.Neuropsychol.Soc.},
	author = {Crosson, B. and Cato, M. A. and Sadek, J. R. and Gokcay, D. and Bauer, R. M. and Fischler, I. S. and Maron, L. and Gopinath, K. and Auerbach, E. J. and Browd, S. R. and Briggs, R. W.},
	year = {2002},
	keywords = {Acoustic Stimulation, Adult, Auditory Perception, clinical, cortex, Emotions, Female, human, Image Processing,Computer-Assisted, Imagination, Laterality, Magnetic Resonance Imaging, Male, physiology, prefrontal cortex, Reaction Time, Semantics, Support,U.S.Gov't,P.H.S.},
	pages = {607--622},
	annote = {{UI} - 22154543NOT {IN} {FILE}}
}

@article{pienaar_methodology_2008,
	title = {A Methodology for Analyzing Curvature in the Developing Brain from Preterm to Adult},
	volume = {18},
	issn = {0899-9457 (Print) 0899-9457 (Linking)},
	shorttitle = {A Methodology for Analyzing Curvature in the Developing Brain from Preterm to Adult},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/19936261},
	doi = {10.1002/ima.v18:1},
	abstract = {The character and timing of gyral development is one manifestation of the complex orchestration of human brain development. The ability to quantify these changes would not only allow for deeper understanding of cortical development, but also conceivably allow for improved detection of pathologies. This paper describes a {FreeSurfer} based image-processing analysis "pipeline" or methodology that inputs an {MRI} volume, corrects possible contrast defects, creates surface reconstructions, and outputs various curvature-based function analyses. A technique of performing neonate reconstructions using {FreeSurfer}, which has not been possible previously due to inverted image contrast in pre-myelinated brains, is described. Once surfaces are reconstructed, the analysis component of the pipeline incorporates several surface-based curvature functions found in literature (principle curvatures, Gaussian, mean curvature, "curvedness", and Willmore Bending Energy). We consider the problem of analyzing curvatures from different sized brains by introducing a Gaussian-curvature based variable-radius filter. Segmented volume data is also analyzed for folding measures: a gyral folding index (gyrification-white index {GWI}), and a gray-white matter junction folding index ({WMF}). A very simple curvature-based classifier is proposed that has the potential to discriminate between certain classes of subjects. We also present preliminary results of this curvature analysis pipeline on nine neonate subjects (30.4 weeks through 40.3 weeks Corrected Gestational Age), 3 children (2, 3, and 7 years) and 3 adults (33, 37, and 39 years). Initial results demonstrate that curvature measures and functions across our subjects peaked at term, with a gradual decline through early childhood and further decline continuing through to adults. We can also discriminate older neonates, children, and adults based on curvature analysis. Using a variable radius Gaussian-curvature filter, we also observed that the per-unit bending energy of neonate brain surfaces was also much higher than the children and adults.},
	number = {1},
	journal = {Int J Imaging Syst Technol},
	author = {Pienaar, R. and Fischl, B. and Caviness, V. and Makris, N. and Grant, P. E.},
	month = jun,
	year = {2008},
	pages = {42--68},
	annote = {Pienaar, {RFischl}, {BCaviness}, {VMakris}, {NGrant}, P {EENGR}01 {RR}016594-01A1/{RR}/{NCRR} {NIH} {HHS}/2008/06/01 00:00Int J Imaging Syst Technol. 2008 Jun 1;18(1):42-68.},
	file = {Pienaar-2008-A Methodology for Analyzing Curva:/autofs/cluster/freesurfer/zotero/storage/8AVVV75X/Pienaar-2008-A Methodology for Analyzing Curva.pdf:application/pdf;PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/SE6G3ABX/PIENAAR et al. - 2008 - A METHODOLOGY FOR ANALYZING CURVATURE IN THE DEVEL.pdf:application/pdf}
}

@article{cerasa_met158_2010,
	title = {Met158 variant of the catechol-O-methyltransferase genotype is associated with thicker cortex in adult brain},
	volume = {167},
	issn = {03064522},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S030645221000268X},
	doi = {10.1016/j.neuroscience.2010.02.040},
	language = {en},
	number = {3},
	urldate = {2014-08-23},
	journal = {Neuroscience},
	author = {Cerasa, A. and Cherubini, A. and Quattrone, A. and Gioia, M.C. and Tarantino, P. and Annesi, G. and Assogna, F. and Caltagirone, C. and Spalletta, G.},
	month = may,
	year = {2010},
	keywords = {Adult, Aged, Amino Acid Substitution, Body Patterning, Catechol O-Methyltransferase, Cerebral Cortex, {DNA} Mutational Analysis, Dopamine, Female, Genetic Testing, Genetic Variation, Genotype, Humans, Male, Methionine, Middle Aged, Organogenesis, Phenotype, Point Mutation, Polymorphism, Genetic, Prefrontal Cortex, Temporal Lobe, Young Adult},
	pages = {809--814}
}

@article{gold_differing_2005,
	title = {Differing neuropsychological and neuroanatomical correlates of abnormal reading in early-stage semantic dementia and dementia of the Alzheimer type},
	volume = {43},
	issn = {0028-3932 (Print) 0028-3932 (Linking)},
	shorttitle = {Differing neuropsychological and neuroanatomical correlates of abnormal reading in early-stage semantic dementia and dementia of the Alzheimer type},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/15716156 http://www.sciencedirect.com/science/article/pii/S0028393204002659},
	doi = {10.1016/j.neuropsychologia.2004.10.005},
	abstract = {Individuals with semantic dementia ({SD}) were differentiated neuropsychologically from individuals with dementia of the Alzheimer type ({DAT}) at very mild-to-mild stages (clinical dementia rating 0.5 or 1). A picture naming and recognition memory experiment provided a particularly useful probe for early identification, with {SD} individuals showing preserved picture recognition memory and impaired naming, and {DAT} individuals tending to show the reverse dissociation. The identification of an early {SD} group provided the opportunity to inform models of reading by exploring the influence of isolated lexical semantic impairment on reading regular words. Results demonstrated prolonged latency in both {SD} and {DAT} group reading compared to a control group but exaggerated influence of frequency and length only for the {SD} group. The {SD} reading pattern was associated with focal atrophy of the left temporal pole. These cognitive-neuroanatomical findings suggest a role for the left temporal pole in lexical/semantic components of reading and demonstrate that cortical thickness differences in the left temporal pole correlate with prolonged latency associated with increased reliance on sublexical components of reading.},
	language = {eng},
	number = {6},
	journal = {Neuropsychologia},
	author = {Gold, B. T. and Balota, D. A. and Cortese, M. J. and Sergent-Marshall, S. D. and Snyder, A. Z. and Salat, D. H. and Fischl, B. and Dale, A. M. and Morris, J. C. and Buckner, R. L.},
	year = {2005},
	keywords = {Aged, Aged, 80 and over, Alzheimer Disease/complications/*physiopathology, *Brain Mapping, Dementia/complications/*physiopathology, Dyslexia/complications/physiopathology, Female, Functional Laterality/physiology, Humans, Magnetic Resonance Imaging, Male, Middle Aged, Neuropsychological Tests, Reaction Time, *Reading, Recognition (Psychology)/*physiology, Reference Values, Semantics, Temporal Lobe/physiology/physiopathology},
	pages = {833--46},
	annote = {Gold, Brian {TBalota}, Dave {ACortese}, Michael {JSergent}-Marshall, Susan {DSnyder}, Abraham {ZSalat}, David {HFischl}, {BruceDale}, Anders {MMorris}, John {CBuckner}, Randy {LengAG}03991/{AG}/{NIA} {NIH} {HHS}/{AG}05681/{AG}/{NIA} {NIH} {HHS}/{MH}57506/{MH}/{NIMH} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01-{RR}13609/{RR}/{NCRR} {NIH} {HHS}/Comparative {StudyResearch} Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov'{tResearch} Support, U.S. Gov't, P.H.S.England2005/02/18 09:00Neuropsychologia. 2005;43(6):833-46. Epub 2004 Dec 8.}
}

@article{ford_relation_2014,
	title = {The relation between structural and functional connectivity depends on age and on task goals},
	volume = {8},
	url = {http://journal.frontiersin.org/Journal/10.3389/fnhum.2014.00307/abstract},
	doi = {10.3389/fnhum.2014.00307},
	abstract = {The last decade has seen an increase in neuroimaging studies examining structural (i.e., structural integrity of white matter tracts) and functional connectivity (e.g., correlations in neural activity throughout the brain). Although structural and functional connectivity changes have often been measured independently, examining the relation between these two measures is critical to understanding the specific function of neural networks and the ways they may differ across tasks and individuals. The current study addressed this question by examining the effect of age (treated as a continuous variable) and emotional valence on the relation between functional and structural connectivity. As prior studies have suggested that prefrontal regions may guide and regulate emotional memory search via functional connections with the amygdala, the current analysis focused on functional connectivity between the left amygdala and the left prefrontal cortex, and structural integrity of the uncinate fasciculus, a white matter tract connecting prefrontal and temporal regions. Participants took part in a scanned retrieval task in which they recalled positive, negative, and neutral images associated with neutral titles. Aging was associated with a significant increase in the relation between measures of structural integrity (specifically, fractional anisotropy, or {FA}) along the uncinate fasciculus and functional connectivity between the left ventral prefrontal cortex and amygdala during positive event retrieval, but not negative or neutral retrieval. Notably, during negative event retrieval, age was linked to stronger structure-function relations between the amygdala and the dorsal anterior cingulate cortex, such that increased structural integrity predicted stronger negative functional connectivity in older adults only. These findings suggest that young and older adults may utilize a structural pathway to engage different retrieval and regulatory strategies, even when structural integrity along that pathway does not differ.},
	urldate = {2014-08-25},
	journal = {Frontiers in Human Neuroscience},
	author = {Ford, Jaclyn Hennessey and Kensinger, Elizabeth},
	year = {2014},
	keywords = {Aging, Amygdala, diffusion weighted imaging, emotion, functional {MRI}, Prefrontal Cortex},
	pages = {307},
	file = {Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/2KDUPDVJ/Ford and Kensinger - 2014 - The relation between structural and functional con.pdf:application/pdf}
}

@article{walhovd_neuroanatomical_2005,
	title = {Neuroanatomical aging: Universal but not uniform},
	volume = {26},
	shorttitle = {Neuroanatomical aging: Universal but not uniform},
	number = {9},
	journal = {Neurobiology of Aging},
	author = {Walhovd, Kristine B and Fjell, Anders Martin and Reinvang, Ivar and Lundervold, Arvid and Dale, Anders M and Quinn, Brian T and Salat, David and Nikos, Makris and Fischl, Bruce},
	year = {2005},
	pages = {1279--1282}
}

@inproceedings{segonne_active_2005,
	title = {Active Contours Under Topology Control - Genus Preserving Level Sets},
	shorttitle = {Active Contours Under Topology Control - Genus Preserving Level Sets},
	author = {Ségonne, F. and Pons, J.P. and Grimson, E. and Fischl, B.},
	year = {2005}
}

@article{sigalovsky_mapping_2006,
	title = {Mapping an intrinsic {MR} property of gray matter in auditory cortex of living humans: A possible marker for primary cortex and hemispheric differences},
	volume = {32},
	issn = {1053-8119},
	shorttitle = {Mapping an intrinsic {MR} property of gray matter in auditory cortex of living humans},
	url = {http://www.sciencedirect.com/science/article/pii/S1053811906005702},
	doi = {10.1016/j.neuroimage.2006.05.023},
	abstract = {Recently, magnetic resonance properties of cerebral gray matter have been spatially mapped – in vivo – over the cortical surface. In one of the first neuroscientific applications of this approach, this study explores what can be learned about auditory cortex in living humans by mapping longitudinal relaxation rate (R1), a property related to myelin content. Gray matter R1 (and thickness) showed repeatable trends, including the following:(1)
Regions of high R1 were always found overlapping posteromedial Heschl's gyrus. They also sometimes occurred in planum temporale and never in other parts of the superior temporal lobe. We hypothesize that the high R1 overlapping Heschl's gyrus (which likely indicates dense gray matter myelination) reflects auditory koniocortex (i.e., primary cortex), a heavily myelinated area that shows comparable overlap with the gyrus. High R1 overlapping Heschl's gyrus was identified in every instance suggesting that R1 may ultimately provide a marker for koniocortex in individuals. Such a marker would be significant for auditory neuroimaging, which has no standard means (anatomic or physiologic) for localizing cortical areas in individual subjects.
(2)
Inter-hemispheric comparisons revealed greater R1 on the left on Heschl's gyrus, planum temporale, superior temporal gyrus and superior temporal sulcus. This asymmetry suggests greater gray matter myelination in left auditory cortex, which may be a substrate for the left hemisphere's specialized processing of speech, language, and rapid acoustic changes.


These results indicate that in vivo R1 mapping can provide new insights into the structure of human cortical gray matter and its relation to function.},
	number = {4},
	urldate = {2014-08-23},
	journal = {{NeuroImage}},
	author = {Sigalovsky, Irina S. and Fischl, Bruce and Melcher, Jennifer R.},
	month = oct,
	year = {2006},
	keywords = {Brain asymmetry, Brodmann areas, Cortical thickness, Dyslexia, {MRI}, Primary auditory cortex, T1, Temporal processing},
	pages = {1524--1537},
	file = {ScienceDirect Snapshot:/autofs/cluster/freesurfer/zotero/storage/HPQ4Q397/S1053811906005702.html:text/html}
}

@article{cerasa_mao_2011,
	title = {{MAO} A {VNTR} polymorphism and amygdala volume in healthy subjects},
	volume = {191},
	issn = {0165-1781},
	url = {https://surfer.nmr.mgh.harvard.edu/pub/articles/Psych_Res_Neuroimaging_2011.pdf},
	doi = {10.1016/j.pscychresns.2010.11.002},
	abstract = {The X-linked Monoamine Oxidase A ({MAO} A) gene presents a well known functional polymorphism consisting of a variable number of tandem repeats ({VNTR}) (long and short variants) previously associated with altered neural function of the amygdala. Using automatic subcortical segmentation (Freesurfer), we investigated whether amygdala volume could be influenced by this genotype. We studied 109 healthy subjects (age range 18-80 years; 59 male and 50 female), 74 carrying the {MAO} A High-activity allele and 35 the {MAO} A Low-activity allele. No significant effect of the {MAO} A polymorphism or interaction effect between polymorphism × gender was found on amygdalar volume. Thus, our findings suggest that the reported impact of the {MAO} A polymorphism on amygdala function is not coupled with consistent volumetric changes in healthy subjects. Future studies are needed to investigate whether the association between volume of the amygdala and the {MAO} A {VNTR} polymorphism is influenced by social/psychological variables, such as impulsivity, trauma history and cigarette smoking behaviour, not taken into account in this work.},
	language = {eng},
	number = {2},
	journal = {Psychiatry Research},
	author = {Cerasa, Antonio and Quattrone, Aldo and Gioia, Maria C. and Magariello, Angela and Muglia, Maria and Assogna, Francesca and Bernardini, Sergio and Caltagirone, Carlo and Bossù, Paola and Spalletta, Gianfranco},
	month = feb,
	year = {2011},
	pmid = {21236646},
	keywords = {Adolescent, Adolescent, Adult, Adult, Aged, Aged, Aged, 80 and over, Aged, 80 and over, Amygdala, Amygdala/*anatomy \& histology, Female, Female, Gene Frequency, Gene Frequency, Genotype, Genotype, Humans, Humans, Image Processing, Computer-Assisted, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Magnetic Resonance Imaging/methods, Male, Male, Middle Aged, Middle Aged, Minisatellite Repeats, Minisatellite Repeats/*genetics, Monoamine Oxidase, Monoamine Oxidase/*genetics, Polymorphism, Genetic, Polymorphism, Genetic/*genetics, Sex Factors, Sex Factors, Statistics, Nonparametric, Statistics, Nonparametric, Young Adult, Young Adult},
	pages = {87--91},
	annote = {Cerasa, {AntonioQuattrone}, {AldoGioia}, Maria {CMagariello}, {AngelaMuglia}, {MariaAssogna}, {FrancescaBernardini}, {SergioCaltagirone}, {CarloBossu}, {PaolaSpalletta}, {GianfrancoengIreland}2011/01/18 06:00Psychiatry Res. 2011 Feb 28;191(2):87-91. doi: 10.1016/j.pscychresns.2010.11.002. Epub 2011 Jan 13.}
}

@article{lehmann_reduced_2010,
	title = {Reduced cortical thickness in the posterior cingulate gyrus is characteristic of both typical and atypical Alzheimer's disease},
	volume = {20},
	issn = {1875-8908},
	doi = {10.3233/JAD-2010-1401},
	abstract = {Alzheimer's disease ({AD}) and frontotemporal lobar degeneration ({FTLD}) can be difficult to differentiate clinically due to overlapping symptoms. Subject classification in research studies is often based on clinical rather than pathological criteria which may mean some subjects are misdiagnosed and misclassified. Recently, methods measuring cortical thickness using magnetic resonance imaging have been suggested to be effective in differentiating between clinically-defined {AD} and frontotemporal dementia ({FTD}) in addition to showing disease-related patterns of atrophy. In this study we used {FreeSurfer}, a freely-available and automated software tool, to measure cortical thickness in 28 pathologically-confirmed {AD} patients, of which 11 had a typical amnestic presentation and 17 an atypical presentation during life, 23 pathologically-confirmed {FTLD} subjects, and 25 healthy controls. Patients with {AD} pathology, irrespective of clinical diagnosis, showed reduced cortical thickness bilaterally in the medial temporal lobe, posterior cingulate gyrus, precuneus, posterior parietal lobe, and frontal pole compared with controls. We further showed that lower cortical thickness in the posterior cingulate gyrus, parietal lobe, and frontal pole is suggestive of {AD} pathology in patients with behavioral or language deficits. In contrast, lower cortical thickness in the anterior temporal lobe and frontal lobe is indicative of the presence of {FTLD} pathology in patients with a clinical presentation of {FTD}. Reduced cortical thickness in the posterior cingulate gyrus is characteristic of {AD} pathology in patients with typical and atypical clinical presentations of {AD}, and may assist a clinical distinction of {AD} pathology from {FTLD} pathology.},
	language = {eng},
	number = {2},
	journal = {Journal of Alzheimer's disease: {JAD}},
	author = {Lehmann, Manja and Rohrer, Jonathan D. and Clarkson, Matthew J. and Ridgway, Gerard R. and Scahill, Rachael I. and Modat, Marc and Warren, Jason D. and Ourselin, Sebastien and Barnes, Josephine and Rossor, Martin N. and Fox, Nick C.},
	year = {2010},
	pmid = {20182057},
	keywords = {Aged, Alzheimer Disease, Brain Mapping, Cerebral Cortex, Databases, Factual, Female, Frontotemporal Lobar Degeneration, Functional Laterality, Gyrus Cinguli, Humans, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Male, Mental Status Schedule, Middle Aged},
	pages = {587--598},
	file = {MetaPress Snapshot:/autofs/cluster/freesurfer/zotero/storage/I9FQ8KGS/157p836584666515.html:text/html}
}

@article{mendola_representation_1999,
	title = {The representation of illusory and real contours in human cortical visual areas revealed by functional magnetic resonance imaging},
	volume = {19},
	issn = {1529-2401 (Electronic) 0270-6474 (Linking)},
	shorttitle = {The representation of illusory and real contours in human cortical visual areas revealed by functional magnetic resonance imaging},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/10493756},
	abstract = {Illusory contours (perceived edges that exist in the absence of local stimulus borders) demonstrate that perception is an active process, creating features not present in the light patterns striking the retina. Illusory contours are thought to be processed using mechanisms that partially overlap with those of "real" contours, but questions about the neural substrate of these percepts remain. Here, we employed functional magnetic resonance imaging to obtain physiological signals from human visual cortex while subjects viewed different types of contours, both real and illusory. We sampled these signals independently from nine visual areas, each defined by retinotopic or other independent criteria. Using both within- and across-subject analysis, we found evidence for overlapping sites of processing; most areas responded to most types of contours. However, there were distinctive differences in the strength of activity across areas and contour types. Two types of illusory contours differed in the strength of activation of the retinotopic areas, but both types activated crudely retinotopic visual areas, including V3A, V4v, V7, and V8, bilaterally. The extent of activation was largely invariant across a range of stimulus sizes that produce illusory contours perceptually, but it was related to the spatial frequency of displaced-grating stimuli. Finally, there was a striking similarity in the pattern of results for the illusory contour-defined shape and a similar shape defined by stereoscopic depth. These and other results suggest a role in surface perception for this lateral occipital region that includes V3A, V4v, V7, and V8.},
	language = {eng},
	number = {19},
	journal = {J Neurosci},
	author = {Mendola, J. D. and Dale, A. M. and Fischl, B. and Liu, A. K. and Tootell, R. B.},
	month = oct,
	year = {1999},
	keywords = {*Brain Mapping, Computer Graphics, Form Perception/*physiology, Humans, Magnetic Resonance Imaging/methods, Neurons/physiology, Occipital Lobe/*physiology, Optical Illusions/*physiology, Photic Stimulation, Retina/physiology, Vision, Binocular/physiology, Visual Cortex/*physiology},
	pages = {8560--72},
	annote = {Mendola, J {DDale}, A {MFischl}, {BLiu}, A {KTootell}, R {BengEY}07980/{EY}/{NEI} {NIH} {HHS}/Research Support, Non-U.S. Gov'{tResearch} Support, U.S. Gov't, P.H.S.1999/09/24J Neurosci. 1999 Oct 1;19(19):8560-72.},
	file = {Mendola-1999-The representation of illusory an:/autofs/cluster/freesurfer/zotero/storage/9CVV35SP/Mendola-1999-The representation of illusory an.pdf:application/pdf}
}

@article{fischl_high-resolution_1999,
	title = {High-resolution inter-subject averaging and a coordinate system for the cortical surface.},
	volume = {8},
	shorttitle = {High-resolution inter-subject averaging and a coordinate system for the cortical surface.},
	url = {https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl99-morphing.pdf},
	number = {4},
	journal = {Human Brain Mapping},
	author = {Fischl, B and Sereno, M.I. and Tootell, R.B.H. and Dale, A.M.},
	year = {1999},
	keywords = {fs\_Intersubject-averaging},
	pages = {272--284}
}

@article{buckner_evidence_2004,
	title = {Evidence for Distinct Effects of Aging and Alzheimer's Disease on Hippocampal Volume},
	volume = {Submitted},
	shorttitle = {Evidence for Distinct Effects of Aging and Alzheimer's Disease on Hippocampal Volume},
	journal = {Journal of Neuroscience},
	author = {Buckner, Randy L. and Quinn, Brian T. and Salat, David and Head, Denise and Snyder, Abraham Z. and Busa, Evelina and Goate, Alison and Morris, John C. and Dale, Anders M. and Fischl, Bruce},
	year = {2004}
}

@article{ronan_intrinsic_2011,
	title = {{INTRINSIC} {CURVATURE}: A {MARKER} {OF} {MILLIMETER}-{SCALE} {TANGENTIAL} {CORTICO}-{CORTICAL} {CONNECTIVITY}?},
	volume = {21},
	issn = {0129-0657},
	shorttitle = {{INTRINSIC} {CURVATURE}},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3446200/},
	abstract = {In this paper, we draw a link between cortical intrinsic curvature and the distributions of tangential connection lengths. We suggest that differential rates of surface expansion not only lead to intrinsic curvature of the cortical sheet, but also to differential inter-neuronal spacing. We propose that there follows a consequential change in the profile of neuronal connections: specifically an enhancement of the tendency towards proportionately more short connections. Thus, the degree of cortical intrinsic curvature may have implications for short-range connectivity.},
	number = {5},
	urldate = {2014-08-25},
	journal = {International journal of neural systems},
	author = {RONAN, LISA and PIENAAR, RUDOLPH and WILLIAMS, GUY and BULLMORE, ED and CROW, TIM J. and ROBERTS, NEIL and JONES, PETER B. and SUCKLING, JOHN and FLETCHER, PAUL C.},
	month = oct,
	year = {2011},
	pmid = {21956929},
	pmcid = {PMC3446200},
	pages = {351--366},
	file = {PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/R778AADP/RONAN et al. - 2011 - INTRINSIC CURVATURE A MARKER OF MILLIMETER-SCALE .pdf:application/pdf}
}

@article{yeo_learning_2010,
	title = {Learning task-optimal registration cost functions for localizing cytoarchitecture and function in the cerebral cortex},
	volume = {29},
	issn = {1558-254X (Electronic) 0278-0062 (Linking)},
	shorttitle = {Learning task-optimal registration cost functions for localizing cytoarchitecture and function in the cerebral cortex},
	url = {http://people.csail.mit.edu/ythomas/publications/2010TaskOptimal-TMI.pdf},
	doi = {10.1109/TMI.2010.2049497},
	abstract = {Image registration is typically formulated as an optimization problem with multiple tunable, manually set parameters. We present a principled framework for learning thousands of parameters of registration cost functions, such as a spatially-varying tradeoff between the image dissimilarity and regularization terms. Our approach belongs to the classic machine learning framework of model selection by optimization of cross-validation error. This second layer of optimization of cross-validation error over and above registration selects parameters in the registration cost function that result in good registration as measured by the performance of the specific application in a training data set. Much research effort has been devoted to developing generic registration algorithms, which are then specialized to particular imaging modalities, particular imaging targets and particular postregistration analyses. Our framework allows for a systematic adaptation of generic registration cost functions to specific applications by learning the "free" parameters in the cost functions. Here, we consider the application of localizing underlying cytoarchitecture and functional regions in the cerebral cortex by alignment of cortical folding. Most previous work assumes that perfectly registering the macro-anatomy also perfectly aligns the underlying cortical function even though macro-anatomy does not completely predict brain function. In contrast, we learn 1) optimal weights on different cortical folds or 2) optimal cortical folding template in the generic weighted sum of squared differences dissimilarity measure for the localization task. We demonstrate state-of-the-art localization results in both histological and functional magnetic resonance imaging data sets.},
	number = {7},
	journal = {{IEEE} Trans Med Imaging},
	author = {Yeo, B. T. and Sabuncu, M. R. and Vercauteren, T. and Holt, D. J. and Amunts, K. and Zilles, K. and Golland, P. and Fischl, B.},
	month = jul,
	year = {2010},
	keywords = {*Algorithms, Brain Mapping/*methods, Brain/*physiology, Cerebral Cortex/*physiology, fs\_Intersubject-averaging, fs\_Misc-methodology, Humans, Image Enhancement/methods, Image Interpretation, Computer-Assisted/*methods, Information Storage and Retrieval/*methods, Magnetic Resonance Imaging/*methods, Pattern Recognition, Automated/*methods, Reproducibility of Results, Sensitivity and Specificity},
	pages = {1424--41},
	annote = {Yeo, B T {ThomasSabuncu}, Mert {RVercauteren}, {TomHolt}, Daphne {JAmunts}, {KatrinZilles}, {KarlGolland}, {PolinaFischl}, {BruceengAG}02238/{AG}/{NIA} {NIH} {HHS}/K25 {EB}013649/{EB}/{NIBIB} {NIH} {HHS}/P41 {EB}015902/{EB}/{NIBIB} {NIH} {HHS}/P41 {RR}013218/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075/{RR}/{NCRR} {NIH} {HHS}/P41-{RR}13218/{RR}/{NCRR} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 {AG}022381/{AG}/{NIA} {NIH} {HHS}/R01 {EB}001550/{EB}/{NIBIB} {NIH} {HHS}/R01 {EB}006758/{EB}/{NIBIB} {NIH} {HHS}/R01 {NS}051826/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}052585/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}052585-01/{NS}/{NINDS} {NIH} {HHS}/R01 {RR}016594/{RR}/{NCRR} {NIH} {HHS}/R01 {RR}16594-01A1/{RR}/{NCRR} {NIH} {HHS}/R01-{NS}051826/{NS}/{NINDS} {NIH} {HHS}/R01EB001550/{EB}/{NIBIB} {NIH} {HHS}/R01EB006758/{EB}/{NIBIB} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/U24-{RR}021382/{RR}/{NCRR} {NIH} {HHS}/U54 {EB}005149/{EB}/{NIBIB} {NIH} {HHS}/U54-{EB}005149/{EB}/{NIBIB} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov'{tResearch} Support, U.S. Gov't, Non-P.H.S.2010/06/10 06:00IEEE Trans Med Imaging. 2010 Jul;29(7):1424-41. doi: 10.1109/{TMI}.2010.2049497. Epub 2010 Jun 7.},
	file = {Yeo-2010-Learning task-optimal registration co:/autofs/cluster/freesurfer/zotero/storage/ADECKCW6/Yeo-2010-Learning task-optimal registration co.pdf:application/pdf}
}

@article{f._segonne_genetic_2005,
	title = {Genetic algorithm for the topology correction of cortical surfaces.},
	shorttitle = {Genetic algorithm for the topology correction of cortical surfaces.},
	number = {393-405},
	journal = {{IPMI}},
	author = {F. Segonne, E. Grimson {and} B. Fischl},
	year = {2005}
}

@article{aganj_removing_2013,
	title = {On removing interpolation and resampling artifacts in rigid image registration},
	volume = {22},
	issn = {1941-0042 (Electronic) 1057-7149 (Linking)},
	shorttitle = {On removing interpolation and resampling artifacts in rigid image registration},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/23076044},
	doi = {10.1109/TIP.2012.2224356},
	abstract = {We show that image registration using conventional interpolation and summation approximations of continuous integrals can generally fail because of resampling artifacts. These artifacts negatively affect the accuracy of registration by producing local optima, altering the gradient, shifting the global optimum, and making rigid registration asymmetric. In this paper, after an extensive literature review, we demonstrate the causes of the artifacts by comparing inclusion and avoidance of resampling analytically. We show the sum-of-squared-differences cost function formulated as an integral to be more accurate compared with its traditional sum form in a simple case of image registration. We then discuss aliasing that occurs in rotation, which is due to the fact that an image represented in the Cartesian grid is sampled with different rates in different directions, and propose the use of oscillatory isotropic interpolation kernels, which allow better recovery of true global optima by overcoming this type of aliasing. Through our experiments on brain, fingerprint, and white noise images, we illustrate the superior performance of the integral registration cost function in both the Cartesian and spherical coordinates, and also validate the introduced radial interpolation kernel by demonstrating the improvement in registration.},
	number = {2},
	urldate = {2014-08-21},
	journal = {{IEEE} Trans Image Process},
	author = {Aganj, I. and Yeo, B. T. and Sabuncu, M. R. and Fischl, B.},
	month = feb,
	year = {2013},
	keywords = {Algorithms, *Artifacts, Brain/anatomy \& histology, Dermatoglyphics, fs\_Misc-methodology, Humans, Image Processing, Computer-Assisted/*methods, Magnetic Resonance Imaging},
	pages = {816--27},
	annote = {Aganj, {ImanYeo}, Boon Thye {ThomasSabuncu}, Mert {RFischl}, Bruceeng1K25EB013649-01/{EB}/{NIBIB} {NIH} {HHS}/1KL2RR025757-01/{RR}/{NCRR} {NIH} {HHS}/1R01NS070963/{NS}/{NINDS} {NIH} {HHS}/1R21NS072652-01/{NS}/{NINDS} {NIH} {HHS}/1S10RR019307/{RR}/{NCRR} {NIH} {HHS}/1S10RR023043/{RR}/{NCRR} {NIH} {HHS}/1S10RR023401/{RR}/{NCRR} {NIH} {HHS}/5U01-{MH}093765/{MH}/{NIMH} {NIH} {HHS}/{AG}022381/{AG}/{NIA} {NIH} {HHS}/{AT}005728-01/{AT}/{NCCAM} {NIH} {HHS}/K25 {EB}013649/{EB}/{NIBIB} {NIH} {HHS}/P41 {RR}006009/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075/{RR}/{NCRR} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 {EB}006758/{EB}/{NIBIB} {NIH} {HHS}/R01 {NS}052585/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}070963/{NS}/{NINDS} {NIH} {HHS}/R01 {RR}016594/{RR}/{NCRR} {NIH} {HHS}/R01EB006758/{EB}/{NIBIB} {NIH} {HHS}/R01NS052585-01/{NS}/{NINDS} {NIH} {HHS}/R21 {NS}072652/{NS}/{NINDS} {NIH} {HHS}/S10 {RR}019307/{RR}/{NCRR} {NIH} {HHS}/S10 {RR}023401/{RR}/{NCRR} {NIH} {HHS}/U24RR021382/{RR}/{NCRR} {NIH} {HHS}/U54 {EB}005149/{EB}/{NIBIB} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov't2012/10/19 06:00IEEE Trans Image Process. 2013 Feb;22(2):816-27. doi: 10.1109/{TIP}.2012.2224356. Epub 2012 Oct 11.},
	file = {Aganj-2013-On removing interpolation and resa1:/autofs/cluster/freesurfer/zotero/storage/PW8UCQVS/Aganj-2013-On removing interpolation and resa1.pdf:application/pdf}
}

@article{sailer_focal_2003,
	title = {Focal thinning of the cerebral cortex in multiple sclerosis},
	volume = {126},
	issn = {0006-8950 (Print) 0006-8950 (Linking)},
	shorttitle = {Focal thinning of the cerebral cortex in multiple sclerosis},
	url = {http://brain.oxfordjournals.org/content/126/8/1734.full.pdf},
	doi = {10.1093/brain/awg175},
	abstract = {Brain atrophy as determined by quantitative {MRI} can be used to characterize disease progression in multiple sclerosis. Many studies have addressed white matter ({WM}) alterations leading to atrophy, while changes of the cerebral cortex have been studied to a lesser extent. In vivo, the cerebral cortex has been difficult to study due to its complex structure and regional variability. Measurement of cerebral cortex thickness at different disease stages may provide new insights into grey matter ({GM}) pathology. In the present investigation, we evaluated in vivo cortical thickness and its relationship to disability, disease duration, {WM} T2 hyper-intense and T1 hypo-intense lesion volumes. High-resolution {MRI} brain scans were obtained in 20 patients with clinically definite multiple sclerosis and 15 age-matched normal subjects. A novel method of automated surface reconstruction yielded measurements of the cortical thickness for each subject's entire brain and computed cross-subject statistics based on the cortical anatomy. Statistical thickness difference maps were generated by performing t-tests between patient and control groups and individual thickness measures were submitted to analyses of variance to investigate the relationship between cortical thickness and clinical variables. The mean overall thickness of the cortical ribbon was reduced in multiple sclerosis patients compared with controls [2.30 mm ({SD} 0.14) versus 2.48 mm ({SD} 0.11)], showing a significant main effect of group (controls versus patients). In patients, we found significant main effects for disability, disease duration, T2 and T1 lesion volumes. The visualization of statistical difference maps of the cortical {GM} thickness on inflated brains across the cortical surface revealed a distinct distribution of significant focal thinning of the cerebral cortex in addition to the diffuse cortical atrophy. Focal cortical thinning in frontal [2.37 mm ({SD} 0.17) versus 2.73 mm ({SD} 0.25)] and in temporal [2.65 mm ({SD} 0.15) versus 2.95 mm ({SD} 0.11)] brain regions was observed, even early in the course of the disease or in patients with mild disability. Patients with longstanding disease or severe disability, however, presented additionally with focal thinning of the motor cortex area [2.35 mm ({SD} 0.19) versus 2.74 mm ({SD} 0.15)]. We conclude that in vivo measurement of cortical thickness is feasible in patients suffering from multiple sclerosis. The data provide new insight into the cortical pathology in multiple sclerosis patients, revealing focal cortical thinning beside an overall reduction of the cortical thickness with disease progression.},
	language = {eng},
	number = {Pt 8},
	journal = {Brain},
	author = {Sailer, M. and Fischl, B. and Salat, D. and Tempelmann, C. and Schonfeld, M. A. and Busa, E. and Bodammer, N. and Heinze, H. J. and Dale, A.},
	month = aug,
	year = {2003},
	keywords = {Adult, Adult, Atrophy, Atrophy, Cerebral Cortex, Cerebral Cortex/*pathology, Disease Progression, Disease Progression, Female, Female, Humans, Humans, Image Processing, Computer-Assisted, Image Processing, Computer-Assisted/methods, Magnetic Resonance Imaging, Magnetic Resonance Imaging, Male, Male, Middle Aged, Middle Aged, Multiple Sclerosis, Multiple Sclerosis/*pathology, Severity of Illness Index, Severity of Illness Index, Time Factors, Time Factors},
	pages = {1734--44},
	annote = {Sailer, {MichaelFischl}, {BruceSalat}, {DavidTempelmann}, {ClausSchonfeld}, Mircea {ArielBusa}, {EvelinaBodammer}, {NilsHeinze}, Hans-{JochenDale}, Anderseng1R01 {RR} 16594-01A1/{RR}/{NCRR} {NIH} {HHS}/P41 {RR} 14075/{RR}/{NCRR} {NIH} {HHS}/Research Support, U.S. Gov't, P.H.S.England2003/06/14 05:00Brain. 2003 Aug;126(Pt 8):1734-44. Epub 2003 Jun 4.},
	file = {Sailer-2003-Focal thinning of the cerebral cor:/autofs/cluster/freesurfer/zotero/storage/ZS82FH6G/Sailer-2003-Focal thinning of the cerebral cor.pdf:application/pdf}
}

@article{clarkson_comparison_2011,
	title = {A comparison of voxel and surface based cortical thickness estimation methods},
	volume = {57},
	issn = {1095-9572},
	doi = {10.1016/j.neuroimage.2011.05.053},
	abstract = {Cortical thickness estimation performed in-vivo via magnetic resonance imaging is an important technique for the diagnosis and understanding of the progression of neurodegenerative diseases. Currently, two different computational paradigms exist, with methods generally classified as either surface or voxel-based. This paper provides a much needed comparison of the surface-based method {FreeSurfer} and two voxel-based methods using clinical data. We test the effects of computing regional statistics using two different atlases and demonstrate that this makes a significant difference to the cortical thickness results. We assess reproducibility, and show that {FreeSurfer} has a regional standard deviation of thickness difference on same day scans that is significantly lower than either a Laplacian or Registration based method and discuss the trade off between reproducibility and segmentation accuracy caused by bending energy constraints. We demonstrate that voxel-based methods can detect similar patterns of group-wise differences as well as {FreeSurfer} in typical applications such as producing group-wise maps of statistically significant thickness change, but that regional statistics can vary between methods. We use a Support Vector Machine to classify patients against controls and did not find statistically significantly different results with voxel based methods compared to {FreeSurfer}. Finally we assessed longitudinal performance and concluded that currently {FreeSurfer} provides the most plausible measure of change over time, with further work required for voxel based methods.},
	language = {eng},
	number = {3},
	journal = {{NeuroImage}},
	author = {Clarkson, Matthew J. and Cardoso, M. Jorge and Ridgway, Gerard R. and Modat, Marc and Leung, Kelvin K. and Rohrer, Jonathan D. and Fox, Nick C. and Ourselin, Sébastien},
	month = aug,
	year = {2011},
	pmid = {21640841},
	keywords = {Aged, Alzheimer Disease, Brain, Brain Mapping, Female, Frontotemporal Dementia, fs\_Validation-Evaluations, Humans, Image Interpretation, Computer-Assisted, Magnetic Resonance Imaging, Male, Reproducibility of Results},
	pages = {856--865}
}

@article{dale_improved_1993,
	title = {Improved localization of cortical activity by combining {EEG} and {MEG} with {MRI} cortical surface reconstruction: A linear approach.},
	volume = {5},
	url = {http://nmr.mgh.harvard.edu/~fischl/reprints/dalesereno93-ms.pdf},
	journal = {Journal of Cognitive Neuroscience},
	author = {Dale, A. M. and Sereno, M. I.},
	year = {1993},
	keywords = {fs\_Surface-reconstruction},
	pages = {162--176}
}

@article{ghosh_evaluating_2010,
	title = {Evaluating the validity of volume-based and surface-based brain image registration for developmental cognitive neuroscience studies in children 4 to 11 years of age},
	volume = {53},
	issn = {1095-9572 (Electronic) 1053-8119 (Linking)},
	shorttitle = {Evaluating the validity of volume-based and surface-based brain image registration for developmental cognitive neuroscience studies in children 4 to 11 years of age},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/20621657},
	doi = {10.1016/j.neuroimage.2010.05.075},
	abstract = {Understanding the neurophysiology of human cognitive development relies on methods that enable accurate comparison of structural and functional neuroimaging data across brains from people of different ages. A fundamental question is whether the substantial brain growth and related changes in brain morphology that occur in early childhood permit valid comparisons of brain structure and function across ages. Here we investigated whether valid comparisons can be made in children from ages 4 to 11, and whether there are differences in the use of volume-based versus surface-based registration approaches for aligning structural landmarks across these ages. Regions corresponding to the calcarine sulcus, central sulcus, and Sylvian fissure in both the hemispheres were manually labeled on T1-weighted structural magnetic resonance images from 31 children ranging in age from 4.2 to 11.2years old. Quantitative measures of shape similarity and volumetric-overlap of these manually labeled regions were calculated when brains were aligned using a 12-parameter affine transform, {SPM}'s nonlinear normalization, a diffeomorphic registration ({ANTS}), and {FreeSurfer}'s surface-based registration. Registration error for normalization into a common reference framework across participants in this age range was lower than commonly used functional imaging resolutions. Surface-based registration provided significantly better alignment of cortical landmarks than volume-based registration. In addition, registering children's brains to a common space does not result in an age-associated bias between older and younger children, making it feasible to accurately compare structural properties and patterns of brain activation in children from ages 4 to 11.},
	number = {1},
	journal = {Neuroimage},
	author = {Ghosh, S. S. and Kakunoori, S. and Augustinack, J. and Nieto-Castanon, A. and Kovelman, I. and Gaab, N. and Christodoulou, J. A. and Triantafyllou, C. and Gabrieli, J. D. and Fischl, B.},
	month = oct,
	year = {2010},
	keywords = {Aging, Aging/*pathology, Algorithms, *Algorithms, Brain, Brain/*anatomy \& histology/*growth \& development, Child, Preschool, Child, Preschool, Cognition, Cognition/physiology, Female, Female, fs\_Validation-Evaluations, Humans, Humans, Image Enhancement, Image Enhancement/methods, Image Interpretation, Computer-Assisted, Image Interpretation, Computer-Assisted/*methods, Imaging, Three-Dimensional, Imaging, Three-Dimensional/*methods, Male, Male, Neurosciences, Neurosciences/methods, Reproducibility of Results, Reproducibility of Results, Sensitivity and Specificity, Sensitivity and Specificity, *Subtraction Technique, Subtraction Technique},
	pages = {85--93},
	annote = {Ghosh, Satrajit {SKakunoori}, {SitaAugustinack}, {JeanNieto}-Castanon, {AlfonsoKovelman}, {IouliaGaab}, {NadineChristodoulou}, Joanna {ATriantafyllou}, {ChristinaGabrieli}, John D {EFischl}, {BruceengAG}02238/{AG}/{NIA} {NIH} {HHS}/P41-{RR}1407/{RR}/{NCRR} {NIH} {HHS}/R01 {NS}052585-01/{NS}/{NINDS} {NIH} {HHS}/R01EB006758/{EB}/{NIBIB} {NIH} {HHS}/R03 {EB}008673-01/{EB}/{NIBIB} {NIH} {HHS}/R03EB008673/{EB}/{NIBIB} {NIH} {HHS}/U54 {EB}005149/{EB}/{NIBIB} {NIH} {HHS}/Evaluation {StudiesResearch} Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov'{tValidation} Studies2010/07/14 06:00Neuroimage. 2010 Oct 15;53(1):85-93. doi: 10.1016/j.neuroimage.2010.05.075. Epub 2010 Jun 4.},
	file = {Ghosh-2010-Evaluating the validity of volume-b:/autofs/cluster/freesurfer/zotero/storage/JQ3SWNFW/Ghosh-2010-Evaluating the validity of volume-b.pdf:application/pdf}
}

@article{fjell_morphometric_2008,
	title = {Morphometric Changes in the Episodic Memory Network and Tau Pathologic Features Correlate with Memory Performance in Patients with Mild Cognitive Impairment},
	volume = {29},
	issn = {0195-6108, 1936-959X},
	url = {http://www.ajnr.org/content/29/6/1183},
	doi = {10.3174/ajnr.A1059},
	abstract = {{BACKGROUND} {AND} {PURPOSE}: Mild cognitive impairment ({MCI}) may affect several cognitive domains, including attention and reasoning, but is often first characterized by memory deficits. The purpose of this study was to ask these 2 questions: 1) Can levels of {CSF} tau proteins and amyloid beta 42 peptide explain thinning of the cerebral cortex in patients with {MCI}? 2) How are brain morphometry, {CSF} biomarkers, and apolipoprotein E ({APOE}) allelic variation related to episodic memory function in {MCI}?
{MATERIALS} {AND} {METHODS}: Hippocampal volume and cortical thickness were estimated by {MR} imaging and compared for patients with {MCI} (n = 18) and healthy controls (n = 18). In addition, regions of interest ({ROIs}) were selected in areas where the {MCI} group had atrophy and which overlapped with the episodic memory network (temporal, entorhinal, inferior parietal, precuneus/posterior cingulate, and frontal). Relationships among morphometry, {CSF} biomarkers, {APOE}, and memory were tested. The analyses were repeated with an independent sample of patients with {MCI} (n = 19).
{RESULTS}: Patients with {MCI} and pathologic {CSF} values had hippocampal atrophy. However, both patients with pathologic and patients with nonpathologic {CSF} had a thinner cortex outside the hippocampal area. {CSF} pathology was related to hippocampal volume, whereas relationships with cortical thickness were found mainly in one of the samples. Morphometry correlated robustly with memory performance across {MCI} samples, whereas less stable results were found for tau protein.
{CONCLUSION}: The differences in hippocampal volume between the {MCI} and the healthy control groups were only found in patients with pathologic {CSF} biomarkers, whereas differences in cortical thickness were also found for patients without such pathologic features. Morphometry in areas in the episodic memory network was robustly correlated with memory performance. It is speculated that atrophy in these areas may be associated with the memory problems seen in {MCI}.},
	language = {en},
	number = {6},
	urldate = {2014-08-23},
	journal = {American Journal of Neuroradiology},
	author = {Fjell, A. M. and Walhovd, K. B. and Amlien, I. and Bjørnerud, A. and Reinvang, I. and Gjerstad, L. and Cappelen, T. and Willoch, F. and Due-Tønnessen, P. and Grambaite, R. and Skinningsrud, A. and Stenset, V. and Fladby, T.},
	month = jun,
	year = {2008},
	pmid = {18544670},
	pages = {1183--1189},
	file = {Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/Q2HDT8UE/Fjell et al. - 2008 - Morphometric Changes in the Episodic Memory Networ.pdf:application/pdf;Snapshot:/autofs/cluster/freesurfer/zotero/storage/8CPE8KD8/1183.html:text/html}
}

@article{montoliu_focal_2012,
	title = {Focal cortical damage parallels cognitive impairment in minimal hepatic encephalopathy},
	volume = {61},
	issn = {1095-9572},
	doi = {10.1016/j.neuroimage.2012.03.041},
	abstract = {Little attention has been paid to cortical integrity in patients with minimal hepatic encephalopathy ({MHE}), although cognitive functions affected in early stages of liver disease are mainly allocated in different neocortical structures. Here we used cortical surface-based analysis techniques to investigate if patterns of cortical thinning accompany the mildest form of {HE}. To aim this goal, cortical thickness obtained from high-resolution 3T magnetic resonance imaging ({MRI}) was measured in patients with no {MHE} ({NMHE}), {MHE}, and healthy controls. Further correlation analyses were performed to examine whether scores in the critical flicker frequency ({CFF}) test, and blood ammonia levels accounted for the loss of cortical integrity in different stages of liver disease. Finally, we assessed group differences in volume of different subcortical regions and their potential relationships with {CFF} scores/blood ammonia levels. Results showed a focal thinning of the superior temporal cortex and precuneus in {MHE} patients when compared with {NMHE} and controls. Relationships between blood ammonia levels and cortical thickness of the calcarine sulcus accounted for impaired visual judgment in patients with {MHE} when compared to {NMHE}. Regression analyses between cortical thickness and {CFF} predicted differences between controls and the two groups of {HE} patients, but failed to discriminate between patients with {NMHE} and {MHE}. Taking together, these findings provide the first report of cortical thinning in {MHE} patients, and they yield novel insights into the neurobiological basis of cognitive impairment associated with early stages of liver diseases.},
	language = {eng},
	number = {4},
	journal = {{NeuroImage}},
	author = {Montoliu, Carmina and Gonzalez-Escamilla, Gabriel and Atienza, Mercedes and Urios, Amparo and Gonzalez, Olga and Wassel, Abdallah and Aliaga, Roberto and Giner-Duran, Remedios and Serra, Miguel A. and Rodrigo, Jose M. and Belloch, Vicente and Felipo, Vicente and Cantero, Jose L.},
	month = jul,
	year = {2012},
	pmid = {22465844},
	keywords = {Cerebral Cortex, Cognition Disorders, Early Diagnosis, Female, Hepatic Encephalopathy, Humans, Image Interpretation, Computer-Assisted, Magnetic Resonance Imaging, Male, Middle Aged, Neuropsychological Tests},
	pages = {1165--1175}
}

@misc{center_for_history_and_new_media_zotero_????,
	title = {Zotero Quick Start Guide},
	url = {http://zotero.org/support/quick_start_guide},
	author = {{Center for History and New Media}},
	annote = {Welcome to Zotero!View the Quick Start Guide to learn how to begin collecting, managing, citing, and sharing your research sources.Thanks for installing Zotero.}
}

@article{isaacs_effect_2008,
	title = {The effect of early human diet on caudate volumes and {IQ}},
	volume = {63},
	issn = {0031-3998},
	url = {https://surfer.nmr.mgh.harvard.edu/ftp/articles/caudate.pdf},
	doi = {10.1203/PDR.0b013e318163a271},
	abstract = {Early nutrition in animals affects both behavior and brain structure. In humans, randomized trials show that early nutrition affects later cognition, notably in males. We hypothesized that early nutrition also influences brain structure, measurable using magnetic resonance imaging. Prior research suggested that the caudate nucleus may be especially vulnerable to early environment and that its size relates to {IQ}. To test the hypothesis that the caudate nucleus could be a neural substrate for cognitive effects of early nutrition, we compared two groups of adolescents, assigned a Standard- or High-nutrient diet in the postnatal weeks after preterm birth. Groups had similar birth status and neonatal course. Scans and {IQ} data were obtained from 76 adolescents and volumes of several subcortical structures were calculated. The High-nutrient group had significantly larger caudate volumes and higher Verbal {IQ} ({VIQ}). Caudate volumes correlated significantly with {VIQ} in the Standard-nutrient group only. Caudate volume was influenced by early nutrition and related selectively to {VIQ} in males, but not in females. Our findings may partly explain the effects of early diet on cognition and the predominant effects in males. They are among the first to show that human brain structure can be influenced by early nutrition.},
	language = {eng},
	number = {3},
	journal = {Pediatric Research},
	author = {Isaacs, Elizabeth B. and Gadian, David G. and Sabatini, Stuart and Chong, Wui K. and Quinn, Brian T. and Fischl, Bruce R. and Lucas, Alan},
	month = mar,
	year = {2008},
	pmid = {18287970},
	keywords = {Adolescent, Adolescent, Adolescent Development, Adolescent Development, Adult, Adult, Brain Mapping, Brain Mapping/methods, Caudate Nucleus, Caudate Nucleus/growth \& development/*physiology, Child Development, Child Development, Cognition, *Cognition, Cohort Studies, Cohort Studies, Diet, *Diet, Female, Female, Gestational Age, Gestational Age, Humans, Humans, *Infant Formula, Infant Formula, Infant, Newborn, Infant, Newborn, *Infant Nutritional Physiological Phenomena, Infant Nutritional Physiological Phenomena, *Infant, Premature, Infant, Premature, Intelligence, *Intelligence, Intelligence Tests, Intelligence Tests, Magnetic Resonance Imaging, Magnetic Resonance Imaging, Male, Male, *Milk, Human, Milk, Human, Organ Size, Organ Size, Randomized Controlled Trials as Topic, Randomized Controlled Trials as Topic, Sex Factors, Sex Factors, Time Factors, Time Factors},
	pages = {308--314},
	annote = {Isaacs, Elizabeth {BGadian}, David {GSabatini}, {StuartChong}, Wui {KQuinn}, Brian {TFischl}, Bruce {RLucas}, {AlanengP}41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 {EB}001550/{EB}/{NIBIB} {NIH} {HHS}/R01 {NS}052585-01/{NS}/{NINDS} {NIH} {HHS}/R01 {RR}16594-01AI/{AI}/{NIAID} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/U54 {EB}005149/{EB}/{NIBIB} {NIH} {HHS}/Medical Research Council/United {KingdomWellcome} Trust/United {KingdomComparative} {StudyResearch} Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov'{tResearch} Support, U.S. Gov't, Non-P.H.S.2008/02/22 09:00Pediatr Res. 2008 Mar;63(3):308-14. doi: 10.1203/{PDR}.0b013e318163a271.},
	file = {Isaacs-2008-The effect of early human diet on:/autofs/cluster/freesurfer/zotero/storage/R2BQDJ3D/Isaacs-2008-The effect of early human diet on.pdf:application/pdf}
}

@article{pardoe_sample_2013,
	title = {Sample Size Estimates for Well-Powered Cross-Sectional Cortical Thickness Studies},
	volume = {34},
	issn = {1065-9471},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3500581/},
	doi = {10.1002/hbm.22120},
	abstract = {Introduction
Cortical thickness mapping is a widely used method for the analysis of neuroanatomical differences between subject groups. We applied power analysis methods over a range of image processing parameters to derive a model that allows researchers to calculate the number of subjects required to ensure a well-powered cross-sectional cortical thickness study.

Methods
0.9-mm isotropic T1-weighted 3D {MPRAGE} {MRI} scans from 98 controls (53 females, age 29.1 ± 9.7 years) were processed using Freesurfer 5.0. Power analyses were carried out using vertex-wise variance estimates from the coregistered cortical thickness maps, systematically varying processing parameters. A genetic programming approach was used to derive a model describing the relationship between sample size and processing parameters. The model was validated on four Alzheimer’s Disease Neuroimaging Initiative control datasets (mean 126.5 subjects/site, age 76.6 ± 5.0 years).

Results
Approximately 50 subjects per group are required to detect a 0.25-mm thickness difference; less than 10 subjects per group are required for differences of 1 mm (two-sided test, 10 mm smoothing, α = 0.05). Sample size estimates were heterogeneous over the cortical surface. The model yielded sample size predictions within 2–6\% of that determined experimentally using independent data from four other datasets. Fitting parameters of the model to data from each site reduced the estimation error to less than 2\%.

Conclusions
The derived model provides a simple tool for researchers to calculate how many subjects should be included in a well-powered cortical thickness analysis.},
	number = {11},
	urldate = {2014-08-23},
	journal = {Human brain mapping},
	author = {Pardoe, Heath R. and Abbott, David F. and Jackson, Graeme D.},
	month = nov,
	year = {2013},
	pmid = {22807270},
	pmcid = {PMC3500581},
	keywords = {Adult, Anatomy, Cross-Sectional/*methods, Brain Mapping/methods, Cerebral Cortex/*anatomy \& histology, Cohort Studies, Data Interpretation, Statistical, Female, Genetic Processes, Humans, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Male, Models, Neurological, Reproducibility of Results, *Sample Size, Young Adult},
	annote = {Pardoe, Heath {RAbbott}, David {FJackson}, Graeme {DengNIH}-{NINDS} R37-31146/{PHS} {HHS}/R37 {NS}031146/{NS}/{NINDS} {NIH} {HHS}/U01 {AG}024904/{AG}/{NIA} {NIH} {HHS}/{UL}1 {TR}000128/{TR}/{NCATS} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov't2012/07/19 06:00Hum Brain Mapp. 2013 Nov;34(11):3000-9. doi: 10.1002/hbm.22120. Epub 2012 Jul 17.},
	file = {Pardoe-2013-Sample size estimates for well-po1:/autofs/cluster/freesurfer/zotero/storage/8MP4B97D/Pardoe-2013-Sample size estimates for well-po1.pdf:application/pdf;PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/3GM8JCEM/Pardoe et al. - 2013 - Sample Size Estimates for Well-Powered Cross-Secti.pdf:application/pdf}
}

@article{walhovd_volumetric_2007,
	title = {Volumetric cerebral characteristics of children exposed to opiates and other substances in utero},
	volume = {36},
	issn = {1053-8119},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2039875/},
	doi = {10.1016/j.neuroimage.2007.03.070},
	abstract = {Morphometric cerebral characteristics were studied in children with prenatal poly-substance exposure (n =14) compared to controls (n = 14) without such exposure. Ten of the substance exposed children were born to mothers who used opiates (heroin) throughout the pregnancy. Groups were compared across 16 brain measures: cortical gray matter, cerebral white matter, hippocampus, amygdala, thalamus, accumbens area, caudate, putamen, pallidum, brainstem, cerebellar cortex, cerebellar white matter, lateral ventricles, inferior lateral ventricles, and the 3rd and 4th ventricles. In addition, continuous measurement of thickness across the entire cortical mantle was performed. Volumetric characteristics were correlated with ability and questionnaire assessments 2 years prior to scan. Compared to controls, the substance-exposed children had smaller intracranial and brain volumes, including smaller cerebral cortex, amygdala, accumbens area, putamen, pallidum, brainstem, cerebellar cortex, cerebellar white matter, and inferior lateral ventricles, and thinner cortex of the right anterior cingulate and lateral orbitofrontal cortex. Pallidum and putamen appeared especially reduced in the subgroup exposed to opiates. Only volumes of the right anterior cingulate, the right lateral orbitofrontal cortex and the accumbens area, showed some association with ability and questionnaire measures. The sample studied is rare, and hence small, so conclusions cannot be drawn with certainty. Morphometric group differences were observed, but associations with previous behavioral assessment were generally weak. Some of the volumetric differences, particularly thinner cortex in part of the right lateral orbitofrontal cortex, may be moderately involved in cognitive and behavioral difficulties more frequently experienced by opiate and poly-substance exposed children.},
	number = {4},
	urldate = {2014-08-25},
	journal = {{NeuroImage}},
	author = {Walhovd, K. B. and Moe, V. and Slinning, K. and Due-T?nnessen, P. and Bj?rnerud, A. and Dale, A. M. and van der Kouwe, A. and Quinn, B. T. and Kosofsky, B. and Greve, D. and Fischl, B.},
	month = jul,
	year = {2007},
	pmid = {17513131},
	pmcid = {PMC2039875},
	keywords = {Attention Deficit Disorder with Hyperactivity/chemically, Brain/*drug effects/pathology, Cerebral Cortex/drug effects/pathology, Child, Child Behavior Disorders/chemically induced/diagnosis/pathology, Child, Preschool, Developmental Disabilities/*chemically induced/diagnosis/pathology, Dominance, Cerebral/physiology, Female, Follow-Up Studies, Heroin/*toxicity, Humans, *Image Processing, Computer-Assisted, *Imaging, Three-Dimensional, induced/diagnosis/pathology, Intelligence/drug effects, Internal-External Control, Learning Disorders/*chemically induced/diagnosis, *Magnetic Resonance Imaging, Male, Narcotics/*toxicity, Neuropsychological Tests, Pregnancy, *Prenatal Exposure Delayed Effects, Reference Values, Social Adjustment, Statistics as Topic, Street Drugs/*toxicity, Wechsler Scales},
	pages = {1331--1344},
	annote = {Walhovd, K {BMoe}, {VSlinning}, {KDue}-Tonnessen, {PBjornerud}, {ADale}, A Mvan der Kouwe, {AQuinn}, B {TKosofsky}, {BGreve}, {DFischl}, {BengBIRN}002/{PHS} {HHS}/K02 {DA}000354-08/{DA}/{NIDA} {NIH} {HHS}/P41 {RR}014075/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-075753/{RR}/{NCRR} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 {DA}017905-03/{DA}/{NIDA} {NIH} {HHS}/R01 {EB}001550-04/{EB}/{NIBIB} {NIH} {HHS}/R01 {EB}006758/{EB}/{NIBIB} {NIH} {HHS}/R01 {EB}006758-01A1/{EB}/{NIBIB} {NIH} {HHS}/R01 {NS}052585/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}052585-01A1/{NS}/{NINDS} {NIH} {HHS}/R01 {RR}016594/{RR}/{NCRR} {NIH} {HHS}/R01 {RR}016594-01A1/{RR}/{NCRR} {NIH} {HHS}/R01-{NS}39581/{NS}/{NINDS} {NIH} {HHS}/R01-{RR}13609/{RR}/{NCRR} {NIH} {HHS}/R01-{RR}16594/{RR}/{NCRR} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/U24 {RR}021382-037971/{RR}/{NCRR} {NIH} {HHS}/U54 {EB}005149-04/{EB}/{NIBIB} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov't2007/05/22 09:00Neuroimage. 2007 Jul 15;36(4):1331-44. Epub 2007 Apr 25.},
	file = {PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/FJQ68SUN/Walhovd et al. - 2007 - Volumetric cerebral characteristics of children ex.pdf:application/pdf;Walhovd-2007-Volumetric cerebral characteristi:/autofs/cluster/freesurfer/zotero/storage/X2SKNP8W/Walhovd-2007-Volumetric cerebral characteristi.pdf:application/pdf}
}

@article{ly_cortical_2012,
	title = {Cortical thinning in psychopathy},
	volume = {169},
	issn = {0002-953X},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3815681/},
	doi = {10.1176/appi.ajp.2012.11111627},
	abstract = {Objective
Psychopathy is a personality disorder associated with severely antisocial behavior and a host of cognitive and affective deficits. The neuropathological basis of the disorder has not been clearly established. Cortical thickness is a sensitive measure of brain structure that has been used to identify neurobiological abnormalities in a number of psychiatric disorders. The purpose of this study is to evaluate cortical thickness and corresponding functional connectivity in criminal psychopaths.

Method
Using T1 {MRI} data, we computed cortical thickness maps in a sample of adult male prison inmates selected based on psychopathy diagnosis (n=21 psychopathic inmates, n=31 non-psychopathic inmates). Using rest-{fMRI} data from a subset of these inmates (n=20 psychopathic inmates, n=20 non-psychopathic inmates), we then computed functional connectivity within networks exhibiting significant thinning among psychopaths.

Results
Relative to non-psychopaths, psychopaths exhibited significantly thinner cortex in a number of regions, including left insula and dorsal anterior cingulate cortex, bilateral precentral gyrus, bilateral anterior temporal cortex, and right inferior frontal gyrus. These neurostructural differences were not due to differences in age, {IQ}, or substance abuse. Psychopaths also exhibited a corresponding reduction in functional connectivity between left insula and left dorsal anterior cingulate cortex.

Conclusions
Psychopathy is associated with a distinct pattern of cortical thinning and reduced functional connectivity.},
	number = {7},
	urldate = {2014-08-23},
	journal = {The American journal of psychiatry},
	author = {Ly, Martina and Motzkin, Julian C. and Philippi, Carissa L. and Kirk, Gregory R. and Newman, Joseph P. and Kiehl, Kent A. and Koenigs, Michael},
	month = jul,
	year = {2012},
	pmid = {22581200},
	pmcid = {PMC3815681},
	file = {PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/M6CVUDTI/Ly et al. - 2012 - Cortical thinning in psychopathy.pdf:application/pdf}
}

@article{wonderlick_reliability_2009,
	title = {Reliability of {MRI}-derived cortical and subcortical morphometric measures: effects of pulse sequence, voxel geometry, and parallel imaging.},
	volume = {44},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2739882/},
	doi = {10.1016/j.neuroimage.2008.10.037},
	abstract = {Advances in magnetic resonance imaging ({MRI}) have contributed greatly to the study of neurodegenerative processes, psychiatric disorders, and normal human development, but the effect of such improvements on the reliability of downstream morphometric measures has not been extensively studied. We examined how},
	language = {eng},
	number = {4},
	journal = {{NeuroImage}},
	author = {Wonderlick, J. S. and Ziegler, D. A. and Hosseini-Varnamkhasti, P. and Locascio, J. J. and Bakkour, A. and van der Kouwe, A. and Triantafyllou, C. and Corkin, S. and Dickerson, B. C.},
	month = feb,
	year = {2009},
	pmid = {19038349},
	pmcid = {PMC2739882},
	keywords = {Adult, *Algorithms, *Artifacts, Cerebral Cortex/*anatomy \& histology, Female, fs\_Misc-methodology, Humans, Image Enhancement/methods, Image Interpretation, Computer-Assisted/*methods, Imaging, Three-Dimensional/*methods, Magnetic Resonance Imaging/*methods, Male, Reproducibility of Results, Sensitivity and Specificity},
	pages = {1324--1333}
}

@article{desikan_automated_2009,
	title = {Automated {MRI} measures identify individuals with mild cognitive impairment and Alzheimer's disease},
	volume = {132},
	issn = {0006-8950, 1460-2156},
	url = {http://brain.oxfordjournals.org/content/132/8/2048},
	doi = {10.1093/brain/awp123},
	abstract = {Mild cognitive impairment can represent a transitional state between normal ageing and Alzheimer's disease. Non-invasive diagnostic methods are needed to identify mild cognitive impairment individuals for early therapeutic interventions. Our objective was to determine whether automated magnetic resonance imaging-based measures could identify mild cognitive impairment individuals with a high degree of accuracy. Baseline volumetric T1-weighted magnetic resonance imaging scans of 313 individuals from two independent cohorts were examined using automated software tools to identify the volume and mean thickness of 34 neuroanatomic regions. The first cohort included 49 older controls and 48 individuals with mild cognitive impairment, while the second cohort included 94 older controls and 57 mild cognitive impairment individuals. Sixty-five patients with probable Alzheimer's disease were also included for comparison. For the discrimination of mild cognitive impairment, entorhinal cortex thickness, hippocampal volume and supramarginal gyrus thickness demonstrated an area under the curve of 0.91 (specificity 94\%, sensitivity 74\%, positive likelihood ratio 12.12, negative likelihood ratio 0.29) for the first cohort and an area under the curve of 0.95 (specificity 91\%, sensitivity 90\%, positive likelihood ratio 10.0, negative likelihood ratio 0.11) for the second cohort. For the discrimination of Alzheimer's disease, these three measures demonstrated an area under the curve of 1.0. The three magnetic resonance imaging measures demonstrated significant correlations with clinical and neuropsychological assessments as well as with cerebrospinal fluid levels of tau, hyperphosphorylated tau and abeta 42 proteins. These results demonstrate that automated magnetic resonance imaging measures can serve as an in vivo surrogate for disease severity, underlying neuropathology and as a non-invasive diagnostic method for mild cognitive impairment and Alzheimer's disease.},
	language = {en},
	number = {8},
	urldate = {2014-08-25},
	journal = {Brain},
	author = {Desikan, Rahul S. and Cabral, Howard J. and Hess, Christopher P. and Dillon, William P. and Glastonbury, Christine M. and Weiner, Michael W. and Schmansky, Nicholas J. and Greve, Douglas N. and Salat, David H. and Buckner, Randy L. and Fischl, Bruce},
	month = aug,
	year = {2009},
	pmid = {19460794},
	keywords = {Adolescent, Adult, Aged, Aged, 80 and over, Alzheimer Disease/*diagnosis/pathology/psychology, Alzheimer's disease, Biological Markers/cerebrospinal fluid, Brain Mapping/methods, Cerebral Cortex/pathology, Cognition Disorders/*diagnosis/etiology/pathology, diagnostic marker, Disease Progression, Early Diagnosis, Epidemiologic Methods, Female, Humans, Image Interpretation, Computer-Assisted/methods, Magnetic Resonance Imaging/methods, Male, Middle Aged, mild cognitive impairment, {MRI}, Neuropsychological Tests, Prognosis, Young Adult},
	pages = {2048--2057},
	annote = {Desikan, Rahul {SCabral}, Howard {JHess}, Christopher {PDillon}, William {PGlastonbury}, Christine {MWeiner}, Michael {WSchmansky}, Nicholas {JGreve}, Douglas {NSalat}, David {HBuckner}, Randy {LFischl}, {BruceengAG}021910/{AG}/{NIA} {NIH} {HHS}/P01 {AG}03991/{AG}/{NIA} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/P50 {AG}05681/{AG}/{NIA} {NIH} {HHS}/R01 {AG}021910-05/{AG}/{NIA} {NIH} {HHS}/R01 {AG}034556-01/{AG}/{NIA} {NIH} {HHS}/R01 {EB}001550/{EB}/{NIBIB} {NIH} {HHS}/R01 {RR} 16594-01A1/{RR}/{NCRR} {NIH} {HHS}/U01 {AG}024904/{AG}/{NIA} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/Howard Hughes Medical Institute/Multicenter {StudyResearch} Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov'{tResearch} Support, U.S. Gov't, Non-P.H.S.England2009/05/23 09:00Brain. 2009 Aug;132(Pt 8):2048-57. doi: 10.1093/brain/awp123. Epub 2009 May 21.},
	file = {Desikan-2009-Automated MRI measures identify i:/autofs/cluster/freesurfer/zotero/storage/MFIIS66R/Desikan-2009-Automated MRI measures identify i.pdf:application/pdf;Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/UTZEQ8P5/Desikan et al. - 2009 - Automated MRI measures identify individuals with m.pdf:application/pdf;Snapshot:/autofs/cluster/freesurfer/zotero/storage/RSU8ZBH8/2048.html:text/html}
}

@article{kikinis_gray_2010,
	title = {Gray matter volume reduction in rostral middle frontal gyrus in patients with chronic schizophrenia},
	volume = {123},
	issn = {1573-2509 (Electronic)},
	shorttitle = {Gray matter volume reduction in rostral middle frontal gyrus in patients with chronic schizophrenia},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/20822884},
	doi = {10.1016/j.schres.2010.07.027},
	abstract = {The dorsolateral prefrontal cortex ({DLPFC}) is a brain region that has figured prominently in studies of schizophrenia and working memory, yet the exact neuroanatomical localization of this brain region remains to be defined. {DLPFC} primarily involves the superior frontal gyrus and middle frontal gyrus ({MFG}). The latter, however is not a single neuroanatomical entity but instead is comprised of rostral (anterior, middle, and posterior) and caudal regions. In this study we used structural {MRI} to develop a method for parcellating {MFG} into its component parts. We focused on this region of {DLPFC} because it includes {BA}46, a region involved in working memory. We evaluated volume differences in {MFG} in 20 patients with chronic schizophrenia and 20 healthy controls. Mid-rostral {MFG} ({MR}-{MFG}) was delineated within the rostral {MFG} using anterior and posterior neuroanatomical landmarks derived from cytoarchitectonic definitions of {BA}46. Gray matter volumes of {MR}-{MFG} were then compared between groups, and a significant reduction in gray matter volume was observed (p{\textless}0.008), but not in other areas of {MFG} (i.e., anterior or posterior rostral {MFG}, or caudal regions of {MFG}). Our results demonstrate that volumetric alterations in {MFG} gray matter are localized exclusively to {MR}-{MFG}. 3D reconstructions of the cortical surface made it possible to follow {MFG} into its anterior part, where other approaches have failed. This method of parcellation offers a more precise way of measuring {MR}-{MFG} that will likely be important in further documentation of {DLPFC} anomalies in schizophrenia.},
	number = {2-3},
	journal = {Schizophr Res},
	author = {Kikinis, Z. and Fallon, J. H. and Niznikiewicz, M. and Nestor, P. and Davidson, C. and Bobrow, L. and Pelavin, P. E. and Fischl, B. and Yendiki, A. and McCarley, R. W. and Kikinis, R. and Kubicki, M. and Shenton, M. E.},
	month = nov,
	year = {2010},
	keywords = {Adult, Case-Control Studies, Chronic Disease, Diagnostic and Statistical Manual of Mental Disorders, Frontal Lobe/*pathology, Humans, Image Processing, Computer-Assisted/methods, Imaging, Three-Dimensional/methods, *Magnetic Resonance Imaging/methods, Male, Middle Aged, Prefrontal Cortex/pathology, Schizophrenia/*pathology},
	pages = {153--9},
	annote = {Kikinis, {ZFallon}, J {HNiznikiewicz}, {MNestor}, {PDavidson}, {CBobrow}, {LPelavin}, P {EFischl}, {BYendiki}, {AMcCarley}, R {WKikinis}, {RKubicki}, {MShenton}, M {EengK}05 {MH} 070047/{MH}/{NIMH} {NIH} {HHS}/K05 {MH}070047-06/{MH}/{NIMH} {NIH} {HHS}/P41 {RR} 019703/{RR}/{NCRR} {NIH} {HHS}/P41 {RR} 13218/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}013218-12/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}019703/{RR}/{NCRR} {NIH} {HHS}/P50 {MH} 080272/{MH}/{NIMH} {NIH} {HHS}/P50 {MH}080272-01/{MH}/{NIMH} {NIH} {HHS}/P50 {MH}080272-04/{MH}/{NIMH} {NIH} {HHS}/R01 {MH} 052807/{MH}/{NIMH} {NIH} {HHS}/R01 {MH} 40799/{MH}/{NIMH} {NIH} {HHS}/R01 {MH} 50747/{MH}/{NIMH} {NIH} {HHS}/R01 {MH}040799-13/{MH}/{NIMH} {NIH} {HHS}/R01 {MH}040799-23S1/{MH}/{NIMH} {NIH} {HHS}/R01 {MH}050740-15/{MH}/{NIMH} {NIH} {HHS}/R01 {MH}052807-10/{MH}/{NIMH} {NIH} {HHS}/R01 {MH}052807-15/{MH}/{NIMH} {NIH} {HHS}/U54 {EB}005149/{EB}/{NIBIB} {NIH} {HHS}/U54 {EB}005149-01/{EB}/{NIBIB} {NIH} {HHS}/U54 {EB}005149-03/{EB}/{NIBIB} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov'{tResearch} Support, U.S. Gov't, Non-P.H.S.Netherlands2010/09/09 06:00Schizophr Res. 2010 Nov;123(2-3):153-9. doi: 10.1016/j.schres.2010.07.027. Epub 2010 Sep 6.},
	file = {Kikinis-2010-Gray matter volume reduction in r:/autofs/cluster/freesurfer/zotero/storage/FHIDBN45/Kikinis-2010-Gray matter volume reduction in r.pdf:application/pdf;PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/U5IF5V7W/Kikinis et al. - 2010 - GRAY MATTER VOLUME REDUCTION IN ROSTRAL MIDDLE FRO.pdf:application/pdf}
}

@article{blankstein_complex_2009,
	title = {The complex minds of teenagers: neuroanatomy of personality differs between sexes},
	volume = {47},
	issn = {0028-3932},
	shorttitle = {The complex minds of teenagers},
	doi = {10.1016/j.neuropsychologia.2008.10.014},
	abstract = {Extraversion and neuroticism influence behaviour and mood. Extreme expressions of these personality traits may predispose individuals to developing chronic functional pains and mood disorders that predominantly affect women. We acquired anatomical {MRI} scans and personality scores from healthy male and female adolescents and measured gray matter volume ({GMV}) and cortical thickness to test the hypothesis that neuroticism and extraversion contribute to sex differences in fronto-limbic cortical development during a crucial period of social and biological maturation. In females, extraversion correlated negatively with medial frontal gyrus {GMV} and neuroticism correlated positively with subgenual anterior cingulate cortex {GMV} and cortical thickness. Interestingly, correlations between {GMV} and personality in males showed an opposite effect. Given the association of these cortical areas with social cognition and emotional processing, we suggest that a neuro-maturational divergence during adolescence accounts for the higher prevalence of specific chronic pains and mood disorders in females.},
	language = {eng},
	number = {2},
	journal = {Neuropsychologia},
	author = {Blankstein, Udi and Chen, Jerry Y. W. and Mincic, Adina M. and McGrath, Patricia A. and Davis, Karen D.},
	month = jan,
	year = {2009},
	pmid = {19010338},
	keywords = {Adolescent, Adolescent Behavior, Brain, Cerebral Cortex, Extraversion (Psychology), Female, Gyrus Cinguli, Humans, Image Processing, Computer-Assisted, Limbic System, Magnetic Resonance Imaging, Male, Neurotic Disorders, Personality, Prefrontal Cortex, Sex Characteristics},
	pages = {599--603}
}

@article{leritz_thickness_2011,
	title = {Thickness of the Human Cerebral Cortex is Associated with Metrics of Cerebrovascular Health in a Normative Sample of Community Dwelling Older Adults},
	volume = {54},
	issn = {1053-8119},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3026290/},
	doi = {10.1016/j.neuroimage.2010.10.050},
	abstract = {We examined how wide ranges in levels of risk factors for cerebrovascular disease are associated with thickness of the human cerebral cortex in 115 individuals ages 43–83 with no cerebrovascular or neurologic history. Cerebrovascular risk factors included blood pressure, cholesterol, body mass index, creatinine, and diabetes-related factors. Variables were submitted into a principal components analysis that confirmed four orthogonal factors (Blood Pressure, Cholesterol, Cholesterol/Metabolic and Glucose). T1-weighted {MRI} was used to create models of the cortex for calculation of regional cortical thickness. Increasing blood pressure factor scores were associated with numerous regions of reduced thickness. Increasing glucose scores were modestly associated with areas of regionally decreased thickness. Increasing cholesterol scores, in contrast, were associated with thicker cortex across the whole brain. All findings were primarily independent of age. These results provide evidence that normal and moderately abnormal levels of parameters used to assess cerebrovascular health may impact brain structure, even in the absence of cerebrovascular disease. Our data have important implications for the clinical management of vascular health, as well as for what is currently conceptualized as “normal aging” as they suggest that subclinical levels of risk may impact cortical gray matter before a disease process is evident.},
	number = {4},
	urldate = {2014-08-23},
	journal = {{NeuroImage}},
	author = {Leritz, Elizabeth C. and Salat, David H. and Williams, Victoria J. and Schnyer, David M. and Rudolph, James L. and Lipsitz, Lewis and Fischl, Bruce and McGlinchey, Regina E. and Milberg, William P.},
	month = feb,
	year = {2011},
	pmid = {21035552},
	pmcid = {PMC3026290},
	keywords = {Adult, Aged, Aged, 80 and over, Aging/blood/*pathology, Blood Glucose/*physiology, Blood Pressure, *Body Mass Index, Cerebral Cortex/*pathology, Cerebrovascular Disorders/pathology/physiopathology, Cholesterol/*blood, Creatinine/blood, Female, Humans, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Male, Middle Aged, Risk Factors},
	pages = {2659--2671},
	annote = {Leritz, Elizabeth {CSalat}, David {HWilliams}, Victoria {JSchnyer}, David {MRudolph}, James {LLipsitz}, {LewisFischl}, {BruceMcGlinchey}, Regina {EMilberg}, William {PengAG}02238/{AG}/{NIA} {NIH} {HHS}/{BIRN}002/{PHS} {HHS}/K01AG24898/{AG}/{NIA} {NIH} {HHS}/K23 {NS}062148-01/{NS}/{NINDS} {NIH} {HHS}/K23 {NS}062148-02S1/{NS}/{NINDS} {NIH} {HHS}/K23 {NS}062148-02S2/{NS}/{NINDS} {NIH} {HHS}/K23 {NS}062148-05/{NS}/{NINDS} {NIH} {HHS}/K23NS062148/{NS}/{NINDS} {NIH} {HHS}/K23NS06214802S1/{NS}/{NINDS} {NIH} {HHS}/P01AG004390/{AG}/{NIA} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/P60AG08812/{AG}/{NIA} {NIH} {HHS}/R01EB006758/{EB}/{NIBIB} {NIH} {HHS}/R01NR010827/{NR}/{NINR} {NIH} {HHS}/R01NS052585/{NS}/{NINDS} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/U54 {EB}005149/{EB}/{NIBIB} {NIH} {HHS}/U54 {EB}005149-07/{EB}/{NIBIB} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov'{tResearch} Support, U.S. Gov't, Non-P.H.S.2010/11/03 06:00Neuroimage. 2011 Feb 14;54(4):2659-71. doi: 10.1016/j.neuroimage.2010.10.050. Epub 2010 Oct 28.},
	file = {Leritz-2011-Thickness of the human cerebral co:/autofs/cluster/freesurfer/zotero/storage/RWX9V7NQ/Leritz-2011-Thickness of the human cerebral co.pdf:application/pdf;PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/ZCVHX7JA/Leritz et al. - 2011 - Thickness of the Human Cerebral Cortex is Associat.pdf:application/pdf}
}

@article{dasilva_colocalized_2008,
	title = {Colocalized Structural and Functional Changes in the Cortex of Patients with Trigeminal Neuropathic Pain},
	volume = {3},
	issn = {1932-6203},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2561059/},
	doi = {10.1371/journal.pone.0003396},
	abstract = {Background
Recent data suggests that in chronic pain there are changes in gray matter consistent with decreased brain volume, indicating that the disease process may produce morphological changes in the brains of those affected. However, no study has evaluated cortical thickness in relation to specific functional changes in evoked pain. In this study we sought to investigate structural (gray matter thickness) and functional (blood oxygenation dependent level – {BOLD}) changes in cortical regions of precisely matched patients with chronic trigeminal neuropathic pain ({TNP}) affecting the right maxillary (V2) division of the trigeminal nerve. The model has a number of advantages including the evaluation of specific changes that can be mapped to known somatotopic anatomy.

Methodology/Principal Findings
Cortical regions were chosen based on sensory (Somatosensory cortex ({SI} and {SII}), motor ({MI}) and posterior insula), or emotional ({DLPFC}, Frontal, Anterior Insula, Cingulate) processing of pain. Both structural and functional (to brush-induced allodynia) scans were obtained and averaged from two different imaging sessions separated by 2–6 months in all patients. Age and gender-matched healthy controls were also scanned twice for cortical thickness measurement. Changes in cortical thickness of {TNP} patients were frequently colocalized and correlated with functional allodynic activations, and included both cortical thickening and thinning in sensorimotor regions, and predominantly thinning in emotional regions.

Conclusions
Overall, such patterns of cortical thickness suggest a dynamic functionally-driven plasticity of the brain. These structural changes, which correlated with the pain duration, age-at-onset, pain intensity and cortical activity, may be specific targets for evaluating therapeutic interventions.},
	number = {10},
	urldate = {2014-08-23},
	journal = {{PLoS} {ONE}},
	author = {DaSilva, Alexandre F. and Becerra, Lino and Pendse, Gautam and Chizh, Boris and Tully, Shannon and Borsook, David},
	month = oct,
	year = {2008},
	pmid = {18923647},
	pmcid = {PMC2561059},
	file = {PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/Q4A5S5NB/DaSilva et al. - 2008 - Colocalized Structural and Functional Changes in t.pdf:application/pdf}
}

@article{feczko_mri-based_2009,
	title = {An {MRI}-based method for measuring volume, thickness and surface area of entorhinal, perirhinal, and posterior parahippocampal cortex.},
	volume = {30},
	url = {https://surfer.nmr.mgh.harvard.edu/pub/articles/dickerson2007_methods.pdf},
	doi = {10.1016/j.neurobiolaging.2007.07.023},
	abstract = {Several quantitative {MRI}-based protocols have been developed for measuring the volume of entorhinal ({ERC}), perirhinal ({PRC}), and posterior parahippocampal ({PPHC}) cortex. However, since the volume of a cortical region is a composite measure, relating directly to both thickness and surface area, it would be ideal  to be able to quantify all of these morphometric measures, particularly since disease-related processes, such as Alzheimer's disease ({AD}), may preferentially affect thickness. This study describes a novel protocol for measuring the thickness, surface area, and volume of these three medial temporal lobe ({MTL}) subregions. Participants included 29 younger normal subjects (ages 18-30), 47 older normal subjects (ages 66-90), and 29 patients with mild {AD} (ages 56-90). Cortical surface models were reconstructed from the gray/white and gray/cerebrospinal fluid boundaries, and a hybrid visualization approach was implemented to trace the {ERC}, {PRC}, and {PPHC} using both orthogonal {MRI} slice- and  cortical surface-based visualization of landmarks. Anatomic variants of the collateral sulcus ({CS}) were classified in all 105 participants, and the relationship between {CS} variants and corresponding morphometric measures was examined. One {CS} variant - deep, uninterrupted {CS} not connected with nearby sulci - was the most common configuration and was associated with thinner cortex within the {ERC} and {PRC} regions. This novel protocol enables the reliable measurement of  both the thickness and surface area of {ERC}, {PRC}, and {PPHC}.},
	language = {eng},
	number = {3},
	journal = {Neurobiology of aging},
	author = {Feczko, Eric and Augustinack, Jean C. and Fischl, Bruce and Dickerson, Bradford C.},
	month = mar,
	year = {2009},
	pmid = {17850926},
	pmcid = {PMC3665765},
	keywords = {Adolescent, Adult, Aged, Aged, 80 and over, Alzheimer Disease/diagnosis/pathology, Entorhinal Cortex/*anatomy \& histology/growth \& development/pathology, Female, fs\_Misc-methodology, Hippocampus/*anatomy \& histology/growth \& development/pathology, Humans, Magnetic Resonance Imaging/*methods/standards, Male, Middle Aged, Organ Size, Parahippocampal Gyrus/*anatomy \& histology/growth \& development/pathology, Young Adult},
	pages = {420--431}
}

@article{joyner_common_2009,
	title = {A common {MECP}2 haplotype associates with reduced cortical surface area in humans in two independent populations},
	volume = {106},
	issn = {0027-8424},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2741277/},
	doi = {10.1073/pnas.0901866106},
	abstract = {The gene {MECP}2 is a well-known determinant of brain structure. Mutations in the {MECP}2 protein cause microencephalopathy and are associated with several neurodevelopmental disorders that affect both brain morphology and cognition. Although mutations in {MECP}2 result in severe neurological phenotypes, the effect of common variation in this genetic region is unknown. We find that common sequence variations in a region in and around {MECP}2 show association with structural brain size measures in 2 independent cohorts, a discovery sample from the Thematic Organized Psychosis research group, and a replication sample from the Alzheimer's Disease Neuroimaging Initiative. The most statistically significant replicated association (P {\textless} 0.025 in both cohorts) involved the minor allele of {SNP} rs2239464 with reduced cortical surface area, and the finding was specific to male gender in both populations. Variations in the {MECP}2 region were associated with cortical surface area but not cortical thickness. Secondary analysis showed that this allele was also associated with reduced surface area in specific cortical regions (cuneus, fusiform gyrus, pars triangularis) in both populations.},
	number = {36},
	urldate = {2014-08-24},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	author = {Joyner, Alexander H. and J., Cooper Roddey and Bloss, Cinnamon S. and Bakken, Trygve E. and Rimol, Lars M. and Melle, Ingrid and Agartz, Ingrid and Djurovic, Srdjan and Topol, Eric J. and Schork, Nicholas J. and Andreassen, Ole A. and Dale, Anders M.},
	month = sep,
	year = {2009},
	pmid = {19717458},
	pmcid = {PMC2741277},
	pages = {15483--15488},
	file = {PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/JHS3A5W8/Joyner et al. - 2009 - A common MECP2 haplotype associates with reduced c.pdf:application/pdf}
}

@article{barnes_head_2010,
	title = {Head size, age and gender adjustment in {MRI} studies: a necessary nuisance?},
	volume = {53},
	issn = {1095-9572},
	shorttitle = {Head size, age and gender adjustment in {MRI} studies},
	doi = {10.1016/j.neuroimage.2010.06.025},
	abstract = {Imaging studies of cerebral volumes often adjust for factors such as age that may confound between-subject comparisons. However the use of nuisance covariates in imaging studies is inconsistent, which can make interpreting results across studies difficult. Using magnetic resonance images of 78 healthy controls we assessed the effects of age, gender, head size and scanner upgrade on region of interest ({ROI}) volumetry, cortical thickness and voxel-based morphometric ({VBM}) measures. We found numerous significant associations between these variables and volumetric measures: cerebral volumes and cortical thicknesses decreased with increasing age, men had larger volumes and smaller thicknesses than women, and increasing head size was associated with larger volumes. The relationships between most {ROIs} and head size volumes were non-linear. With age, gender, head size and upgrade in one model we found that volumes and thicknesses decreased with increasing age, women had larger volumes than men ({VBM}, whole-brain and white matter volumes), increasing head size was associated with larger volumes but not cortical thickness, and scanner upgrade had an effect on thickness and some volume measures. The effects of gender on cortical thickness when adjusting for head size, age and upgrade showed some non-significant effect (women{\textgreater}men), whereas the independent effect of head size showed little pattern. We conclude that age and head size should be considered in {ROI} volume studies, age, gender and upgrade should be considered for cortical thickness studies and all variables require consideration for {VBM} analyses. Division of all volumes by head size is unlikely to be adequate owing to their non-proportional relationship.},
	language = {eng},
	number = {4},
	journal = {{NeuroImage}},
	author = {Barnes, Josephine and Ridgway, Gerard R. and Bartlett, Jonathan and Henley, Susie M. D. and Lehmann, Manja and Hobbs, Nicola and Clarkson, Matthew J. and MacManus, David G. and Ourselin, Sebastien and Fox, Nick C.},
	month = dec,
	year = {2010},
	pmid = {20600995},
	keywords = {Adult, Aged, Aged, 80 and over, Age Factors, Brain, Female, fs\_Validation-Evaluations, Head, Humans, Image Interpretation, Computer-Assisted, Magnetic Resonance Imaging, Male, Middle Aged, Organ Size, Sex Factors, Young Adult},
	pages = {1244--1255}
}

@article{bernal-rusiel_spatiotemporal_2013,
	title = {Spatiotemporal linear mixed effects modeling for the mass-univariate analysis of longitudinal neuroimage data},
	volume = {81},
	issn = {1095-9572 (Electronic) 1053-8119 (Linking)},
	shorttitle = {Spatiotemporal linear mixed effects modeling for the mass-univariate analysis of longitudinal neuroimage data},
	url = {http://www.sciencedirect.com/science/article/pii/S1053811913005430},
	doi = {10.1016/j.neuroimage.2013.05.049},
	abstract = {We present an extension of the Linear Mixed Effects ({LME}) modeling approach to be applied to the mass-univariate analysis of longitudinal neuroimaging ({LNI}) data. The proposed method, called spatiotemporal {LME} or {ST}-{LME}, builds on the flexible {LME} framework and exploits the spatial structure in image data. We instantiated {ST}-{LME} for the analysis of cortical surface measurements (e.g. thickness) computed by {FreeSurfer}, a widely-used brain Magnetic Resonance Image ({MRI}) analysis software package. We validate the proposed {ST}-{LME} method and provide a quantitative and objective empirical comparison with two popular alternative methods, using two brain {MRI} datasets obtained from the Alzheimer's disease neuroimaging initiative ({ADNI}) and Open Access Series of Imaging Studies ({OASIS}). Our experiments revealed that {ST}-{LME} offers a dramatic gain in statistical power and repeatability of findings, while providing good control of the false positive rate.},
	language = {en},
	urldate = {2014-08-21},
	journal = {Neuroimage},
	author = {Bernal-Rusiel, J. L. and Reuter, M. and Greve, D. N. and Fischl, B. and Sabuncu, M. R. and Alzheimer's Disease Neuroimaging, Initiative},
	month = nov,
	year = {2013},
	keywords = {Brain/*pathology/physiology, fs\_Longitudinal-processing, Humans, Image Interpretation, Computer-Assisted/*methods, Linear Models, longitudinal processing, Magnetic Resonance Imaging, *Models, Neurological, *Software},
	pages = {358--70},
	annote = {Bernal-Rusiel, Jorge {LReuter}, {MartinGreve}, Douglas {NFischl}, {BruceSabuncu}, Mert Reng1K25EB013649-01/{EB}/{NIBIB} {NIH} {HHS}/1R01NS070963/{NS}/{NINDS} {NIH} {HHS}/1R21NS072652-01/{NS}/{NINDS} {NIH} {HHS}/1S10RR019307/{RR}/{NCRR} {NIH} {HHS}/1S10RR023043/{RR}/{NCRR} {NIH} {HHS}/1S10RR023401/{RR}/{NCRR} {NIH} {HHS}/2R01NS042861-06A1/{NS}/{NINDS} {NIH} {HHS}/5P01NS058793-03/{NS}/{NINDS} {NIH} {HHS}/5U01-{MH}093765/{MH}/{NIMH} {NIH} {HHS}/{AG}022381/{AG}/{NIA} {NIH} {HHS}/K25 {EB}013649/{EB}/{NIBIB} {NIH} {HHS}/P41 {EB}015896/{EB}/{NIBIB} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 {NS}052585-01/{NS}/{NINDS} {NIH} {HHS}/R01-{HD}071664/{HD}/{NICHD} {NIH} {HHS}/R01EB006758/{EB}/{NIBIB} {NIH} {HHS}/{RC}1 {AT}005728-01/{AT}/{NCCAM} {NIH} {HHS}/U01 {AG}024904/{AG}/{NIA} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov'{tResearch} Support, U.S. Gov't, Non-P.H.S.2013/05/25 06:00Neuroimage. 2013 Nov 1;81:358-70. doi: 10.1016/j.neuroimage.2013.05.049. Epub 2013 May 20.}
}

@article{becker_amyloid-?_2011,
	title = {Amyloid-? Associated Cortical Thinning in Clinically Normal Elderly},
	volume = {69},
	issn = {0364-5134},
	shorttitle = {Amyloid-?},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3117980/},
	doi = {10.1002/ana.22333},
	abstract = {Objective
Both amyloid-β (Aβ) deposition and brain atrophy are associated with Alzheimer's disease ({AD}) and the disease process likely begins many years before symptoms appear. We sought to determine whether clinically normal ({CN}) older individuals with Aβ deposition revealed by positron emission tomography ({PET}) imaging using Pittsburgh Compound B ({PiB}) also have evidence of both cortical thickness and hippocampal volume reductions in a pattern similar to that seen in {AD}.

Methods
A total of 119 older individuals (87 {CN} subjects and 32 patients with mild {AD}) underwent {PiB} {PET} and high-resolution structural magnetic resonance imaging ({MRI}). Regression models were used to relate {PiB} retention to cortical thickness and hippocampal volume.

Results
We found that {PiB} retention in {CN} subjects was (1) age-related and (2) associated with cortical thickness reductions, particularly in parietal and posterior cingulate regions extending into the precuneus, in a pattern similar to that observed in mild {AD}. Hippocampal volume reduction was variably related to Aβ deposition.

Interpretation
We conclude that Aβ deposition is associated with a pattern of cortical thickness reduction consistent with {AD} prior to the development of cognitive impairment. {ANN} {NEUROL} 2010;},
	number = {6},
	urldate = {2014-08-23},
	journal = {Annals of Neurology},
	author = {Becker, J Alex and Hedden, Trey and Carmasin, Jeremy and Maye, Jacqueline and Rentz, Dorene M and Putcha, Deepti and Fischl, Bruce and Greve, Douglas N and Marshall, Gad A and Salloway, Stephen and Marks, Donald and Buckner, Randy L and Sperling, Reisa A and Johnson, Keith A},
	month = jun,
	year = {2011},
	pmid = {21437929},
	pmcid = {PMC3117980},
	keywords = {Aged, Aged, 80 and over, Age Factors, Aging/*pathology, Alzheimer Disease/pathology/radionuclide imaging, Amyloid beta-Peptides/*metabolism, Analysis of Variance, Aniline Compounds/diagnostic use, Brain Mapping, Cerebral Cortex/*metabolism/radionuclide imaging, Female, Hippocampus/metabolism/radionuclide imaging, Humans, Magnetic Resonance Imaging, Male, Middle Aged, Positron-Emission Tomography, Statistics as Topic, Thiazoles/diagnostic use},
	pages = {1032--1042},
	annote = {Becker, J {AlexHedden}, {TreyCarmasin}, {JeremyMaye}, {JacquelineRentz}, Dorene {MPutcha}, {DeeptiFischl}, {BruceGreve}, Douglas {NMarshall}, Gad {ASalloway}, {StephenMarks}, {DonaldBuckner}, Randy {LSperling}, Reisa {AJohnson}, Keith Aeng1K23AG033634/{AG}/{NIA} {NIH} {HHS}/K23 {AG}033634-03/{AG}/{NIA} {NIH} {HHS}/K24 {AG}035007/{AG}/{NIA} {NIH} {HHS}/K24 {AG}035007-02/{AG}/{NIA} {NIH} {HHS}/P01 {AG}036694-01/{AG}/{NIA} {NIH} {HHS}/P01-{AG}036694/{AG}/{NIA} {NIH} {HHS}/P50-{AG}00513421/{AG}/{NIA} {NIH} {HHS}/R01 {AG}027435-02S1/{AG}/{NIA} {NIH} {HHS}/R01 {AG}034556/{AG}/{NIA} {NIH} {HHS}/R01 {AG}034556-02/{AG}/{NIA} {NIH} {HHS}/R01 {AG}034556-03/{AG}/{NIA} {NIH} {HHS}/R01 {AG}037497-01/{AG}/{NIA} {NIH} {HHS}/R01 {AG}037497-02/{AG}/{NIA} {NIH} {HHS}/R01-{AG}021910/{AG}/{NIA} {NIH} {HHS}/R01-{AG}027435-S1/{AG}/{NIA} {NIH} {HHS}/Howard Hughes Medical Institute/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov't2011/03/26 06:00Ann Neurol. 2011 Jun;69(6):1032-42. doi: 10.1002/ana.22333. Epub 2011 Mar 17.},
	file = {Becker-2011-Amyloid-beta associated cortical t:/autofs/cluster/freesurfer/zotero/storage/BZ9MGJXZ/Becker-2011-Amyloid-beta associated cortical t.pdf:application/pdf;PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/D2MHPDGN/Becker et al. - 2011 - Amyloid- Associated Cortical Thinning in Clinical.pdf:application/pdf;PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/IR43TVQD/Becker et al. - 2011 - Amyloid- Associated Cortical Thinning in Clinical.pdf:application/pdf}
}

@article{rimol_cortical_2012,
	title = {Cortical volume, surface area, and thickness in schizophrenia and bipolar disorder},
	volume = {71},
	issn = {1873-2402},
	doi = {10.1016/j.biopsych.2011.11.026},
	abstract = {{BACKGROUND}: Magnetic resonance imaging studies have shown that structural brain abnormalities are present in both schizophrenia and bipolar disorder. Most previous studies have focused on brain tissue volumes, but advances in neuroimaging data processing have made it possible to separate cortical area and cortical thickness. The purpose of the present study was to provide a more complete picture of cortical morphometric differences in schizophrenia and bipolar disorder, decomposing cortical volume into its constituent parts, cortical thickness and cortical area.
{METHODS}: We analyzed magnetic resonance imaging images from a sample of 173 patients with schizophrenia, 139 patients with bipolar disorder, and 207 healthy control subjects. Maps of cortical volume, area, and thickness across the continuous cortical surface were generated within groups and compared between the groups.
{RESULTS}: There were widespread reductions in cortical volume in schizophrenia relative to healthy control subjects and patients with bipolar disorder type I. These reductions were mainly driven by cortical thinning, but there were also cortical area reductions in more circumscribed regions, which contributed to the observed volume reductions.
{CONCLUSIONS}: The current surface-based methodology allows for a distinction between cortical thinning and reduction in cortical area and reveals that cortical thinning is the most important factor in volume reduction in schizophrenia. Cortical area reduction was not observed in bipolar disorder type I and may be unique to schizophrenia.},
	language = {eng},
	number = {6},
	journal = {Biological Psychiatry},
	author = {Rimol, Lars M. and Nesvåg, Ragnar and Hagler, Don J. and Bergmann, Orjan and Fennema-Notestine, Christine and Hartberg, Cecilie B. and Haukvik, Unn K. and Lange, Elisabeth and Pung, Chris J. and Server, Andres and Melle, Ingrid and Andreassen, Ole A. and Agartz, Ingrid and Dale, Anders M.},
	month = mar,
	year = {2012},
	pmid = {22281121},
	keywords = {Adolescent, Adult, Aged, Bipolar Disorder, Brain Mapping, Cerebral Cortex, Female, Humans, Image Processing, Computer-Assisted, Longitudinal Studies, Magnetic Resonance Imaging, Male, Middle Aged, Organ Size, Schizophrenia, Young Adult},
	pages = {552--560}
}

@article{ecker_describing_2010,
	title = {Describing the Brain in Autism in Five Dimensions—Magnetic Resonance Imaging-Assisted Diagnosis of Autism Spectrum Disorder Using a Multiparameter Classification Approach},
	volume = {30},
	issn = {0270-6474, 1529-2401},
	url = {http://www.jneurosci.org/content/30/32/10612},
	doi = {10.1523/JNEUROSCI.5413-09.2010},
	abstract = {Autism spectrum disorder ({ASD}) is a neurodevelopmental condition with multiple causes, comorbid conditions, and a wide range in the type and severity of symptoms expressed by different individuals. This makes the neuroanatomy of autism inherently difficult to describe. Here, we demonstrate how a multiparameter classification approach can be used to characterize the complex and subtle structural pattern of gray matter anatomy implicated in adults with {ASD}, and to reveal spatially distributed patterns of discriminating regions for a variety of parameters describing brain anatomy. A set of five morphological parameters including volumetric and geometric features at each spatial location on the cortical surface was used to discriminate between people with {ASD} and controls using a support vector machine ({SVM}) analytic approach, and to find a spatially distributed pattern of regions with maximal classification weights. On the basis of these patterns, {SVM} was able to identify individuals with {ASD} at a sensitivity and specificity of up to 90\% and 80\%, respectively. However, the ability of individual cortical features to discriminate between groups was highly variable, and the discriminating patterns of regions varied across parameters. The classification was specific to {ASD} rather than neurodevelopmental conditions in general (e.g., attention deficit hyperactivity disorder). Our results confirm the hypothesis that the neuroanatomy of autism is truly multidimensional, and affects multiple and most likely independent cortical features. The spatial patterns detected using {SVM} may help further exploration of the specific genetic and neuropathological underpinnings of {ASD}, and provide new insights into the most likely multifactorial etiology of the condition.},
	language = {en},
	number = {32},
	urldate = {2014-08-25},
	journal = {The Journal of Neuroscience},
	author = {Ecker, Christine and Marquand, Andre and Mourão-Miranda, Janaina and Johnston, Patrick and Daly, Eileen M. and Brammer, Michael J. and Maltezos, Stefanos and Murphy, Clodagh M. and Robertson, Dene and Williams, Steven C. and Murphy, Declan G. M.},
	month = aug,
	year = {2010},
	pmid = {20702694},
	pages = {10612--10623},
	file = {Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/BM5KDJ43/Ecker et al. - 2010 - Describing the Brain in Autism in Five Dimensions—.pdf:application/pdf;Snapshot:/autofs/cluster/freesurfer/zotero/storage/9HIW3ENZ/10612.html:text/html}
}

@article{wozniak_tractography_2014,
	title = {Tractography reveals diffuse white matter abnormalities in Myotonic Dystrophy Type 1},
	volume = {341},
	issn = {1878-5883},
	doi = {10.1016/j.jns.2014.04.005},
	abstract = {Cerebral involvement in Myotonic Dystrophy Type 1 ({DM}1) is well-established but not well characterized. This study applied new Diffusion Tensor Imaging ({DTI}) tractography to characterize white matter disturbance in adults with {DM}1. Forty-five participants with {DM}1 and 44 control participants had {MRIs} on a Siemens 3T {TIM} Trio scanner. Data were processed with {TRActs} Constrained by {UnderLying} Anatomy ({TRACULA}) and 7 tracts were evaluated. Bilateral disturbances in white matter integrity were seen in all tracts in participants with {DM}1 compared to controls. There were no right-left hemisphere differences. The resulting {DTI} metrics were correlated with cognitive functioning, particularly working memory and processing speed. Motor speed was not significantly correlated with white matter microstructural integrity and, thus, was not the core explanation for the working memory and processing speed findings. White matter integrity was correlated with important clinical variables including the muscular impairment rating scale ({MIRS}). {CTG} repeat length was moderately associated with white matter status in corticospinal tract and cingulum. Sleepiness (Epworth Sleepiness Scale) was moderately associated with white matter status in the superior longitudinal fasciculus and cingulum. Overall, the results add to an emerging literature showing widespread white matter disturbances in both early-onset and adult-onset {DM}1. Results suggest that further investigation of white matter pathology is warranted in {DM}1 and that non-invasive measures such as {DTI} have a potentially important clinical value in characterizing the status of individuals with {DM}1.},
	language = {eng},
	number = {1-2},
	journal = {Journal of the Neurological Sciences},
	author = {Wozniak, Jeffrey R. and Mueller, Bryon A. and Lim, Kelvin O. and Hemmy, Laura S. and Day, John W.},
	month = jun,
	year = {2014},
	pmid = {24768314},
	pmcid = {PMC4042407},
	pages = {73--78}
}

@article{schaer_surface-based_2008,
	title = {A surface-based approach to quantify local cortical gyrification.},
	volume = {27},
	url = {http://ltswww.epfl.ch/~schaer/Schaer_TMI.pdf},
	doi = {10.1109/TMI.2007.903576},
	abstract = {The high complexity of cortical convolutions in humans is very challenging both for engineers to measure and compare it, and for biologists and physicians to understand it. In this paper, we propose a surface-based method for the quantification of cortical gyrification. Our method uses accurate 3-D cortical reconstruction and computes local measurements of gyrification at thousands of points over the whole cortical surface. The potential of our method to identify and localize precisely gyral abnormalities is illustrated by a clinical study on  a group of children affected by 22q11 Deletion Syndrome, compared to control individuals.},
	language = {eng},
	number = {2},
	journal = {{IEEE} transactions on medical imaging},
	author = {Schaer, Marie and Cuadra, Meritxell Bach and Tamarit, Lucas and Lazeyras, Francois and Eliez, Stephan and Thiran, Jean-Philippe},
	month = feb,
	year = {2008},
	pmid = {18334438},
	keywords = {Algorithms, *Algorithms, *Artificial Intelligence, Artificial Intelligence, Cerebral Cortex, Cerebral Cortex/*anatomy \& histology, Child, Child, Computer Simulation, Computer Simulation, Female, Female, fs\_LGI, Humans, Humans, Image Enhancement, Image Enhancement/methods, Image Interpretation, Computer-Assisted, Image Interpretation, Computer-Assisted/*methods, Imaging, Three-Dimensional, Imaging, Three-Dimensional/*methods, Magnetic Resonance Imaging, Magnetic Resonance Imaging/*methods, Male, Male, Models, Neurological, Models, Neurological, Pattern Recognition, Automated, Pattern Recognition, Automated/*methods, Reproducibility of Results, Reproducibility of Results, Sensitivity and Specificity, Sensitivity and Specificity},
	pages = {161--170}
}

@article{oliveira_use_2010,
	title = {Use of {SVM} methods with surface-based cortical and volumetric subcortical measurements to detect Alzheimer's disease},
	volume = {19},
	issn = {1875-8908},
	url = {https://surfer.nmr.mgh.harvard.edu/pub/articles/Oliveira_JAD2010.pdf},
	doi = {10.3233/JAD-2010-1322},
	abstract = {Here, we examine morphological changes in cortical thickness of patients with Alzheimer's disease ({AD}) using image analysis algorithms for brain structure segmentation and study automatic classification of {AD} patients using cortical and volumetric data. Cortical thickness of {AD} patients (n=14) was measured using {MRI} cortical surface-based analysis and compared with healthy subjects (n=20). Data was analyzed using an automated algorithm for tissue segmentation and classification. A Support Vector Machine ({SVM}) was applied over the volumetric measurements of subcortical and cortical structures to separate {AD} patients from controls. The group analysis showed cortical thickness reduction in the superior temporal lobe, parahippocampal gyrus, and enthorhinal cortex in both hemispheres. We also found cortical thinning in the isthmus of cingulate gyrus and middle temporal gyrus at the right hemisphere, as well as a reduction of the cortical mantle in areas previously shown to be associated with {AD}. We also confirmed that automatic classification algorithms ({SVM}) could be helpful to distinguish {AD} patients from healthy controls. Moreover, the same areas implicated in the pathogenesis of {AD} were the main parameters driving the classification algorithm. While the patient sample used in this study was relatively small, we expect that using a database of regional volumes derived from {MRI} scans of a large number of subjects will increase the {SVM} power of {AD} patient identification.},
	language = {eng},
	number = {4},
	journal = {Journal of Alzheimer's disease: {JAD}},
	author = {Oliveira, Pedro Paulo de Magalhães and Nitrini, Ricardo and Busatto, Geraldo and Buchpiguel, Carlos and Sato, João Ricardo and Amaro, Edson},
	year = {2010},
	pmid = {20061613},
	keywords = {Aged, Aged, 80 and over, Alzheimer Disease, Automatic Data Processing, Cerebral Cortex, Cognition Disorders, Diagnosis, Differential, Humans, Magnetic Resonance Imaging, Neuropsychological Tests},
	pages = {1263--1272}
}

@article{mulder_hippocampal_2014,
	title = {Hippocampal volume change measurement: quantitative assessment of the reproducibility of expert manual outlining and the automated methods {FreeSurfer} and {FIRST}},
	volume = {92},
	issn = {1095-9572 (Electronic) 1053-8119 (Linking)},
	shorttitle = {Hippocampal volume change measurement},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/24521851},
	doi = {10.1016/j.neuroimage.2014.01.058},
	abstract = {{BACKGROUND}: To measure hippocampal volume change in Alzheimer's disease ({AD}) or mild cognitive impairment ({MCI}), expert manual delineation is often used because of its supposed accuracy. It has been suggested that expert outlining yields poorer reproducibility as compared to automated methods, but this has not been investigated. {AIM}: To determine the reproducibilities of expert manual outlining and two common automated methods for measuring hippocampal atrophy rates in healthy aging, {MCI} and {AD}. {METHODS}: From the Alzheimer's Disease Neuroimaging Initiative ({ADNI}), 80 subjects were selected: 20 patients with {AD}, 40 patients with mild cognitive impairment ({MCI}) and 20 healthy controls ({HCs}). Left and right hippocampal volume change between baseline and month-12 visit was assessed by using expert manual delineation, and by the automated software packages {FreeSurfer} (longitudinal processing stream) and {FIRST}. To assess reproducibility of the measured hippocampal volume change, both back-to-back ({BTB}) {MPRAGE} scans available for each visit were analyzed. Hippocampal volume change was expressed in {muL}, and as a percentage of baseline volume. Reproducibility of the 1-year hippocampal volume change was estimated from the {BTB} measurements by using linear mixed model to calculate the limits of agreement ({LoA}) of each method, reflecting its measurement uncertainty. Using the delta method, approximate p-values were calculated for the pairwise comparisons between methods. Statistical analyses were performed both with inclusion and exclusion of visibly incorrect segmentations. {RESULTS}: Visibly incorrect automated segmentation in either one or both scans of a longitudinal scan pair occurred in 7.5\% of the hippocampi for {FreeSurfer} and in 6.9\% of the hippocampi for {FIRST}. After excluding these failed cases, reproducibility analysis for 1-year percentage volume change yielded {LoA} of +/-7.2\% for {FreeSurfer}, +/-9.7\% for expert manual delineation, and +/-10.0\% for {FIRST}. Methods ranked the same for reproducibility of 1-year {muL} volume change, with {LoA} of +/-218 {muL} for {FreeSurfer}, +/-319 {muL} for expert manual delineation, and +/-333 {muL} for {FIRST}. Approximate p-values indicated that reproducibility was better for {FreeSurfer} than for manual or {FIRST}, and that manual and {FIRST} did not differ. Inclusion of failed automated segmentations led to worsening of reproducibility of both automated methods for 1-year raw and percentage volume change. {CONCLUSION}: Quantitative reproducibility values of 1-year microliter and percentage hippocampal volume change were roughly similar between expert manual outlining, {FIRST} and {FreeSurfer}, but {FreeSurfer} reproducibility was statistically significantly superior to both manual outlining and {FIRST} after exclusion of failed segmentations.},
	language = {en},
	urldate = {2014-08-21},
	journal = {Neuroimage},
	author = {Mulder, E. R. and de Jong, R. A. and Knol, D. L. and van Schijndel, R. A. and Cover, K. S. and Visser, P. J. and Barkhof, F. and Vrenken, H. and Alzheimer's Disease Neuroimaging, Initiative},
	month = may,
	year = {2014},
	keywords = {fs\_Validation-Evaluations},
	pages = {169--81},
	annote = {Mulder, Emma Rde Jong, Remko {AKnol}, Dirk Lvan Schijndel, Ronald {ACover}, Keith {SVisser}, Pieter {JBarkhof}, {FrederikVrenken}, {HugoengK}01 {AG}030514/{AG}/{NIA} {NIH} {HHS}/P30 {AG}010129/{AG}/{NIA} {NIH} {HHS}/U01 {AG}024904/{AG}/{NIA} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov't2014/02/14 06:00Neuroimage. 2014 May 15;92:169-81. doi: 10.1016/j.neuroimage.2014.01.058. Epub 2014 Feb 9.}
}

@article{fischl_automated_2001,
	title = {Automated manifold surgery: constructing geometrically accurate and topologically correct models of the human cerebral cortex},
	volume = {20},
	issn = {0278-0062 (Print) 0278-0062 (Linking)},
	shorttitle = {Automated manifold surgery: constructing geometrically accurate and topologically correct models of the human cerebral cortex},
	url = {https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl01-topology-fixing.pdf},
	doi = {10.1109/42.906426},
	abstract = {Highly accurate surface models of the cerebral cortex are becoming increasingly important as tools in the investigation of the functional organization of the human brain. The construction of such models is difficult using current neuroimaging technology due to the high degree of cortical folding. Even single voxel misclassifications can result in erroneous connections being created between adjacent banks of a sulcus, resulting in a topologically inaccurate model. These topological defects cause the cortical model to no longer be homeomorphic to a sheet, preventing the accurate inflation, flattening, or spherical morphing of the reconstructed cortex. Surface deformation techniques can guarantee the topological correctness of a model, but are time-consuming and may result in geometrically inaccurate models. In order to address this need we have developed a technique for taking a model of the cortex, detecting and fixing the topological defects while leaving that majority of the model intact, resulting in a surface that is both geometrically accurate and topologically correct.},
	number = {1},
	journal = {{IEEE} Trans Med Imaging},
	author = {Fischl, B. and Liu, A. and Dale, A. M.},
	month = jan,
	year = {2001},
	keywords = {Cerebral Cortex/*anatomy \& histology, fs\_Surface-reconstruction, Humans, *Image Processing, Computer-Assisted, *Imaging, Three-Dimensional, Magnetic Resonance Imaging/*methods},
	pages = {70--80},
	annote = {Fischl, {BLiu}, {ADale}, A {MengP}41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01-{NS}39581/{NS}/{NINDS} {NIH} {HHS}/R01-{RR}13609/{RR}/{NCRR} {NIH} {HHS}/Research Support, U.S. Gov't, P.H.S.2001/04/11 10:00IEEE Trans Med Imaging. 2001 Jan;20(1):70-80.}
}

@article{fischl_cortical_2008,
	title = {Cortical folding patterns and predicting cytoarchitecture},
	volume = {18},
	issn = {1460-2199 (Electronic) 1047-3211 (Linking)},
	shorttitle = {Cortical folding patterns and predicting cytoarchitecture},
	url = {https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl_cerebralcortex2008.pdf},
	doi = {10.1093/cercor/bhm225},
	abstract = {The human cerebral cortex is made up of a mosaic of structural areas, frequently referred to as Brodmann areas ({BAs}). Despite the widespread use of cortical folding patterns to perform ad hoc estimations of the locations of the {BAs}, little is understood regarding 1) how variable the position of a given {BA} is with respect to the folds, 2) whether the location of some {BAs} is more variable than others, and 3) whether the variability is related to the level of a {BA} in a putative cortical hierarchy. We use whole-brain histology of 10 postmortem human brains and surface-based analysis to test how well the folds predict the locations of the {BAs}. We show that higher order cortical areas exhibit more variability than primary and secondary areas and that the folds are much better predictors of the {BAs} than had been previously thought. These results further highlight the significance of cortical folding patterns and suggest a common mechanism for the development of the folds and the cytoarchitectonic fields.},
	number = {8},
	journal = {Cereb Cortex},
	author = {Fischl, B. and Rajendran, N. and Busa, E. and Augustinack, J. and Hinds, O. and Yeo, B. T. and Mohlberg, H. and Amunts, K. and Zilles, K.},
	month = aug,
	year = {2008},
	keywords = {Brain Mapping/*methods, Cerebral Cortex/*cytology/*physiology, fs\_Cortical-parcellation, Humans, Predictive Value of Tests},
	pages = {1973--80},
	annote = {Fischl, {BruceRajendran}, {NiranjiniBusa}, {EvelinaAugustinack}, {JeanHinds}, {OliverYeo}, B T {ThomasMohlberg}, {HartmutAmunts}, {KatrinZilles}, {KarlengP}41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 {EB}001550/{EB}/{NIBIB} {NIH} {HHS}/R01 {NS}052585-01/{NS}/{NINDS} {NIH} {HHS}/R01 {RR}16594-01A1/{RR}/{NCRR} {NIH} {HHS}/R01EB006758/{EB}/{NIBIB} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/U54 {EB}005149/{EB}/{NIBIB} {NIH} {HHS}/Comparative {StudyResearch} Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov'{tNew} York, N.Y. : 19912007/12/15 09:00Cereb Cortex. 2008 Aug;18(8):1973-80. Epub 2007 Dec 12.},
	file = {Fischl-2008-Cortical folding patterns and pred:/autofs/cluster/freesurfer/zotero/storage/IV5F9SXP/Fischl-2008-Cortical folding patterns and pred.pdf:application/pdf}
}

@article{winkler_measuring_2012,
	title = {Measuring and comparing brain cortical surface area and other areal quantities},
	volume = {61},
	issn = {1095-9572 (Electronic) 1053-8119 (Linking)},
	shorttitle = {Measuring and comparing brain cortical surface area and other areal quantities},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/22446492},
	doi = {10.1016/j.neuroimage.2012.03.026},
	abstract = {Structural analysis of {MRI} data on the cortical surface usually focuses on cortical thickness. Cortical surface area, when considered, has been measured only over gross regions or approached indirectly via comparisons with a standard brain. Here we demonstrate that direct measurement and comparison of the surface area of the cerebral cortex at a fine scale is possible using mass conservative interpolation methods. We present a framework for analyses of the cortical surface area, as well as for any other measurement distributed across the cortex that is areal by nature. The method consists of the construction of a mesh representation of the cortex, registration to a common coordinate system and, crucially, interpolation using a pycnophylactic method. Statistical analysis of surface area is done with power-transformed data to address lognormality, and inference is done with permutation methods. We introduce the concept of facewise analysis, discuss its interpretation and potential applications.},
	number = {4},
	journal = {Neuroimage},
	author = {Winkler, A. M. and Sabuncu, M. R. and Yeo, B. T. and Fischl, B. and Greve, D. N. and Kochunov, P. and Nichols, T. E. and Blangero, J. and Glahn, D. C.},
	month = jul,
	year = {2012},
	keywords = {Brain Mapping/*methods, Cerebral Cortex/*anatomy \& histology, Humans, Image Interpretation, Computer-Assisted/*methods, *Magnetic Resonance Imaging},
	pages = {1428--43},
	annote = {Winkler, Anderson {MSabuncu}, Mert {RYeo}, B T {ThomasFischl}, {BruceGreve}, Douglas {NKochunov}, {PeterNichols}, Thomas {EBlangero}, {JohnGlahn}, David Ceng1 {KL}2 {RR}025757-01/{RR}/{NCRR} {NIH} {HHS}/1R01-{NS}070963/{NS}/{NINDS} {NIH} {HHS}/1R21-{NS}072652-01/{NS}/{NINDS} {NIH} {HHS}/1S10RR019307/{RR}/{NCRR} {NIH} {HHS}/1S10RR023043/{RR}/{NCRR} {NIH} {HHS}/1S10RR023401/{RR}/{NCRR} {NIH} {HHS}/{AG}022381/{AG}/{NIA} {NIH} {HHS}/{EB}006395/{EB}/{NIBIB} {NIH} {HHS}/K01 {EB}006395/{EB}/{NIBIB} {NIH} {HHS}/K01 {EB}006395-02/{EB}/{NIBIB} {NIH} {HHS}/K25 {EB}013649/{EB}/{NIBIB} {NIH} {HHS}/{MH}0708143/{MH}/{NIMH} {NIH} {HHS}/{MH}078111/{MH}/{NIMH} {NIH} {HHS}/{MH}083824/{MH}/{NIMH} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 {MH}078111/{MH}/{NIMH} {NIH} {HHS}/R01 {MH}078143-01/{MH}/{NIMH} {NIH} {HHS}/R01 {MH}083824-01/{MH}/{NIMH} {NIH} {HHS}/R01-{NS}052585-01/{NS}/{NINDS} {NIH} {HHS}/R01EB006758/{EB}/{NIBIB} {NIH} {HHS}/R37 {MH}059490/{MH}/{NIMH} {NIH} {HHS}/{RC}1AT005728-01/{AT}/{NCCAM} {NIH} {HHS}/S10 {RR}029392/{RR}/{NCRR} {NIH} {HHS}/U24RR021382/{RR}/{NCRR} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov't2012/03/27 06:00Neuroimage. 2012 Jul 16;61(4):1428-43. doi: 10.1016/j.neuroimage.2012.03.026. Epub 2012 Mar 15.},
	file = {PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/DT9ZMM6X/Winkler et al. - 2012 - Measuring and comparing brain cortical surface are.pdf:application/pdf;Winkler-2012-Measuring and comparing brain cor:/autofs/cluster/freesurfer/zotero/storage/3KMHISBX/Winkler-2012-Measuring and comparing brain cor.pdf:application/pdf}
}

@article{makris_human_2006,
	title = {Human cerebral cortex: a system for the integration of volume- and surface-based representations},
	volume = {33},
	issn = {1053-8119 (Print) 1053-8119 (Linking)},
	shorttitle = {Human cerebral cortex: a system for the integration of volume- and surface-based representations},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/16920366},
	doi = {10.1016/j.neuroimage.2006.04.220},
	abstract = {We describe an {MRI}-based system for topological analysis followed by measurements of topographic features for the human cerebral cortex that takes as its starting point volumetric segmentation data. This permits interoperation between volume-based and surface-based topographic analysis and extends the functionality of many existing segmentation schemes. We demonstrate the utility of these operations in individual as well as to group analysis. The methodology integrates analyses of cortical segmentation data generated by manual and semi-automated volumetric morphometry routines (such as the program cardviews) with the procedures of the {FreeSurfer} program to generate a cortical ribbon of the cerebrum and perform cortical topographic measurements (including thickness, surface area and curvature) in individual subjects as well as in subject populations. This system allows the computation of topographical cortical measurements for segmentation data generated from manual and semi-automated volumetric sources other than {FreeSurfer}. These measurements can be regionally specific and integrated with systems of cortical parcellation that subdivides the neocortex into gyral-based parcellation units ({PUs}). This system of topographical analysis of the cerebral cortex is consistent with current views of cortical development and neural systems organization of the human and non-human primate brain.},
	number = {1},
	journal = {Neuroimage},
	author = {Makris, N. and Kaiser, J. and Haselgrove, C. and Seidman, L. J. and Biederman, J. and Boriel, D. and Valera, E. M. and Papadimitriou, G. M. and Fischl, B. and Caviness, Jr., V. S. and Kennedy, D. N.},
	month = oct,
	year = {2006},
	keywords = {Adult, Algorithms, Cerebral Cortex/*anatomy \& histology, Diffusion Magnetic Resonance Imaging, Female, Functional Laterality/physiology, Humans, Image Processing, Computer-Assisted/statistics \& numerical data, Magnetic Resonance Imaging, Male, Middle Aged, Reproducibility of Results, Software},
	pages = {139--53},
	annote = {Makris, {NikosKaiser}, {JonathanHaselgrove}, {ChristianSeidman}, Larry {JBiederman}, {JosephBoriel}, {DeniseValera}, Eve {MPapadimitriou}, George {MFischl}, {BruceCaviness}, Verne S {JrKennedy}, David {NengF}32 {MH}065040-01A1/{MH}/{NIMH} {NIH} {HHS}/{HD} 62152/{HD}/{NICHD} {NIH} {HHS}/{MH} 57934/{MH}/{NIMH} {NIH} {HHS}/{MH}-16259/{MH}/{NIMH} {NIH} {HHS}/P41RR14075/{RR}/{NCRR} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov't2006/08/22 09:00Neuroimage. 2006 Oct 15;33(1):139-53. Epub 2006 Aug 22.}
}

@article{du_different_2007,
	title = {Different regional patterns of cortical thinning in Alzheimer's disease and frontotemporal dementia},
	volume = {130},
	issn = {0006-8950},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1853284/},
	doi = {10.1093/brain/awm016},
	abstract = {Alzheimer’s disease and frontotemporal dementia ({FTD}) can be difficult to differentiate clinically because of overlapping symptoms. Distinguishing the two dementias based on volumetric measurements of brain atrophy with {MRI} has been only partially successful. Whether {MRI} measurements of cortical thinning improve the differentiation between Alzheimer’s disease and {FTD} is unclear. In this study, we measured cortical thickness using a set of automated tools (Freesurfer) to reconstruct the brain’s cortical surface from T1-weighted structural {MRI} data in 22 patients with Alzheimer’s disease, 19 patients with {FTD} and 23 cognitively normal subjects. The goals were to detect the characteristic patterns of cortical thinning in these two types of dementia, to test the relationship between cortical thickness and cognitive impairment, to determine if measurement of cortical thickness is better than that of cortical volume for differentiating between these dementias and normal ageing and improving the classification of Alzheimer’s disease and {FTD} based on neuropsychological scores alone. Compared to cognitively normal subjects, Alzheimer’s disease patients had a thinner cortex primarily in bilateral, frontal, parietal, temporal and occipital lobes (P {\textless} 0.001), while {FTD} patients had a thinner cortex in bilateral, frontal and temporal regions and some thinning in inferior parietal regions and the posterior cingulate (P{\textless} 0.001). Compared to {FTD} patients, Alzheimer’s disease patients had a thinner cortex (P{\textless} 0.001) in parts of bilateral parietal and precuneus regions. Cognitive impairment was negatively correlated with cortical thickness of frontal, parietal and temporal lobes in Alzheimer’s disease, while similar correlations were not significant in {FTD}. Measurement of cortical thickness was similar to that of cortical volume in differentiating between normal ageing, Alzheimer’s disease and {FTD}. Furthermore, cortical thickness measurements significantly improved the classification between Alzheimer’s disease and {FTD} based on neuropsychological scores alone, including the Mini-Mental State Examination and a modified version of the Trail-Making Test. In conclusion, the characteristic patterns of cortical thinning in Alzheimer’s disease and {FTD} suggest that cortical thickness may be a useful surrogate marker for these types of dementia.},
	number = {Pt 4},
	urldate = {2014-08-23},
	journal = {Brain : a journal of neurology},
	author = {Du, An-Tao and Schuff, Norbert and Kramer, Joel H. and Rosen, Howard J. and Gorno-Tempini, Maria Luisa and Rankin, Katherine and Miller, Bruce L. and Weiner, Michael W.},
	month = apr,
	year = {2007},
	pmid = {17353226},
	pmcid = {PMC1853284},
	pages = {1159--1166},
	file = {PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/JZJC3IFV/Du et al. - 2007 - Different regional patterns of cortical thinning i.pdf:application/pdf}
}

@article{sabuncu_generative_2010,
	title = {A generative model for image segmentation based on label fusion},
	volume = {29},
	issn = {1558-254X (Electronic) 0278-0062 (Linking)},
	shorttitle = {A generative model for image segmentation based on label fusion},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/20562040},
	doi = {10.1109/TMI.2010.2050897},
	abstract = {We propose a nonparametric, probabilistic model for the automatic segmentation of medical images, given a training set of images and corresponding label maps. The resulting inference algorithms rely on pairwise registrations between the test image and individual training images. The training labels are then transferred to the test image and fused to compute the final segmentation of the test subject. Such label fusion methods have been shown to yield accurate segmentation, since the use of multiple registrations captures greater inter-subject anatomical variability and improves robustness against occasional registration failures. To the best of our knowledge, this manuscript presents the first comprehensive probabilistic framework that rigorously motivates label fusion as a segmentation approach. The proposed framework allows us to compare different label fusion algorithms theoretically and practically. In particular, recent label fusion or multiatlas segmentation algorithms are interpreted as special cases of our framework. We conduct two sets of experiments to validate the proposed methods. In the first set of experiments, we use 39 brain {MRI} scans-with manually segmented white matter, cerebral cortex, ventricles and subcortical structures-to compare different label fusion algorithms and the widely-used {FreeSurfer} whole-brain segmentation tool. Our results indicate that the proposed framework yields more accurate segmentation than {FreeSurfer} and previous label fusion algorithms. In a second experiment, we use brain {MRI} scans of 282 subjects to demonstrate that the proposed segmentation tool is sufficiently sensitive to robustly detect hippocampal volume changes in a study of aging and Alzheimer's Disease.},
	number = {10},
	journal = {{IEEE} Trans Med Imaging},
	author = {Sabuncu, M. R. and Yeo, B. T. and Van Leemput, K. and Fischl, B. and Golland, P.},
	month = oct,
	year = {2010},
	keywords = {*Algorithms, Brain/*anatomy \& histology, Computer Simulation, fs\_Misc-methodology, Humans, Image Enhancement/methods, Image Interpretation, Computer-Assisted/*methods, Magnetic Resonance Imaging/*methods, *Models, Anatomic, Models, Neurological, Pattern Recognition, Automated/*methods, Reproducibility of Results, Sensitivity and Specificity, *Subtraction Technique},
	pages = {1714--29},
	annote = {Sabuncu, Mert {RYeo}, B T {ThomasVan} Leemput, {KoenFischl}, {BruceGolland}, {PolinaengP}41 {RR}013218-04/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-06/{RR}/{NCRR} {NIH} {HHS}/P41-{RR}13218/{RR}/{NCRR} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 {EB}001550/{EB}/{NIBIB} {NIH} {HHS}/R01 {EB}001550-01/{EB}/{NIBIB} {NIH} {HHS}/R01 {EB}006758-01A1/{EB}/{NIBIB} {NIH} {HHS}/R01 {NS}051826-01/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}052585-01/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}052585-02/{NS}/{NINDS} {NIH} {HHS}/R01 {RR}016594-02/{RR}/{NCRR} {NIH} {HHS}/R01 {RR}16594-01A1/{RR}/{NCRR} {NIH} {HHS}/R01-{NS}051826/{NS}/{NINDS} {NIH} {HHS}/R01EB006758/{EB}/{NIBIB} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/U24 {RR}021382-01/{RR}/{NCRR} {NIH} {HHS}/U24-{RR}021382/{RR}/{NCRR} {NIH} {HHS}/U54 {EB}005149-06/{EB}/{NIBIB} {NIH} {HHS}/U54-{EB}005149/{EB}/{NIBIB} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov'{tResearch} Support, U.S. Gov't, Non-P.H.S.2010/06/22 06:00IEEE Trans Med Imaging. 2010 Oct;29(10):1714-29. doi: 10.1109/{TMI}.2010.2050897. Epub 2010 Jun 17.},
	file = {Sabuncu-2010-A generative model for image segm:/autofs/cluster/freesurfer/zotero/storage/V4X5U4MD/Sabuncu-2010-A generative model for image segm.pdf:application/pdf}
}

@inproceedings{van_leemput_model-based_2009,
	title = {Model-Based Segmentation of Hippocampal Subfields in Ultra-High Resolution In Vivo {MRI}.},
	volume = {accepted},
	author = {Van Leemput, K and {A. Bakkour} and {T. Benner} and {G. Wiggins} and {L.L. Wald} and {J. Augustinack} and {B.C. Dickerson} and {P. Golland} and Fischl., B.},
	year = {2009}
}

@article{glasser_minimal_2013,
	title = {The minimal preprocessing pipelines for the Human Connectome Project},
	volume = {80},
	issn = {1095-9572},
	doi = {10.1016/j.neuroimage.2013.04.127},
	abstract = {The Human Connectome Project ({HCP}) faces the challenging task of bringing multiple magnetic resonance imaging ({MRI}) modalities together in a common automated preprocessing framework across a large cohort of subjects. The {MRI} data acquired by the {HCP} differ in many ways from data acquired on conventional 3 Tesla scanners and often require newly developed preprocessing methods. We describe the minimal preprocessing pipelines for structural, functional, and diffusion {MRI} that were developed by the {HCP} to accomplish many low level tasks, including spatial artifact/distortion removal, surface generation, cross-modal registration, and alignment to standard space. These pipelines are specially designed to capitalize on the high quality data offered by the {HCP}. The final standard space makes use of a recently introduced {CIFTI} file format and the associated grayordinate spatial coordinate system. This allows for combined cortical surface and subcortical volume analyses while reducing the storage and processing requirements for high spatial and temporal resolution data. Here, we provide the minimum image acquisition requirements for the {HCP} minimal preprocessing pipelines and additional advice for investigators interested in replicating the {HCP}'s acquisition protocols or using these pipelines. Finally, we discuss some potential future improvements to the pipelines.},
	language = {eng},
	journal = {{NeuroImage}},
	author = {Glasser, Matthew F. and Sotiropoulos, Stamatios N. and Wilson, J. Anthony and Coalson, Timothy S. and Fischl, Bruce and Andersson, Jesper L. and Xu, Junqian and Jbabdi, Saad and Webster, Matthew and Polimeni, Jonathan R. and Van Essen, David C. and Jenkinson, Mark and {WU-Minn HCP Consortium}},
	month = oct,
	year = {2013},
	pmid = {23668970},
	pmcid = {PMC3720813},
	keywords = {Algorithms, Brain, Connectome, Diffusion Tensor Imaging, Humans, Image Interpretation, Computer-Assisted, Models, Anatomic, Models, Neurological, Nerve Net},
	pages = {105--124}
}

@article{sarica_tractography_2014,
	title = {Tractography in amyotrophic lateral sclerosis using a novel probabilistic tool: A study with tract-based reconstruction compared to voxel-based approach},
	volume = {224},
	issn = {0165-0270},
	shorttitle = {Tractography in amyotrophic lateral sclerosis using a novel probabilistic tool},
	url = {http://www.sciencedirect.com/science/article/pii/S0165027014000028},
	doi = {10.1016/j.jneumeth.2013.12.014},
	abstract = {{AbstractBackground}
Diffusion tensor imaging ({DTI}) is one of the most sensitive {MRI} tools for detecting subtle cerebral white matter abnormalities in amyotrophic lateral sclerosis ({ALS}). Nowadays a plethora of {DTI} tools have been proposed, but very few methods have been translated into clinical practice.
New method
The aim of this study is to validate the objective measurement of fiber tracts as provided by a new unbiased and automated tractography reconstruction tool named as {TRActs} Constrained by {UnderLying} Anatomy ({TRACULA}). The reliability of this tract-based approach was evaluated on a dataset of 14 patients with definite {ALS} compared with 14 age/sex-matched healthy controls. To further corroborate these measurements, we used a well-known voxelwise approach, called tract-based spatial statistics ({TBSS}), on the same dataset.
Results
{TRACULA} showed specific significant alterations of several {DTI} parameters in the corticospinal tract of the {ALS} group with respect to controls.
Comparison with existing method
The same finding was detected using the well-known {TBSS} analysis. Similarly, both methods depicted also additional microstructural changes in the cingulum.
Conclusions
{DTI} tractography metrics provided by {TRACULA} perfectly agree with those previously reported in several post-mortem and {DTI} studies, thus demonstrating the accuracy of this method in characterizing the microstructural changes occurring in {ALS}. With further validation (i.e. considering the heterogeneity of other clinical phenotypes), this method has the potential to become useful for clinical practice providing objective measurements that might aid radiologists in the interpretation of {MR} images and improve diagnostic accuracy of {ALS}.},
	urldate = {2014-08-25},
	journal = {Journal of Neuroscience Methods},
	author = {Sarica, Alessia and Cerasa, Antonio and Vasta, Roberta and Perrotta, Paolo and Valentino, Paola and Mangone, Graziella and Guzzi, Pietro H. and Rocca, Federico and Nonnis, Matteo and Cannataro, Mario and Quattrone, Aldo},
	month = mar,
	year = {2014},
	keywords = {Amyotrophic lateral sclerosis, Corticospinal tract, {DTI}, Tractography, {TRACULA}},
	pages = {79--87},
	file = {ScienceDirect Snapshot:/autofs/cluster/freesurfer/zotero/storage/5U8KWXF3/S0165027014000028.html:text/html}
}

@inproceedings{augustinack_detection_2004,
	title = {Detection of Entorhinal Islands using 7T {MRI}},
	shorttitle = {Detection of Entorhinal Islands using 7T {MRI}},
	author = {Augustinack, Jean and Kouwe, Andre van der and Salat, David and Wald, Larry and Blackwell, Megan and Wiggins, Chris and Fischl, Bruce},
	year = {2004}
}

@article{ronan_cortical_2011,
	title = {Cortical curvature analysis in {MRI}-negative temporal lobe epilepsy: A surrogate marker for malformations of cortical development: Cortical Morphology Analysis in {MRI}-Negative {TLE}},
	volume = {52},
	issn = {00139580},
	shorttitle = {Cortical curvature analysis in {MRI}-negative temporal lobe epilepsy},
	url = {http://onlinelibrary.wiley.com/enhanced/doi/10.1111/j.1528-1167.2010.02895.x/},
	doi = {10.1111/j.1528-1167.2010.02895.x},
	language = {en},
	number = {1},
	urldate = {2014-08-24},
	journal = {Epilepsia},
	author = {Ronan, Lisa and Scanlon, Cathy and Murphy, Kevin and Maguire, Sinead and Delanty, Norman and Doherty, Colin P. and Fitzsimons, Mary},
	month = jan,
	year = {2011},
	keywords = {Adolescent, Adult, Biological Markers, Brain Mapping/*methods, Cerebral Cortex/*abnormalities/growth \& development/*pathology, Epilepsy, Temporal Lobe/*pathology, Female, Humans, Magnetic Resonance Imaging/*methods, Male, Middle Aged, Young Adult},
	pages = {28--34},
	annote = {Ronan, {LisaScanlon}, {CathyMurphy}, {KevinMaguire}, {SineadDelanty}, {NormanDoherty}, Colin {PFitzsimons}, {MaryengComparative} {StudyResearch} Support, Non-U.S. Gov't2011/01/05 06:00Epilepsia. 2011 Jan;52(1):28-34. doi: 10.1111/j.1528-1167.2010.02895.x. Epub 2010 Dec 27.},
	file = {Cortical curvature analysis in MRI‐negative temporal lobe epilepsy\: A surrogate marker for malformations of cortical development - Ronan - 2010 - Epilepsia - Wiley Online Library:/autofs/cluster/freesurfer/zotero/storage/567RMIVP/j.1528-1167.2010.02895.html:text/html;Ronan-2011-Cortical curvature analysis in MRI1:/autofs/cluster/freesurfer/zotero/storage/7ZKF9FGZ/Ronan-2011-Cortical curvature analysis in MRI1.pdf:application/pdf}
}

@article{saygin_connectivity-based_2011,
	title = {Connectivity-based segmentation of human amygdala nuclei using probabilistic tractography},
	volume = {56},
	issn = {1095-9572 (Electronic) 1053-8119 (Linking)},
	shorttitle = {Connectivity-based segmentation of human amygdala nuclei using probabilistic tractography},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/21396459},
	doi = {10.1016/j.neuroimage.2011.03.006},
	abstract = {The amygdala plays an important role in emotional and social functions, and amygdala dysfunction has been associated with multiple neuropsychiatric disorders, including autism, anxiety, and depression. Although the amygdala is composed of multiple anatomically and functionally distinct nuclei, typical structural magnetic resonance imaging ({MRI}) sequences are unable to discern them. Thus, functional {MRI} ({fMRI}) studies typically average the {BOLD} response over the entire structure, which reveals some aspects of amygdala function as a whole but does not distinguish the separate roles of specific nuclei in humans. We developed a method to segment the human amygdala into its four major nuclei using only diffusion-weighted imaging and connectivity patterns derived mainly from animal studies. We refer to this new method as Tractography-based Segmentation, or {TractSeg}. The segmentations derived from {TractSeg} were topographically similar to their corresponding amygdaloid nuclei, and were validated against a high-resolution scan in which the nucleic boundaries were visible. In addition, nuclei topography was consistent across subjects. {TractSeg} relies on short scan acquisitions and widely accessible software packages, making it attractive for use in healthy populations to explore normal amygdala nucleus function, as well as in clinical and pediatric populations. Finally, it paves the way for implementing this method in other anatomical regions which are also composed of functional subunits that are difficult to distinguish with standard structural {MRI}.},
	number = {3},
	journal = {Neuroimage},
	author = {Saygin, Z. M. and Osher, D. E. and Augustinack, J. and Fischl, B. and Gabrieli, J. D.},
	month = jun,
	year = {2011},
	keywords = {Adult, Amygdala/*anatomy \& histology/physiology, Diffusion Tensor Imaging/*methods, Female, Humans, Image Processing, Computer-Assisted, Male, Models, Neurological, Models, Statistical, Neural Pathways/*anatomy \& histology/physiology, Normal Distribution, Reproducibility of Results, Young Adult},
	pages = {1353--61},
	annote = {Saygin, Zeynep {MOsher}, David {EAugustinack}, {JeanFischl}, {BruceGabrieli}, John D Eeng1R21NS072652-01/{NS}/{NINDS} {NIH} {HHS}/1S10RR019/{RR}/{NCRR} {NIH} {HHS}/1S10RR023043/{RR}/{NCRR} {NIH} {HHS}/1S10RR023401/{RR}/{NCRR} {NIH} {HHS}/{AG}022381/{AG}/{NIA} {NIH} {HHS}/{DA}023427/{DA}/{NIDA} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 {EB}006758-03/{EB}/{NIBIB} {NIH} {HHS}/R01 {NS}052585-01/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}052585-01A1/{NS}/{NINDS} {NIH} {HHS}/R01EB006758/{EB}/{NIBIB} {NIH} {HHS}/R21 {NS}072652-01/{NS}/{NINDS} {NIH} {HHS}/R90 {DA}023427/{DA}/{NIDA} {NIH} {HHS}/R90 {DA}023427-01/{DA}/{NIDA} {NIH} {HHS}/S10 {RR}019307-01/{RR}/{NCRR} {NIH} {HHS}/S10 {RR}023401-01A2/{RR}/{NCRR} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov't2011/03/15 06:00Neuroimage. 2011 Jun 1;56(3):1353-61. doi: 10.1016/j.neuroimage.2011.03.006. Epub 2011 Mar 8.},
	file = {PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/UBIHGH33/Saygin et al. - 2011 - Connectivity-based segmentation of human amygdala .pdf:application/pdf;Saygin-2011-Connectivity-based segmentation of:/autofs/cluster/freesurfer/zotero/storage/6CTQ8PXZ/Saygin-2011-Connectivity-based segmentation of.pdf:application/pdf}
}

@article{scheel_imaging_2011,
	title = {Imaging derived cortical thickness reduction in high-functioning autism: key regions and temporal slope},
	volume = {58},
	issn = {1095-9572},
	shorttitle = {Imaging derived cortical thickness reduction in high-functioning autism},
	doi = {10.1016/j.neuroimage.2011.06.040},
	abstract = {Cortical thickness ({CT}) changes possibly contribute to the complex symptomatology of autism. The aberrant developmental trajectories underlying such differences in certain brain regions and their continuation in adulthood are a matter of intense debate. We studied 28 adults with high-functioning autism ({HFA}) and 28 control subjects matched for age, gender, {IQ} and handedness. A surface-based whole brain analysis utilizing {FreeSurfer} was employed to detect {CT} differences between the two diagnostic groups and to investigate the time course of age-related changes. Direct comparison with control subjects revealed thinner cortex in {HFA} in the posterior superior temporal sulcus ({pSTS}) of the left hemisphere. Considering the time course of {CT} development we found clusters around the {pSTS} and cuneus in the left and the paracentral lobule in the right hemisphere to be thinner in {HFA} with comparable age-related slopes in patients and controls. Conversely, we found clusters around the supramarginal gyrus and inferior parietal lobule ({IPL}) in the left and the precentral and postcentral gyrus in the right hemisphere to be thinner in {HFA}, but with different age-related slopes in patients and controls. In the latter regions {CT} showed a steady decrease in controls but no analogous thinning in {HFA}. {CT} analyses contribute in characterizing neuroanatomical correlates of {HFA}. Reduced {CT} is present in brain regions involved in social cognition. Furthermore, our results demonstrate that aberrant brain development leading to such differences is proceeding throughout adulthood. Discrepancies in prior morphometric studies may be induced by the complex time course of cortical changes.},
	language = {eng},
	number = {2},
	journal = {{NeuroImage}},
	author = {Scheel, Christian and Rotarska-Jagiela, Anna and Schilbach, Leonhard and Lehnhardt, Fritz G. and Krug, Barbara and Vogeley, Kai and Tepest, Ralf},
	month = sep,
	year = {2011},
	pmid = {21749926},
	keywords = {Adult, Age of Onset, Aging, Anatomy, Cross-Sectional, Autistic Disorder, Brain, Cerebral Cortex, Cluster Analysis, Data Interpretation, Statistical, Female, Functional Laterality, Humans, Image Processing, Computer-Assisted, Intelligence, Intelligence Tests, Magnetic Resonance Imaging, Male, Middle Aged, Temporal Lobe, Young Adult},
	pages = {391--400}
}

@article{martinussen_cerebral_2005,
	title = {Cerebral cortex thickness in 15-year-old adolescents with low birth weight measured by an automated {MRI}-based method},
	volume = {128},
	issn = {1460-2156 (Electronic) 0006-8950 (Linking)},
	shorttitle = {Cerebral cortex thickness in 15-year-old adolescents with low birth weight measured by an automated {MRI}-based method},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/16123146},
	doi = {10.1093/brain/awh610},
	abstract = {Infants with low birth weight are at increased risk of perinatal brain injury. Disruption of normal cortical development may have consequences for later motor, behavioural and cognitive development. The aim of this study was to measure cerebral cortical thickness, area and volume with an automated {MRI} technique in 15-year-old adolescents who had low birth weight. Cerebral {MRI} for morphometric analysis was performed on 50 very low birth weight ({VLBW}, birth weight {\textless}/=1500 g), 49 term small for gestational age births ({SGA}, birth weight {\textless}10th percentile at term) and 58 control adolescents. A novel method of cortical surface models yielded measurements of cortical thickness and area for each subject's entire brain and computed cross-subject statistics based on cortical anatomy. The cortical surface models demonstrated regional thinning of the parietal, temporal and occipital lobes in the {VLBW} group, whereas regional thickening was demonstrated in the frontal and occipital lobes. The areas of change were greatest in those with the shortest gestational age at birth and lowest birth weight. Cortical surface area and cortical volume were lower in the {VLBW} than in the Control group. Within the {VLBW} group, there was an association between surface area and estimation of the intelligence quotient {IQ} ({IQ}(est)) and between cortical volume and {IQ}(est). Furthermore, cortical grey matter as a proportion of brain volume was significantly lower in the {VLBW}, but not in the {SGA} group compared with Controls. This observed reorganization of the developing brain offers a unique opportunity to investigate any relationship between changes in cortical anatomy and cognitive and social impairments, and the increase in psychiatric disorders that have been found in {VLBW} children and adolescents.},
	language = {eng},
	number = {Pt 11},
	journal = {Brain},
	author = {Martinussen, M. and Fischl, B. and Larsson, H. B. and Skranes, J. and Kulseng, S. and Vangberg, T. R. and Vik, T. and Brubakk, A. M. and Haraldseth, O. and Dale, A. M.},
	month = nov,
	year = {2005},
	keywords = {Adolescent, Birth Weight, Brain Mapping/methods, Cephalometry/methods, Cerebral Cortex/growth \& development/*pathology, Female, Follow-Up Studies, Humans, Image Processing, Computer-Assisted/methods, *Infant, Low Birth Weight, Infant, Newborn, Infant, Small for Gestational Age, Infant, Very Low Birth Weight, Intelligence, Magnetic Resonance Imaging/methods, Male},
	pages = {2588--96},
	annote = {Martinussen, {MFischl}, {BLarsson}, H {BSkranes}, {JKulseng}, {SVangberg}, T {RVik}, {TBrubakk}, A-{MHaraldseth}, {ODale}, A Meng1-{HD}-1-3127/{HD}/{NICHD} {NIH} {HHS}/1-{HD}-4-2803/{HD}/{NICHD} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01-{NS}39581/{NS}/{NINDS} {NIH} {HHS}/R01-{RR}13609/{RR}/{NCRR} {NIH} {HHS}/R01-{RR}16594/{RR}/{NCRR} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, U.S. Gov't, P.H.S.England2005/08/27 09:00Brain. 2005 Nov;128(Pt 11):2588-96. Epub 2005 Aug 25.},
	file = {Martinussen-2005-Cerebral cortex thickness in1:/autofs/cluster/freesurfer/zotero/storage/Q28W6BPI/Martinussen-2005-Cerebral cortex thickness in1.pdf:application/pdf}
}

@article{blackwell_target-specific_2009,
	title = {Target-specific contrast agents for magnetic resonance microscopy},
	volume = {46},
	issn = {1095-9572 (Electronic) 1053-8119 (Linking)},
	shorttitle = {Target-specific contrast agents for magnetic resonance microscopy},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/19385012},
	abstract = {High-resolution ex vivo magnetic resonance ({MR}) imaging can be used to delineate prominent architectonic features in the human brain, but increased contrast is required to visualize more subtle distinctions. To aid {MR} sensitivity to cell density and myelination, we have begun the development of target-specific paramagnetic contrast agents. This work details the first application of luxol fast blue ({LFB}), an optical stain for myelin, as a white matter-selective {MR} contrast agent for human ex vivo brain tissue. Formalin-fixed human visual cortex was imaged with an isotropic resolution between 80 and 150 microm at 4.7 and 14 T before and after en bloc staining with {LFB}. Longitudinal (R1) and transverse (R2) relaxation rates in {LFB}-stained tissue increased proportionally with myelination at both field strengths. Changes in R1 resulted in larger contrast-to-noise ratios ({CNR}), per unit time, on T1-weighted images between more myelinated cortical layers ({IV}-{VI}) and adjacent, superficial layers (I-{III}) at both field strengths. Specifically, {CNR} for {LFB}-treated samples increased by 229 +/- 13\% at 4.7 T and 269 +/- 25\% at 14 T when compared to controls. Also, additional cortical layers ({IVca}, {IVd}, and Va) were resolvable in 14 T-{MR} images of {LFB}-treated samples but not in control samples. After imaging, samples were sliced in 40-micron sections, mounted, and photographed. Both the macroscopic and microscopic distributions of {LFB} were found to mimic those of traditional histological preparations. Our results suggest target-specific contrast agents will enable more detailed {MR} images with applications in imaging pathological ex vivo samples and constructing better {MR} atlases from ex vivo brains.},
	language = {eng},
	number = {2},
	journal = {Neuroimage},
	author = {Blackwell, M. L. and Farrar, C. T. and Fischl, B. and Rosen, B. R.},
	month = jun,
	year = {2009},
	keywords = {Contrast Media/administration \& dosage, Drug Delivery Systems/methods, Humans, Image Enhancement/*methods, Indoles/administration \& dosage/*diagnostic use, Magnetic Resonance Imaging/*methods, Microscopy/*methods, Nerve Fibers, Myelinated/*ultrastructure, Reproducibility of Results, Sensitivity and Specificity, Visual Cortex/*cytology},
	pages = {382--93},
	annote = {Blackwell, Megan {LFarrar}, Christian {TFischl}, {BruceRosen}, Bruce {RengK}25 {AG}029415-01A1/{AG}/{NIA} {NIH} {HHS}/K25 {AG}029415-02/{AG}/{NIA} {NIH} {HHS}/K25 {AG}029415-03/{AG}/{NIA} {NIH} {HHS}/K25 {AG}029415-04/{AG}/{NIA} {NIH} {HHS}/K25 {AG}029415-05/{AG}/{NIA} {NIH} {HHS}/P41 {RR}014075/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-11/{RR}/{NCRR} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 {EB}001550/{EB}/{NIBIB} {NIH} {HHS}/R01 {EB}001550-04/{EB}/{NIBIB} {NIH} {HHS}/R01 {EB}006758-03/{EB}/{NIBIB} {NIH} {HHS}/R01 {NS}052585-01/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}052585-01A1/{NS}/{NINDS} {NIH} {HHS}/R01EB006758/{EB}/{NIBIB} {NIH} {HHS}/T32 {EB}001680/{EB}/{NIBIB} {NIH} {HHS}/T32 {EB}001680-03/{EB}/{NIBIB} {NIH} {HHS}/T32EB001680/{EB}/{NIBIB} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/U24 {RR}021382-03/{RR}/{NCRR} {NIH} {HHS}/U54 {EB}005149/{EB}/{NIBIB} {NIH} {HHS}/U54 {EB}005149-050017/{EB}/{NIBIB} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov't2009/04/23 09:00Neuroimage. 2009 Jun;46(2):382-93.},
	file = {Blackwell-2009-Target-specific contrast agents:/autofs/cluster/freesurfer/zotero/storage/R7K2W4Z3/Blackwell-2009-Target-specific contrast agents.pdf:application/pdf}
}

@article{rimol_cortical_2010,
	title = {Cortical Thickness is Influenced by Regionally-Specific Genetic Factors},
	volume = {67},
	issn = {0006-3223},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3184643/},
	doi = {10.1016/j.biopsych.2009.09.032},
	abstract = {Background
Although global brain structure is highly heritable, there is still variability in the magnitude of genetic influences on the size of specific regions. Yet, little is known about the patterning of those genetic influences, i.e., whether the same genes influence structure throughout the brain or whether there are regionally-specific sets of genes.

Methods
We mapped the heritability of cortical thickness throughout the brain using 3D structural magnetic resonance imaging in 404 middle-aged male twins. To assess the amount of genetic overlap between regions, we then mapped genetic correlations between three selected seed points and all other points comprising the continuous cortical surface.

Results
There was considerable regional variability in the magnitude of genetic influences on cortical thickness. The primary visual (V1) seed point had strong genetic correlations with posterior sensory and motor areas. The anterior temporal seed point had strong genetic correlations with anterior frontal regions, but not with V1. The middle frontal seed point had strong genetic correlations with inferior parietal regions.

Conclusions
These results provide strong evidence of regionally-specific patterns rather than a single, global genetic factor. The patterns are largely consistent with a division between primary and association cortex, as well as broadly-defined patterns of brain gene expression, neuroanatomical connectivity, and brain maturation trajectories, but no single explanation appears to be sufficient. The patterns do not conform to traditionally-defined brain structure boundaries. This approach can serve as a step toward identifying novel phenotypes for genetic association studies of psychiatric disorders, and normal and pathological cognitive aging.},
	number = {5},
	urldate = {2014-08-23},
	journal = {Biological psychiatry},
	author = {Rimol, Lars M. and Panizzon, Matthew S. and Fennema-Notestine, Christine and Eyler, Lisa T. and Fischl, Bruce and Franz, Carol E. and Hagler, Donald J. and Lyons, Michael J. and Neale, Michael C. and Pacheco, Jennifer and Perry, Michele E. and Schmitt, J. Eric and Grant, Michael D. and Seidman, Larry J. and Thermenos, Heidi W. and Tsuang, Ming T. and Eisen, Seth A. and Kremen, William S. and Dale, Anders M.},
	month = mar,
	year = {2010},
	pmid = {19963208},
	pmcid = {PMC3184643},
	keywords = {Adult, Cerebral Cortex/*anatomy \& histology/*cytology, Female, Genetic Variation/*genetics, Genotype, Humans, Magnetic Resonance Imaging, Male, Phenotype, Twins/genetics},
	pages = {493--499},
	annote = {Rimol, Lars {MPanizzon}, Matthew {SFennema}-Notestine, {ChristineEyler}, Lisa {TFischl}, {BruceFranz}, Carol {EHagler}, Donald {JLyons}, Michael {JNeale}, Michael {CPacheco}, {JenniferPerry}, Michele {ESchmitt}, J {EricGrant}, Michael {DSeidman}, Larry {JThermenos}, Heidi {WTsuang}, Ming {TEisen}, Seth {AKremen}, William {SDale}, Anders {MengAG}018384/{AG}/{NIA} {NIH} {HHS}/{AG}018386/{AG}/{NIA} {NIH} {HHS}/{AG}022381/{AG}/{NIA} {NIH} {HHS}/{AG}022982/{AG}/{NIA} {NIH} {HHS}/R01 {AG}018386-09/{AG}/{NIA} {NIH} {HHS}/R01 {AG}018386-10/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022381-09/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022381-10/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022982/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022982-04/{AG}/{NIA} {NIH} {HHS}/R01 {AG}031224/{AG}/{NIA} {NIH} {HHS}/R01 {AG}031224-01A1/{AG}/{NIA} {NIH} {HHS}/R01 {EB}006758-04/{EB}/{NIBIB} {NIH} {HHS}/R01 {NS}039581/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}039581-01/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}052585-01A1/{NS}/{NINDS} {NIH} {HHS}/R01 {RR}016594-01A1/{RR}/{NCRR} {NIH} {HHS}/R21 {NS}072652-02/{NS}/{NINDS} {NIH} {HHS}/S10 {RR}019307-01/{RR}/{NCRR} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, U.S. Gov't, Non-P.H.S.Twin Study2009/12/08 06:00Biol Psychiatry. 2010 Mar 1;67(5):493-9. doi: 10.1016/j.biopsych.2009.09.032. Epub 2009 Dec 6.},
	file = {PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/JMK5EMSP/Rimol et al. - 2010 - Cortical Thickness is Influenced by Regionally-Spe.pdf:application/pdf;Rimol-2010-Cortical thickness is influenced by:/autofs/cluster/freesurfer/zotero/storage/C2J2T9ZE/Rimol-2010-Cortical thickness is influenced by.pdf:application/pdf}
}

@article{pengas_comparative_2009,
	title = {Comparative reliability of total intracranial volume estimation methods and the influence of atrophy in a longitudinal semantic dementia cohort},
	volume = {19},
	issn = {1552-6569},
	url = {https://surfer.nmr.mgh.harvard.edu/ftp/articles/pengas_g_inpress_2008.pdf},
	doi = {10.1111/j.1552-6569.2008.00246.x},
	abstract = {{BACKGROUND} {AND} {PURPOSE}: Total intracranial volume ({TIV}) as a measure of premorbid brain size is often used to correct volumes of interest for interindividual differences in magnetic resonance imaging ({MRI}) studies. We directly compared the reliability of different {TIV} estimation methods to address whether such methods are influenced by brain atrophy in the neurodegenerative disease, semantic dementia.
{METHODS}: We contrasted several manual approaches using T1-weighted, T2-weighted, and proton density ({PD}) acquisitions with 2 automated methods (statistical parametric mapping 5 [{SPM}5] and {FreeSurfer} [{FS}]) in a cohort of semantic dementia subjects (n= 11) that had been imaged longitudinally.
{RESULTS}: Novel mid-cranial sampling of either {PD} or T2-weighted images were least susceptible to atrophy: of these, the {PD} method was both more precise and more user-friendly. {SPM}5 also produced good results, providing automation for only a small loss in precision compared to the best manual methods. The T1 method that underestimated {TIV} as atrophy progressed was the least reproducible and the most labor-intensive. Fully automated {FS} overestimated {TIV} with progressive atrophy, and the results were even worse after optimizing the transformation.
{CONCLUSION}: The mid-cranial sampling of {PD} images achieved the best combination of precision, reliability, and user-friendliness. {SPM}5 is an attractive alternative if the highest level of precision is not required.},
	language = {eng},
	number = {1},
	journal = {Journal of Neuroimaging: Official Journal of the American Society of Neuroimaging},
	author = {Pengas, George and Pereira, João M. S. and Williams, Guy B. and Nestor, Peter J.},
	month = jan,
	year = {2009},
	pmid = {18494772},
	keywords = {Aged, Analysis of Variance, Atrophy, Brain, Dementia, Female, fs\_Validation-Evaluations, Humans, Image Interpretation, Computer-Assisted, Longitudinal Studies, Magnetic Resonance Imaging, Male, Middle Aged, Organ Size, Reproducibility of Results},
	pages = {37--46}
}

@article{postelnicu_geometry_2007,
	title = {Geometry driven volumetric registration},
	volume = {20},
	issn = {1011-2499 (Print) 1011-2499 (Linking)},
	shorttitle = {Geometry driven volumetric registration},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/17633739},
	abstract = {In this paper, we propose a novel method for the registration of volumetric images of the brain that attempts to maximize the overlap of cortical folds. In order to achieve this, relevant geometrical information is extracted from a surface-based morph and is diffused throughout the volume using the Navier operator of elasticity. The result is a volumetric warp that aligns the folding patterns.},
	journal = {Inf Process Med Imaging},
	author = {Postelnicu, G. and Zollei, L. and Desikan, R. and Fischl, B.},
	year = {2007},
	keywords = {Algorithms, Artificial Intelligence, Brain/*anatomy \& histology, fs\_CVS, Humans, Image Enhancement/*methods, Image Interpretation, Computer-Assisted/*methods, Imaging, Three-Dimensional/*methods, Likelihood Functions, Magnetic Resonance Imaging/*methods, Pattern Recognition, Automated/*methods, Reproducibility of Results, Sensitivity and Specificity, *Subtraction Technique},
	pages = {675--86},
	annote = {Postelnicu, {GheorgheZollei}, {LillaDesikan}, {RahulFischl}, {BruceengP}41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 {EB}001550/{EB}/{NIBIB} {NIH} {HHS}/R01 {NS}052585-01/{NS}/{NINDS} {NIH} {HHS}/R01 {RR}16594-01A1/{RR}/{NCRR} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/U54 {EB}005149/{EB}/{NIBIB} {NIH} {HHS}/Evaluation {StudiesResearch} Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov'{tGermany}2007/07/19 09:00Inf Process Med Imaging. 2007;20:675-86.}
}

@article{saygin_tracking_2013,
	title = {Tracking the Roots of Reading Ability: White Matter Volume and Integrity Correlate with Phonological Awareness in Prereading and Early-Reading Kindergarten Children},
	volume = {33},
	issn = {0270-6474, 1529-2401},
	shorttitle = {Tracking the Roots of Reading Ability},
	url = {http://www.jneurosci.org/content/33/33/13251},
	doi = {10.1523/JNEUROSCI.4383-12.2013},
	abstract = {Developmental dyslexia, an unexplained difficulty in learning to read, has been associated with alterations in white matter organization as measured by diffusion-weighted imaging. It is unknown, however, whether these differences in structural connectivity are related to the cause of dyslexia or if they are consequences of reading difficulty (e.g., less reading experience or compensatory brain organization). Here, in 40 kindergartners who had received little or no reading instruction, we examined the relation between behavioral predictors of dyslexia and white matter organization in left arcuate fasciculus, inferior longitudinal fasciculus, and the parietal portion of the superior longitudinal fasciculus using probabilistic tractography. Higher composite phonological awareness scores were significantly and positively correlated with the volume of the arcuate fasciculus, but not with other tracts. Two other behavioral predictors of dyslexia, rapid naming and letter knowledge, did not correlate with volumes or diffusion values in these tracts. The volume and fractional anisotropy of the left arcuate showed a particularly strong positive correlation with a phoneme blending test. Whole-brain regressions of behavioral scores with diffusion measures confirmed the unique relation between phonological awareness and the left arcuate. These findings indicate that the left arcuate fasciculus, which connects anterior and posterior language regions of the human brain and which has been previously associated with reading ability in older individuals, is already smaller and has less integrity in kindergartners who are at risk for dyslexia because of poor phonological awareness. These findings suggest a structural basis of behavioral risk for dyslexia that predates reading instruction.},
	language = {en},
	number = {33},
	urldate = {2014-08-25},
	journal = {The Journal of Neuroscience},
	author = {Saygin, Zeynep M. and Norton, Elizabeth S. and Osher, David E. and Beach, Sara D. and Cyr, Abigail B. and Ozernov-Palchik, Ola and Yendiki, Anastasia and Fischl, Bruce and Gaab, Nadine and Gabrieli, John D. E.},
	month = aug,
	year = {2013},
	pmid = {23946384},
	pages = {13251--13258},
	file = {Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/WMQ4T76F/Saygin et al. - 2013 - Tracking the Roots of Reading Ability White Matte.pdf:application/pdf;Snapshot:/autofs/cluster/freesurfer/zotero/storage/44NB2RXZ/13251.html:text/html}
}

@article{nishida_detailed_2006,
	title = {Detailed semiautomated {MRI} based morphometry of the neonatal brain: preliminary results},
	volume = {32},
	issn = {1053-8119},
	shorttitle = {Detailed semiautomated {MRI} based morphometry of the neonatal brain},
	url = {https://surfer.nmr.mgh.harvard.edu/ftp/articles/neonatal_morphometry.pdf},
	doi = {10.1016/j.neuroimage.2006.05.020},
	abstract = {In the neonate, regional growth trajectories provide information about the coordinated development of cerebral substructures and help identify regional vulnerability by identifying times of faster growth. Segmentation of magnetic resonance images ({MRI}) has provided detailed information for the myelinated brain but few reports of regional neonatal brain growth exist. We report the method and preliminary results of detailed semiautomated segmentation of 12 normative neonatal brains (gestational age 31.1-42.6 weeks at time of {MRI}) using volumetric T1-weighted images. Accuracy was confirmed by expert review of every segmented image. In 5 brains, repeat segmentation resulted in intraclass correlation coefficients {\textgreater}0.9 (except for the right amygdala) and an average percent voxel overlap of 90.0\%. Artifacts or image quality limited the number of regions segmented in 9/12 data sets and 1/12 was excluded from volumetric analysis due to ventriculomegaly. Brains were segmented into cerebral exterior (N = 8), cerebral lobes (N = 5), lateral ventricles (N = 8), cerebral cortex (N = 6), white matter (N = 6), corpus callosum (N = 7), deep central gray (N = 8), hippocampi (N = 8), amygdalae (N = 8), cerebellar hemispheres (N = 8), vermis (N = 8), midbrain (N = 8), pons (N = 8) and medulla (N = 8). Linear growth (P {\textless} 0.05) was identified in all regions except the cerebral white matter, medulla and ventricles. Striking differences in regional growth rates were noted. These preliminary results are consistent with the heterochronous nature of cerebral development and provide initial estimates of regional brain growth and therefore regional vulnerability in the perinatal time period.},
	language = {eng},
	number = {3},
	journal = {{NeuroImage}},
	author = {Nishida, Mitsuhiro and Makris, Nikolaos and Kennedy, David N. and Vangel, Mark and Fischl, Bruce and Krishnamoorthy, Kalpathy S. and Caviness, Verne S. and Grant, P. Ellen},
	month = sep,
	year = {2006},
	pmid = {16857388},
	keywords = {Algorithms, Brain, Female, Gestational Age, Humans, Image Processing, Computer-Assisted, Infant, Newborn, Magnetic Resonance Imaging, Male, Observer Variation, Posture, Reproducibility of Results},
	pages = {1041--1049}
}

@article{salat_age-related_2005,
	title = {Age-related alterations in white matter microstructure measured by diffusion tensor imaging},
	volume = {26},
	issn = {0197-4580 (Print) 0197-4580 (Linking)},
	shorttitle = {Age-related alterations in white matter microstructure measured by diffusion tensor imaging},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/15917106},
	doi = {10.1016/j.neurobiolaging.2004.09.017},
	abstract = {Cerebral white matter ({WM}) undergoes various degenerative changes with normal aging, including decreases in myelin density and alterations in myelin structure. We acquired whole-head, high-resolution diffusion tensor images ({DTI}) in 38 participants across the adult age span. Maps of fractional anisotropy ({FA}), a measure of {WM} microstructure, were calculated for each participant to determine whether particular fiber systems of the brain are preferentially vulnerable to {WM} degeneration. Regional {FA} measures were estimated from nine regions of interest in each hemisphere and from the genu and splenium of the corpus callosum ({CC}). The results showed significant age-related decline in {FA} in frontal {WM}, the posterior limb of the internal capsule ({PLIC}), and the genu of the {CC}. In contrast, temporal and posterior {WM} was relatively preserved. These findings suggest that {WM} alterations are variable throughout the brain and that particular fiber populations within prefrontal region and {PLIC} are most vulnerable to age-related degeneration.},
	language = {eng},
	number = {8},
	journal = {Neurobiol Aging},
	author = {Salat, D. H. and Tuch, D. S. and Greve, D. N. and van der Kouwe, A. J. and Hevelone, N. D. and Zaleta, A. K. and Rosen, B. R. and Fischl, B. and Corkin, S. and Rosas, H. D. and Dale, A. M.},
	month = aug,
	year = {2005},
	keywords = {Adult, Aged, Aging/*pathology, Anisotropy, Atrophy/pathology/physiopathology, Brain Mapping/methods, Cerebral Cortex/*pathology/physiopathology, Corpus Callosum/pathology, Diffusion Magnetic Resonance Imaging/*methods, Female, Humans, Internal Capsule/pathology, Male, Memory Disorders/*pathology/physiopathology, Middle Aged, Nerve Fibers, Myelinated/*pathology, Neurodegenerative Diseases/pathology/physiopathology, Predictive Value of Tests},
	pages = {1215--27},
	annote = {Salat, D {HTuch}, D {SGreve}, D Nvan der Kouwe, A J {WHevelone}, N {DZaleta}, A {KRosen}, B {RFischl}, {BCorkin}, {SRosas}, H {DianaDale}, A Meng5:P50:{AG}05134/{AG}/{NIA} {NIH} {HHS}/{AG}05886/{AG}/{NIA} {NIH} {HHS}/{AG}14432/{AG}/{NIA} {NIH} {HHS}/{NS}39581/{NS}/{NINDS} {NIH} {HHS}/P41:{RR}14075/{RR}/{NCRR} {NIH} {HHS}/{RR}14075/{RR}/{NCRR} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov'{tResearch} Support, U.S. Gov't, P.H.S.2005/05/27 09:00Neurobiol Aging. 2005 Aug-Sep;26(8):1215-27. Epub 2004 Dec 19.}
}

@article{panizzon_genetic_2012,
	title = {Genetic Influences on Hippocampal Volume Differ as a Function of Testosterone Level in Middle-Aged Men},
	volume = {59},
	issn = {1053-8119},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3230702/},
	doi = {10.1016/j.neuroimage.2011.09.044},
	abstract = {The hippocampus expresses a large number of androgen receptors; therefore, in men it is potentially vulnerable to the gradual age-related decline of testosterone levels. In the present study we sought to elucidate the nature of the relationship between testosterone and hippocampal volume in a sample of middle-aged male twins (average age 55.8 years). We found no evidence for a correlation between testosterone level and hippocampal volume, as well as no indication of shared genetic influences. However, a significant moderating effect of testosterone on the genetic and environmental determinants of hippocampal volume was observed. Genetic influences on hippocampal volume increased substantially as a function of increasing testosterone level, while environmental influences either decreased or remained stable. These findings provide evidence for an apparent gene-by-hormone interaction on hippocampal volume. To the best of our knowledge, this is the first study to demonstrate that the heritability of a brain structure in adults may be modified by an endogenous biological factor.},
	number = {2},
	urldate = {2014-08-25},
	journal = {{NeuroImage}},
	author = {Panizzon, Matthew S. and Hauger, Richard L. and Eaves, Lindon J. and Chen, Chi-Hua and Dale, Anders M. and Eyler, Lisa T. and Fischl, Bruce and Fennema-Notestine, Christine and Franz, Carol E. and Grant, Michael D. and Jacobson, Kristen C. and Jak, Amy J. and Lyons, Michael J. and Mendoza, Sally P. and Neale, Michael C. and Prom-Wormley, Elizabeth and Seidman, Larry J. and Tsuang, Ming T. and Xian, Hong and Kremen, William S.},
	month = jan,
	year = {2012},
	pmid = {21983185},
	pmcid = {PMC3230702},
	keywords = {Hippocampus/*anatomy \& histology/*physiology, Humans, Magnetic Resonance Imaging/methods, Male, Middle Aged, Organ Size/physiology, Testosterone/*blood, Twins/*genetics},
	pages = {1123--1131},
	annote = {Panizzon, Matthew {SHauger}, Richard {LEaves}, Lindon {JChen}, Chi-{HuaDale}, Anders {MEyler}, Lisa {TFischl}, {BruceFennema}-Notestine, {ChristineFranz}, Carol {EGrant}, Michael {DJacobson}, Kristen {CJak}, Amy {JLyons}, Michael {JMendoza}, Sally {PNeale}, Michael {CProm}-Wormley, {ElizabethSeidman}, Larry {JTsuang}, Ming {TXian}, {HongKremen}, William {SengR}01 {AG}018384-01A2/{AG}/{NIA} {NIH} {HHS}/R01 {AG}018386/{AG}/{NIA} {NIH} {HHS}/R01 {AG}018386-01A2/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022381/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022381-01/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022982/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022982-01A1/{AG}/{NIA} {NIH} {HHS}/R01 {AG}18384/{AG}/{NIA} {NIH} {HHS}/R01 {AG}18386/{AG}/{NIA} {NIH} {HHS}/R01 {AG}22381/{AG}/{NIA} {NIH} {HHS}/R01 {AG}22982/{AG}/{NIA} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov'{tResearch} Support, U.S. Gov't, Non-P.H.S.Twin Study2011/10/11 06:00Neuroimage. 2012 Jan 16;59(2):1123-31. doi: 10.1016/j.neuroimage.2011.09.044. Epub 2011 Oct 1.},
	file = {Panizzon-2012-Genetic influences on hippocampa:/autofs/cluster/freesurfer/zotero/storage/K4B3BJ9T/Panizzon-2012-Genetic influences on hippocampa.pdf:application/pdf;PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/DTQHA84E/Panizzon et al. - 2012 - Genetic Influences on Hippocampal Volume Differ as.pdf:application/pdf}
}

@article{rauch_magnetic_2004,
	title = {A magnetic resonance imaging study of cortical thickness in animal phobia},
	volume = {55},
	issn = {1873-2402 (Electronic) 0006-3223 (Linking)},
	shorttitle = {A magnetic resonance imaging study of cortical thickness in animal phobia},
	url = {http://www.nmr.mgh.harvard.edu/~fischl/reprints/rauch_2004_reprint.pdf},
	doi = {10.1016/j.biopsych.2003.12.022},
	abstract = {{BACKGROUND}: Despite the high prevalence of specific phobia ({SP}), its neural substrates remain undetermined. Although an initial series of functional neuroimaging studies have implicated paralimbic and sensory cortical regions in the pathophysiology of {SP}, to date contemporary morphometric neuroimaging methods have not been applied to test specific hypotheses regarding structural abnormalities. {METHODS}: Morphometric magnetic resonance imaging ({MRI}) methods were used to measure regional cortical thickness in 10 subjects with {SP} (animal type) and 20 healthy comparison ({HC}) subjects. {RESULTS}: Consistent with a priori hypotheses, between-group differences in cortical thickness were found within paralimbic and sensory cortical regions. Specifically, in comparison with the {HC} group, the {SP} group exhibited increased cortical thickness in bilateral insular, bilateral pregenual anterior cingulate, and bilateral posterior cingulate cortex as well as left visual cortical regions. {CONCLUSIONS}: Taken together, these structural findings parallel results from initial functional imaging studies that implicate paralimbic and sensory cortical regions in the mediating anatomy of {SP} symptoms. Further research will be necessary to replicate these findings and to determine their specificity as well as their pathophysiologic significance.},
	language = {eng},
	number = {9},
	journal = {Biol Psychiatry},
	author = {Rauch, S. L. and Wright, C. I. and Martis, B. and Busa, E. and McMullin, K. G. and Shin, L. M. and Dale, A. M. and Fischl, B.},
	month = may,
	year = {2004},
	keywords = {Adult, Adult, Animals, Animals, Cerebral Cortex, Cerebral Cortex/anatomy \& histology, Female, Female, Functional Laterality, Functional Laterality/physiology, Gyrus Cinguli, Gyrus Cinguli/anatomy \& histology, Humans, Humans, Limbic System, Limbic System/anatomy \& histology, *Magnetic Resonance Imaging, Magnetic Resonance Imaging, Male, Male, Phobic Disorders, Phobic Disorders/*diagnosis/epidemiology/*psychology, Prevalence, Prevalence, Somatosensory Cortex, Somatosensory Cortex/*anatomy \& histology},
	pages = {946--52},
	annote = {Rauch, Scott {LWright}, Christopher {IMartis}, {BrianBusa}, {EvelinaMcMullin}, Katherine {GShin}, Lisa {MDale}, Anders {MFischl}, {BruceengK}23 {MH}64806/{MH}/{NIMH} {NIH} {HHS}/P41RR14075/{RR}/{NCRR} {NIH} {HHS}/R01 {MH}60219/{MH}/{NIMH} {NIH} {HHS}/{RR}16594/{RR}/{NCRR} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov't2004/04/28 05:00Biol Psychiatry. 2004 May 1;55(9):946-52.}
}

@article{sereno_human_2006,
	title = {A human parietal face area contains aligned head-centered visual and tactile maps},
	volume = {9},
	copyright = {© 2006 Nature Publishing Group},
	issn = {1097-6256},
	url = {http://www.nature.com/neuro/journal/v9/n10/abs/nn1777.html},
	doi = {10.1038/nn1777},
	abstract = {Visually guided eating, biting and kissing, and avoiding objects moving toward the face and toward which the face moves require prompt, coordinated processing of spatial visual and somatosensory information in order to protect the face and the brain. Single-cell recordings in parietal cortex have identified multisensory neurons with spatially restricted, aligned visual and somatosensory receptive fields, but so far, there has been no evidence for a topographic map in this area. Here we mapped the organization of a multisensory parietal face area in humans by acquiring functional magnetic resonance images while varying the polar angle of facial air puffs and close-up visual stimuli. We found aligned maps of tactile and near-face visual stimuli at the highest level of human association cortex—namely, in the superior part of the postcentral sulcus. We show that this area may code the location of visual stimuli with respect to the face, not with respect to the retina.
*{NOTE}: In the version of this article initially published online, there was an error in the affiliation in the html version. The first affiliation should read Department of Cognitive Science, University of California San Diego, La Jolla, California 92093, {USA}. The error has been corrected online.},
	language = {en},
	number = {10},
	urldate = {2014-08-25},
	journal = {Nature Neuroscience},
	author = {Sereno, Martin I. and Huang, Ruey-Song},
	month = oct,
	year = {2006},
	pages = {1337--1343},
	file = {Snapshot:/autofs/cluster/freesurfer/zotero/storage/T7MP9FJH/nn1777.html:text/html}
}

@article{desikan_automated_2010,
	title = {Automated {MRI} measures predict progression to Alzheimer's disease},
	volume = {31},
	issn = {0197-4580},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2902697/},
	doi = {10.1016/j.neurobiolaging.2010.04.023},
	abstract = {The prediction of individuals with mild cognitive impairment ({MCI}) destined to develop Alzheimer's disease ({AD}) is of increasing clinical importance. In this study, using baseline T1-weighted {MRI} scans of 324 {MCI} individuals from two cohorts and automated software tools, we employed factor analyses and Cox proportional hazards models to identify a set of neuroanatomic measures that best predicted the time to progress from {MCI} to {AD}. For comparison, cerebrospinal fluid ({CSF}) assessments of cellular pathology and positron emission tomography ({PET}) measures of metabolic activity were additionally examined. By three years follow-up, 60 {MCI} individuals from the first cohort and 58 {MCI} individuals from the second cohort had progressed to a diagnosis of {AD}. Cox models on the first cohort demonstrated significant effects for the medial temporal factor [Hazards Ratio ({HR}) =0.43\{95\% Confidence Interval ({CI}), 0.32-0.55\}, p {\textless} 0.0001], the fronto-parietoccipital factor [{HR}=0.59\{95\% {CI}, 0.48-0.80\}, p {\textless} 0.001], and the lateral temporal factor [{HR}=0.67 \{95\% {CI}, 0.52-0.87\}, p {\textless} 0.01]. When applied to the second cohort, these Cox models showed significant effects for the medial temporal factor [{HR}=0.44 \{0.32-0.61\}, p {\textless} 0.001] and lateral temporal factor [{HR}=0.49 \{0.38-0.62\}, p {\textless} 0.001]. In a combined Cox model, consisting of individual {CSF}, {PET}, and {MRI} measures that best predicted disease progression, only the medial temporal factor [{HR}=0.53 \{95\% {CI}, 0.34-0.81\}, p {\textless} 0.001] demonstrated a significant effect. These findings illustrate that automated {MRI} measures of the medial temporal cortex accurately and reliably predict time to disease progression, outperform cellular and metabolic measures as predictors of clinical decline, and can potentially serve as a predictive marker for {AD}.},
	number = {8},
	urldate = {2014-08-25},
	journal = {Neurobiology of aging},
	author = {Desikan, Rahul S. and Cabral, Howard J. and Settecase, Fabio and Hess, Christopher P. and Dillon, William P. and Glastonbury, Christine M. and Weiner, Michael W. and Schmansky, Nicholas J. and Salat, David H. and Fischl, Bruce},
	month = aug,
	year = {2010},
	pmid = {20570399},
	pmcid = {PMC2902697},
	keywords = {Aged, Aged, 80 and over, Alzheimer Disease/cerebrospinal fluid/*pathology/psychology, Automation, Laboratory/methods, Cognition Disorders/cerebrospinal fluid/*pathology/psychology, Cohort Studies, *Disease Progression, Female, Follow-Up Studies, Humans, Longitudinal Studies, Magnetic Resonance Imaging/instrumentation/*methods, Male, Predictive Value of Tests, Prospective Studies},
	pages = {1364--1374},
	annote = {Desikan, Rahul {SCabral}, Howard {JSettecase}, {FabioHess}, Christopher {PDillon}, William {PGlastonbury}, Christine {MWeiner}, Michael {WSchmansky}, Nicholas {JSalat}, David {HFischl}, {BruceengAG}021910/{AG}/{NIA} {NIH} {HHS}/P01 {AG}03991/{AG}/{NIA} {NIH} {HHS}/P41 {RR}006009-150400/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-075751/{RR}/{NCRR} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/P50 {AG}05681/{AG}/{NIA} {NIH} {HHS}/R01 {EB}001550/{EB}/{NIBIB} {NIH} {HHS}/R01 {NR}010827/{NR}/{NINR} {NIH} {HHS}/R01 {RR} 16594-01A1/{RR}/{NCRR} {NIH} {HHS}/R01 {RR}016594-01A1/{RR}/{NCRR} {NIH} {HHS}/U01 {AG}024904/{AG}/{NIA} {NIH} {HHS}/U01 {AG}024904-01/{AG}/{NIA} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/Comparative {StudyMulticenter} {StudyResearch} Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov'{tResearch} Support, U.S. Gov't, P.H.S.2010/06/24 06:00Neurobiol Aging. 2010 Aug;31(8):1364-74. doi: 10.1016/j.neurobiolaging.2010.04.023. Epub 2010 Jun 8.},
	file = {Desikan-2010-Automated MRI measures predict pr:/autofs/cluster/freesurfer/zotero/storage/X8ISE695/Desikan-2010-Automated MRI measures predict pr.pdf:application/pdf;PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/VTBWGPC3/Desikan et al. - 2010 - Automated MRI measures predict progression to Alzh.pdf:application/pdf}
}

@article{kim_automatic_2012,
	title = {Automatic hippocampal segmentation in temporal lobe epilepsy: impact of developmental abnormalities},
	volume = {59},
	issn = {1095-9572},
	shorttitle = {Automatic hippocampal segmentation in temporal lobe epilepsy},
	doi = {10.1016/j.neuroimage.2011.11.040},
	abstract = {In drug-resistant temporal lobe epilepsy ({TLE}), detecting hippocampal atrophy on {MRI} is important as it allows defining the surgical target. The performance of automatic segmentation in {TLE} has so far been considered unsatisfactory. In addition to atrophy, about 40\% of patients present with developmental abnormalities (referred to as malrotation) characterized by atypical morphologies of the hippocampus and collateral sulcus. Our purpose was to evaluate the impact of malrotation and atrophy on the performance of three state-of-the-art automated algorithms. We segmented the hippocampus in 66 patients and 35 sex- and age-matched healthy subjects using a region-growing algorithm constrained by anatomical priors ({SACHA}), a freely available atlas-based software ({FreeSurfer}) and a multi-atlas approach ({ANIMAL}-multi). To quantify malrotation, we generated 3D models from manual hippocampal labels and automatically extracted collateral sulci. The accuracy of automated techniques was evaluated relative to manual labeling using the Dice similarity index and surface-based shape mapping, for which we computed vertex-wise displacement vectors between automated and manual segmentations. We then correlated segmentation accuracy with malrotation features and atrophy. {ANIMAL}-multi demonstrated similar accuracy in patients and healthy controls (p {\textgreater} 0.1), whereas {SACHA} and {FreeSurfer} were less accurate in patients (p {\textless} 0.05). Surface-based analysis of contour accuracy revealed that {SACHA} over-estimated the lateral border of malrotated hippocampi (r = 0.61; p {\textless} 0.0001), but performed well in the presence of atrophy ({\textbar}r {\textbar}{\textless} 0.34; p {\textgreater} 0.2). Conversely, {FreeSurfer} and {ANIMAL}-multi were affected by both malrotation ({FreeSurfer}: r = 0.57; p = 0.02, {ANIMAL}-multi: r = 0.50; p = 0.05) and atrophy ({FreeSurfer}: r = 0.78, p {\textless} 0.0001, {ANIMAL}-multi: r = 0.61; p {\textless} 0.0001). Compared to manual volumetry, automated procedures underestimated the magnitude of atrophy (Cohen's d: manual: 1.68; {ANIMAL}-multi: 1.11; {SACHA}: 1.10; {FreeSurfer}: 0.90, p {\textless} 0.0001). In addition, they tended to lateralize the seizure focus less accurately in the presence of malrotation (manual: 64\%; {ANIMAL}-multi: 55\%, p = 0.4; {SACHA}: 50\%, p = 0.1; {FreeSurfer}: 41\%, p = 0.05). Hippocampal developmental anomalies and atrophy had a negative impact on the segmentation performance of three state-of-the-art automated methods. These shape variants should be taken into account when designing segmentation algorithms.},
	language = {eng},
	number = {4},
	journal = {{NeuroImage}},
	author = {Kim, Hosung and Chupin, Marie and Colliot, Olivier and Bernhardt, Boris C. and Bernasconi, Neda and Bernasconi, Andrea},
	month = feb,
	year = {2012},
	pmid = {22155377},
	keywords = {Adolescent, Adult, Algorithms, Atrophy, Epilepsy, Temporal Lobe, Female, fs\_Validation-Evaluations, Hippocampus, Humans, Magnetic Resonance Imaging, Male, Models, Theoretical, Young Adult},
	pages = {3178--3186}
}

@article{pardoe_sodium_2013,
	title = {Sodium valproate use is associated with reduced parietal lobe thickness and brain volume},
	volume = {80},
	issn = {0028-3878},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3908352/},
	doi = {10.1212/WNL.0b013e318292a2e5},
	abstract = {Objective:
We hypothesized that total brain volume, white matter volume, and lobar cortical thickness would be different in epilepsy patients. We studied valproate relative to nonvalproate by using patients with epilepsy and healthy controls.

Methods:
Patients with focal intractable epilepsy from a tertiary epilepsy center were the primary group for analysis. A confirmatory analysis was carried out in an independent group of subjects imaged as part of a community-based study of childhood-onset epilepsy. Total brain volume; white matter volume; and frontal, parietal, occipital, and temporal lobe thickness were measured by processing whole-brain T1-weighted {MRI} using {FreeSurfer} 5.1.

Results:
Total brain volume, white matter volume, and parietal thickness were reduced in the valproate group relative to controls and nonvalproate users (valproate, n = 9; nonvalproate, n = 27; controls, n = 45; all male). These findings were confirmed in an independent group (valproate, n = 7; nonvalproate, n = 70; controls, n = 20; all male).

Conclusions:
Sodium valproate use in epilepsy is associated with parietal lobe thinning, reduced total brain volume, and reduced white matter volume.

Level of evidence:
This study provides Class {IV} evidence that use of valproate in epilepsy is associated with reduced parietal lobe thickness, total brain volume, and white matter volume.},
	number = {20},
	urldate = {2014-08-23},
	journal = {Neurology},
	author = {Pardoe, Heath R. and Berg, Anne T. and Jackson, Graeme D.},
	month = may,
	year = {2013},
	pmid = {23616155},
	pmcid = {PMC3908352},
	keywords = {Adult, Brain/drug effects/pathology, Cohort Studies, Epilepsy/*drug therapy/*pathology, Humans, Male, Middle Aged, Organ Size, Parietal Lobe/*drug effects/*pathology, Valproic Acid/adverse effects/*therapeutic use, Young Adult},
	pages = {1895--1900},
	annote = {Pardoe, Heath {RBerg}, Anne {TJackson}, Graeme {DengResearch} Support, Non-U.S. Gov't2013/04/26 06:00Neurology. 2013 May 14;80(20):1895-900. doi: 10.1212/{WNL}.0b013e318292a2e5. Epub 2013 Apr 24.},
	file = {Pardoe-2013-Sodium valproate use is associate1:/autofs/cluster/freesurfer/zotero/storage/CWRIHNQ5/Pardoe-2013-Sodium valproate use is associate1.pdf:application/pdf;PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/HXATQFK9/Pardoe et al. - 2013 - Sodium valproate use is associated with reduced pa.pdf:application/pdf}
}

@article{sabuncu_event_2014,
	title = {Event time analysis of longitudinal neuroimage data},
	volume = {97},
	issn = {1095-9572 (Electronic) 1053-8119 (Linking)},
	shorttitle = {Event time analysis of longitudinal neuroimage data},
	url = {http://www.sciencedirect.com/science/article/pii/S1053811914002705},
	doi = {10.1016/j.neuroimage.2014.04.015},
	abstract = {This paper presents a method for the statistical analysis of the associations between longitudinal neuroimaging measurements, e.g., of cortical thickness, and the timing of a clinical event of interest, e.g., disease onset. The proposed approach consists of two steps, the first of which employs a linear mixed effects ({LME}) model to capture temporal variation in serial imaging data. The second step utilizes the extended Cox regression model to examine the relationship between time-dependent imaging measurements and the timing of the event of interest. We demonstrate the proposed method both for the univariate analysis of image-derived biomarkers, e.g., the volume of a structure of interest, and the exploratory mass-univariate analysis of measurements contained in maps, such as cortical thickness and gray matter density. The mass-univariate method employs a recently developed spatial extension of the {LME} model. We applied our method to analyze structural measurements computed using {FreeSurfer}, a widely used brain Magnetic Resonance Image ({MRI}) analysis software package. We provide a quantitative and objective empirical evaluation of the statistical performance of the proposed method on longitudinal data from subjects suffering from Mild Cognitive Impairment ({MCI}) at baseline.},
	language = {en},
	urldate = {2014-08-21},
	journal = {Neuroimage},
	author = {Sabuncu, M. R. and Bernal-Rusiel, J. L. and Reuter, M. and Greve, D. N. and Fischl, B. and Alzheimer's Disease Neuroimaging, Initiative},
	month = aug,
	year = {2014},
	keywords = {fs\_Longitudinal-processing, longitudinal processing},
	pages = {9--18},
	annote = {Sabuncu, Mert {RBernal}-Rusiel, Jorge {LReuter}, {MartinGreve}, Douglas {NFischl}, Bruceeng1K25EB013649-01/{EB}/{NIBIB} {NIH} {HHS}/1R01NS070963/{NS}/{NINDS} {NIH} {HHS}/1R21NS072652-01/{NS}/{NINDS} {NIH} {HHS}/1S10RR019307/{RR}/{NCRR} {NIH} {HHS}/1S10RR023043/{RR}/{NCRR} {NIH} {HHS}/1S10RR023401/{RR}/{NCRR} {NIH} {HHS}/2R01NS042861-06A1/{NS}/{NINDS} {NIH} {HHS}/5P01NS058793-03/{NS}/{NINDS} {NIH} {HHS}/5R01AG008122-22/{AG}/{NIA} {NIH} {HHS}/5U01-{MH}093765/{MH}/{NIMH} {NIH} {HHS}/{AG}022381/{AG}/{NIA} {NIH} {HHS}/K25 {EB}013649/{EB}/{NIBIB} {NIH} {HHS}/P41 {EB}015896/{EB}/{NIBIB} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/P41EB015896/{EB}/{NIBIB} {NIH} {HHS}/R01 {EB}006758/{EB}/{NIBIB} {NIH} {HHS}/R01 {NS}052585-01/{NS}/{NINDS} {NIH} {HHS}/R01-{HD}071664/{HD}/{NICHD} {NIH} {HHS}/R01EB006758/{EB}/{NIBIB} {NIH} {HHS}/{RC}1 {AT}005728-01/{AT}/{NCCAM} {NIH} {HHS}/U01 {AG}024904/{AG}/{NIA} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov'{tResearch} Support, U.S. Gov't, P.H.S.2014/04/17 06:00Neuroimage. 2014 Aug 15;97:9-18. doi: 10.1016/j.neuroimage.2014.04.015. Epub 2014 Apr 13.}
}

@article{yeo_shape_2008,
	title = {Shape Analysis with Overcomplete Spherical Wavelets},
	volume = {11},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2720681/},
	abstract = {In this paper, we explore the use of over-complete spherical wavelets in shape analysis of closed 2D surfaces. Previous work has demonstrated, theoretically and practically, the advantages of over-complete over bi-orthogonal spherical wavelets. Here we present a detailed formulation of over-complete wavelets, as well as shape analysis experiments of cortical folding development using them. Our experiments verify in a quantitative fashion existing qualitative theories of neuro-anatomical development. Furthermore, the experiments reveal novel insights into neuro-anatomical development not previously documented.},
	number = {Pt 1},
	urldate = {2014-08-25},
	journal = {Medical image computing and computer-assisted intervention : {MICCAI} ... International Conference on Medical Image Computing and Computer-Assisted Intervention},
	author = {Yeo, B.T. Thomas and Yu, Peng and Grant, P. Ellen and Fischl, Bruce and Golland, Polina},
	year = {2008},
	pmid = {18979780},
	pmcid = {PMC2720681},
	pages = {468--476},
	file = {PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/WBDQV5PW/Yeo et al. - 2008 - Shape Analysis with Overcomplete Spherical Wavelet.pdf:application/pdf}
}

@article{pantazis_comparison_2010,
	title = {Comparison of landmark-based and automatic methods for cortical surface registration},
	volume = {49},
	issn = {1095-9572},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2818237/},
	doi = {10.1016/j.neuroimage.2009.09.027},
	abstract = {Group analysis of structure or function in cerebral cortex typically involves, as a first step, the alignment of cortices. A surface-based approach to this problem treats the cortex as a convoluted surface and coregisters across subjects so that cortical landmarks or features are aligned. This registration can be performed using curves representing sulcal fundi and gyral crowns to constrain the mapping. Alternatively, registration can be based on the alignment of curvature metrics computed over the entire cortical surface. The former approach typically involves some degree of user interaction in defining the sulcal and gyral landmarks while the latter methods can be completely automated. Here we introduce a cortical delineation protocol consisting of 26 consistent landmarks spanning the entire cortical surface. We then compare the performance of a landmark-based registration method that uses this protocol with that of two automatic methods implemented in the software packages {FreeSurfer} and {BrainVoyager}. We compare performance in terms of discrepancy maps between the different methods, the accuracy with which regions of interest are aligned, and the ability of the automated methods to correctly align standard cortical landmarks. Our results show similar performance for {ROIs} in the perisylvian region for the landmark-based method and {FreeSurfer}. However, the discrepancy maps showed larger variability between methods in occipital and frontal cortex and automated methods often produce misalignment of standard cortical landmarks. Consequently, selection of the registration approach should consider the importance of accurate sulcal alignment for the specific task for which coregistration is being performed. When automatic methods are used, the users should ensure that sulci in regions of interest in their studies are adequately aligned before proceeding with subsequent analysis.},
	language = {eng},
	number = {3},
	journal = {{NeuroImage}},
	author = {Pantazis, Dimitrios and Joshi, Anand and Jiang, Jintao and Shattuck, David W. and Bernstein, Lynne E. and Damasio, Hanna and Leahy, Richard M.},
	month = feb,
	year = {2010},
	pmid = {19796696},
	pmcid = {PMC2818237},
	keywords = {Adult, Brain Mapping, Cerebral Cortex, Female, fs\_Validation-Evaluations, Humans, Image Interpretation, Computer-Assisted, Magnetic Resonance Imaging, Male, Young Adult},
	pages = {2479--2493}
}

@article{dickerson_differential_2009,
	title = {Differential effects of aging and Alzheimer's disease on medial temporal lobe cortical thickness and surface area},
	volume = {30},
	issn = {1558-1497 (Electronic) 0197-4580 (Linking)},
	shorttitle = {Differential effects of aging and Alzheimer's disease on medial temporal lobe cortical thickness and surface area},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/17869384},
	doi = {10.1016/j.neurobiolaging.2007.07.022},
	abstract = {The volume of parcellated cortical regions is a composite measure related to both thickness and surface area. It is not clear whether volumetric decreases in medial temporal lobe ({MTL}) cortical regions in aging and Alzheimer's disease ({AD}) are due to thinning, loss of surface area, or both, nor is it clear whether aging and {AD} differ in their effects on these properties. Participants included 28 Younger Normals, 47 Older Normals, and 29 patients with mild {AD}. T1-weighted {MRI} data were analyzed using a novel semi-automated protocol (presented in a companion article) to delineate the boundaries of entorhinal ({ERC}), perirhinal ({PRC}), and posterior parahippocampal ({PPHC}) cortical regions and calculate their mean thickness, surface area, and volume. Compared to Younger Normals, Older Normals demonstrated moderately reduced {ERC} and {PPHC} volumes, which were due primarily to reduced surface area. In contrast, the expected {AD}-related reduction in {ERC} volume was produced by a large reduction in thickness with minimal additional effect (beyond that of aging) on surface area. {PRC} and {PPHC} also showed large {AD}-related reductions in thickness. Of all these {MTL} morphometric measures, {ERC} and {PRC} thinning were the best predictors of poorer episodic memory performance in {AD}. Although the volumes of {MTL} cortical regions may decrease with both aging and {AD}, thickness is relatively preserved in normal aging, while even in its mild clinical stage, {AD} is associated with a large degree of thinning of {MTL} cortex. These differential morphometric effects of aging and {AD} may reflect distinct biologic processes and ultimately may provide insights into the anatomic substrates of change in memory-related functions of {MTL} cortex.},
	language = {eng},
	number = {3},
	journal = {Neurobiol Aging},
	author = {Dickerson, B. C. and Feczko, E. and Augustinack, J. C. and Pacheco, J. and Morris, J. C. and Fischl, B. and Buckner, R. L.},
	month = mar,
	year = {2009},
	keywords = {Adolescent, Adult, Aged, Aged, 80 and over, Aging/*pathology, Alzheimer Disease/diagnosis/*pathology, Cerebral Cortex/pathology, Female, Humans, Male, Middle Aged, Surface Properties, Temporal Lobe/*pathology, Young Adult},
	pages = {432--40},
	annote = {Dickerson, Bradford {CFeczko}, {EricAugustinack}, Jean {CPacheco}, {JenniMorris}, John {CFischl}, {BruceBuckner}, Randy {LengK}23-{AG}22509/{AG}/{NIA} {NIH} {HHS}/P01-{AG}03991/{AG}/{NIA} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/P50-{AG}05681/{AG}/{NIA} {NIH} {HHS}/R01 {AG}029411/{AG}/{NIA} {NIH} {HHS}/R01 {EB}001550/{EB}/{NIBIB} {NIH} {HHS}/R01 {NS}052585-01/{NS}/{NINDS} {NIH} {HHS}/R01 {RR}16594-01A1/{RR}/{NCRR} {NIH} {HHS}/R21 {AG}029840/{AG}/{NIA} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/U24-{RR}021382/{RR}/{NCRR} {NIH} {HHS}/U54 {EB}005149/{EB}/{NIBIB} {NIH} {HHS}/Comparative {StudyResearch} Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov't2007/09/18 09:00Neurobiol Aging. 2009 Mar;30(3):432-40. Epub 2007 Sep 14.},
	file = {Dickerson-2009-Differential effects of aging a:/autofs/cluster/freesurfer/zotero/storage/AS5KRGA6/Dickerson-2009-Differential effects of aging a.pdf:application/pdf;PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/UKVPFT69/Dickerson et al. - 2009 - Differential effects of aging and Alzheimer's dise.pdf:application/pdf}
}

@article{catana_toward_2010,
	title = {Toward implementing an {MRI}-based {PET} attenuation-correction method for neurologic studies on the {MR}-{PET} brain prototype},
	volume = {51},
	issn = {1535-5667 (Electronic) 0161-5505 (Linking)},
	shorttitle = {Toward implementing an {MRI}-based {PET} attenuation-correction method for neurologic studies on the {MR}-{PET} brain prototype},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/20810759},
	doi = {10.2967/jnumed.109.069112},
	abstract = {Several factors have to be considered for implementing an accurate attenuation-correction ({AC}) method in a combined {MR}-{PET} scanner. In this work, some of these challenges were investigated, and an {AC} method based entirely on the {MRI} data obtained with a single dedicated sequence was developed and used for neurologic studies performed with the {MR}-{PET} human brain scanner prototype. {METHODS}: The focus was on the problem of bone-air segmentation, selection of the linear attenuation coefficient for bone, and positioning of the radiofrequency coil. The impact of these factors on {PET} data quantification was studied in simulations and experimental measurements performed on the combined {MR}-{PET} scanner. A novel dual-echo ultrashort echo time ({DUTE}) {MRI} sequence was proposed for head imaging. Simultaneous {MR}-{PET} data were acquired, and the {PET} images reconstructed using the proposed {DUTE} {MRI}-based {AC} method were compared with the {PET} images that had been reconstructed using a {CT}-based {AC} method. {RESULTS}: Our data suggest that incorrectly accounting for the bone tissue attenuation can lead to large underestimations ({\textgreater}20\%) of the radiotracer concentration in the cortex. Assigning a linear attenuation coefficient of 0.143 or 0.151 cm(-1) to bone tissue appears to give the best trade-off between bias and variability in the resulting images. Not identifying the internal air cavities introduces large overestimations ({\textgreater}20\%) in adjacent structures. On the basis of these results, the segmented {CT} {AC} method was established as the silver standard for the segmented {MRI}-based {AC} method. For an integrated {MR}-{PET} scanner, in particular, ignoring the radiofrequency coil attenuation can cause large underestimations (i.e., {\textless}or=50\%) in the reconstructed images. Furthermore, the coil location in the {PET} field of view has to be accurately known. High-quality bone-air segmentation can be performed using the {DUTE} data. The {PET} images obtained using the {DUTE} {MRI}- and {CT}-based {AC} methods compare favorably in most of the brain structures. {CONCLUSION}: A {DUTE} {MRI}-based {AC} method considering all these factors was implemented. Preliminary results suggest that this method could potentially be as accurate as the segmented {CT} method and could be used for quantitative neurologic {MR}-{PET} studies.},
	number = {9},
	journal = {J Nucl Med},
	author = {Catana, C. and van der Kouwe, A. and Benner, T. and Michel, C. J. and Hamm, M. and Fenchel, M. and Fischl, B. and Rosen, B. and Schmand, M. and Sorensen, A. G.},
	month = sep,
	year = {2010},
	keywords = {Adolescent, Adult, Aged, Aged, 80 and over, Bone and Bones/radionuclide imaging, Brain/*radionuclide imaging, Child, Female, Humans, Image Processing, Computer-Assisted/*methods, *Magnetic Resonance Imaging, Male, Middle Aged, Positron-Emission Tomography/*methods, Young Adult},
	pages = {1431--8},
	annote = {Catana, Ciprianvan der Kouwe, {AndreBenner}, {ThomasMichel}, Christian {JHamm}, {MichaelFenchel}, {MatthiasFischl}, {BruceRosen}, {BruceSchmand}, {MatthiasSorensen}, A Gregoryeng1R01CA137254-01A1/{CA}/{NCI} {NIH} {HHS}/R01 {CA}137254/{CA}/{NCI} {NIH} {HHS}/R01 {CA}137254-03/{CA}/{NCI} {NIH} {HHS}/Research Support, N.I.H., Extramural2010/09/03 06:00J Nucl Med. 2010 Sep;51(9):1431-8. doi: 10.2967/jnumed.109.069112.},
	file = {Catana-2010-Toward implementing an MRI-based P:/autofs/cluster/freesurfer/zotero/storage/HZH93PIN/Catana-2010-Toward implementing an MRI-based P.pdf:application/pdf}
}

@article{rosas_cerebral_2008,
	title = {Cerebral cortex and the clinical expression of Huntington's disease: complexity and heterogeneity},
	volume = {131},
	issn = {1460-2156 (Electronic) 0006-8950 (Linking)},
	shorttitle = {Cerebral cortex and the clinical expression of Huntington's disease},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/18337273},
	doi = {10.1093/brain/awn025},
	abstract = {The clinical phenotype of Huntington's disease ({HD}) is far more complex and variable than depictions of it as a progressive movement disorder dominated by neostriatal pathology represent. The availability of novel neuro-imaging methods has enabled us to evaluate cerebral cortical changes in {HD}, which we have found to occur early and to be topographically selective. What is less clear, however, is how these changes influence the clinical expression of the disease. In this study, we used a high-resolution surface based analysis of in vivo {MRI} data to measure cortical thickness in 33 individuals with {HD}, spanning the spectrum of disease and 22 age- and sex-matched controls. We found close relationships between specific functional and cognitive measures and topologically specific cortical regions. We also found that distinct motor phenotypes were associated with discrete patterns of cortical thinning. The selective topographical associations of cortical thinning with clinical features of {HD} suggest that we are not simply correlating global worsening with global cortical degeneration. Our results indicate that cortical involvement contributes to important symptoms, including those that have been ascribed primarily to the striatum, and that topologically selective changes in the cortex might explain much of the clinical heterogeneity found in {HD}. Additionally, a significant association between regional cortical thinning and total functional capacity, currently the leading primary outcome measure used in neuroprotection trials for {HD}, establishes cortical {MRI} morphometry as a potential biomarker of disease progression.},
	language = {en},
	number = {Pt 4},
	urldate = {2014-08-21},
	journal = {Brain},
	author = {Rosas, H. D. and Salat, D. H. and Lee, S. Y. and Zaleta, A. K. and Pappu, V. and Fischl, B. and Greve, D. and Hevelone, N. and Hersch, S. M.},
	month = apr,
	year = {2008},
	keywords = {Adult, Atrophy, Brain Mapping/methods, Cerebral Cortex/*pathology/physiopathology, Cognition Disorders/etiology/pathology, Disease Progression, Female, Humans, Huntington Disease/*pathology/physiopathology/psychology, Image Interpretation, Computer-Assisted/methods, Magnetic Resonance Imaging/methods, Male, Middle Aged, Models, Neurological, Neuropsychological Tests, Phenotype},
	pages = {1057--68},
	annote = {Rosas, H {DianaSalat}, David {HLee}, Stephanie {YZaleta}, Alexandra {KPappu}, {VasanthFischl}, {BruceGreve}, {DougHevelone}, {NathanaelHersch}, Steven {MengAG}024898/{AG}/{NIA} {NIH} {HHS}/{AT}000613/{AT}/{NCCAM} {NIH} {HHS}/{NS}042861/{NS}/{NINDS} {NIH} {HHS}/{NS}045242/{NS}/{NINDS} {NIH} {HHS}/P01 {NS}045242-05/{NS}/{NINDS} {NIH} {HHS}/P01 {NS}045242-050005/{NS}/{NINDS} {NIH} {HHS}/P01 {NS}058793-01A1/{NS}/{NINDS} {NIH} {HHS}/P01 {NS}058793-01A10004/{NS}/{NINDS} {NIH} {HHS}/P01 {NS}058793-01A19001/{NS}/{NINDS} {NIH} {HHS}/P01 {NS}058793-01A19002/{NS}/{NINDS} {NIH} {HHS}/P01NS058793/{NS}/{NINDS} {NIH} {HHS}/P01RR4075/{RR}/{NCRR} {NIH} {HHS}/R01 {AT}000613-05/{AT}/{NCCAM} {NIH} {HHS}/R16594/{PHS} {HHS}/{RR}4075/{RR}/{NCRR} {NIH} {HHS}/U01 {AT}000613-06A1/{AT}/{NCCAM} {NIH} {HHS}/U01 {AT}000613-07/{AT}/{NCCAM} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov'{tEngland}2008/03/14 09:00Brain. 2008 Apr;131(Pt 4):1057-68. doi: 10.1093/brain/awn025. Epub 2008 Mar 12.},
	file = {PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/C4SMQZ7U/Rosas et al. - 2008 - Cerebral cortex and the clinical expression of Hun.pdf:application/pdf;Rosas-2008-Cerebral cortex and the clinical ex:/autofs/cluster/freesurfer/zotero/storage/VMN85NH9/Rosas-2008-Cerebral cortex and the clinical ex.pdf:application/pdf}
}

@article{moore_segregation_2000,
	title = {Segregation of Somatosensory Activation in the Human Rolandic Cortex Using {fMRI}.},
	volume = {84},
	shorttitle = {Segregation of Somatosensory Activation in the Human Rolandic Cortex Using {fMRI}.},
	url = {http://jn.physiology.org/content/jn/84/1/558.full.pdf},
	journal = {Journal of Neurophysiology},
	author = {Moore, Christopher I. and Stern, Chantal E. and Corkin, Suzanne and Fischl, Bruce and Gray, Annette C. and Rosen, Bruce R. and M., Dale.Anders},
	year = {2000},
	pages = {558--569},
	file = {Moore-2000-Segregation of Somatosensory Activa:/autofs/cluster/freesurfer/zotero/storage/P3MPTVMT/Moore-2000-Segregation of Somatosensory Activa.pdf:application/pdf}
}

@article{postelnicu_combined_2009,
	title = {Combined volumetric and surface registration},
	volume = {28},
	issn = {1558-254X (Electronic) 0278-0062 (Linking)},
	shorttitle = {Combined volumetric and surface registration},
	url = {https://surfer.nmr.mgh.harvard.edu/pub/articles/Postelnicu-TMI2009.pdf},
	doi = {10.1109/TMI.2008.2004426},
	abstract = {In this paper, we propose a novel method for the registration of volumetric images of the brain that optimizes the alignment of both cortical and subcortical structures. In order to achieve this, relevant geometrical information is extracted from a surface-based morph and diffused into the volume using the Navier operator of elasticity, resulting in a volumetric warp that aligns cortical folding patterns. This warp field is then refined with an intensity driven optical flow procedure that registers noncortical regions, while preserving the cortical alignment. The result is a combined surface and volume morph ({CVS}) that accurately registers both cortical and subcortical regions, establishing a single coordinate system suitable for the entire brain.},
	number = {4},
	journal = {{IEEE} Trans Med Imaging},
	author = {Postelnicu, G. and Zollei, L. and Fischl, B.},
	month = apr,
	year = {2009},
	keywords = {*Algorithms, Brain/*anatomy \& histology, Databases, Factual, Elastic Modulus, fs\_CVS, Humans, Image Processing, Computer-Assisted/*methods, Magnetic Resonance Imaging/*methods, Poisson Distribution},
	pages = {508--22},
	annote = {Postelnicu, {GheorgheZollei}, {LillaFischl}, {BruceengP}41 {RR}014075-098602/{RR}/{NCRR} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 {AG}018386-09/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022381-01/{AG}/{NIA} {NIH} {HHS}/R01 {EB}006758-01A1/{EB}/{NIBIB} {NIH} {HHS}/R01 {NS}052585-01/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}052585-01A1/{NS}/{NINDS} {NIH} {HHS}/R01 {RR}016594-01A1/{RR}/{NCRR} {NIH} {HHS}/R01 {RR}16594-01A1/{RR}/{NCRR} {NIH} {HHS}/R01EB001550/{EB}/{NIBIB} {NIH} {HHS}/R01EB006758/{EB}/{NIBIB} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/U24 {RR}021382-01/{RR}/{NCRR} {NIH} {HHS}/U54 {EB}005149-05/{EB}/{NIBIB} {NIH} {HHS}/U54EB005149/{EB}/{NIBIB} {NIH} {HHS}/Research Support, N.I.H., Extramural2009/03/11 09:00IEEE Trans Med Imaging. 2009 Apr;28(4):508-22. doi: 10.1109/{TMI}.2008.2004426. Epub 2008 Aug 15.},
	file = {Postelnicu-2009-Combined volumetric and surfac:/autofs/cluster/freesurfer/zotero/storage/FSPFNRFB/Postelnicu-2009-Combined volumetric and surfac.pdf:application/pdf}
}

@article{schaer_congenital_2009,
	title = {Congenital heart disease affects local gyrification in 22q11.2 deletion syndrome},
	volume = {51},
	issn = {00121622, 14698749},
	url = {http://onlinelibrary.wiley.com/enhanced/doi/10.1111/j.1469-8749.2009.03281.x/},
	doi = {10.1111/j.1469-8749.2009.03281.x},
	language = {en},
	number = {9},
	urldate = {2014-08-24},
	journal = {Developmental Medicine \& Child Neurology},
	author = {Schaer, Marie and Glaser, Bronwyn and Cuadra, Meritxell Bach and Debbane, Martin and Thiran, Jean-Philippe and Eliez, Stephan},
	month = sep,
	year = {2009},
	keywords = {Adolescent, Adult, Case-Control Studies, Cerebral Cortex, Child, Cohort Studies, {DiGeorge} Syndrome, Female, Heart Defects, Congenital, Humans, Imaging, Three-Dimensional, Magnetic Resonance Imaging, Male, Organ Size, Young Adult},
	pages = {746--753},
	file = {Congenital heart disease affects local gyrification in 22q11.2 deletion syndrome - SCHAER - 2009 - Developmental Medicine & Child Neurology - Wiley Online Library:/autofs/cluster/freesurfer/zotero/storage/EH9VU5P7/j.1469-8749.2009.03281.html:text/html}
}

@article{lehmann_cortical_2011,
	title = {Cortical thickness and voxel-based morphometry in posterior cortical atrophy and typical Alzheimer's disease},
	volume = {32},
	issn = {1558-1497},
	doi = {10.1016/j.neurobiolaging.2009.08.017},
	abstract = {A significant minority of Alzheimer's disease patients present with posterior cortical atrophy ({PCA}). {PCA} is characterized by visuospatial and visuoperceptual deficits, and relatively preserved memory, whereas patients with typical Alzheimer's disease ({tAD}) mostly present with early episodic memory deficits. We used two unbiased image analysis techniques to assess atrophy patterns in 48 {PCA}, 30 {tAD}, and 50 healthy controls. {FreeSurfer} was used to measure cortical thickness, and volumetric grey matter differences were assessed using voxel-based morphometry ({VBM}). Both {PCA} and {tAD} showed widespread reductions compared with controls using both techniques. Direct comparison of {PCA} and {tAD} revealed thinner cortex predominantly in the right superior parietal lobe in the {PCA} group compared with {tAD}, whereas the {tAD} group showed thinning in the left entorhinal cortex compared with {PCA}. Similar results were obtained in the {VBM} analysis. These distinct patterns of atrophy may have diagnostic utility. In a clinical context, a relatively spared medial temporal lobe in the presence of posterior parietal atrophy may imply {PCA}, and should not discount {AD}.},
	language = {eng},
	number = {8},
	journal = {Neurobiology of Aging},
	author = {Lehmann, Manja and Crutch, Sebastian J. and Ridgway, Gerard R. and Ridha, Basil H. and Barnes, Josephine and Warrington, Elizabeth K. and Rossor, Martin N. and Fox, Nick C.},
	month = aug,
	year = {2011},
	pmid = {19781814},
	keywords = {Aged, Alzheimer Disease, Atrophy, Female, Humans, Magnetic Resonance Imaging, Male, Memory, Middle Aged, Occipital Lobe, Parietal Lobe, Visual Perception},
	pages = {1466--1476}
}

@article{merkley_short_2008,
	title = {{SHORT} {COMMUNICATION}: Diffuse Changes in Cortical Thickness in Pediatric Moderate-to-Severe Traumatic Brain Injury},
	volume = {25},
	issn = {0897-7151},
	shorttitle = {{SHORT} {COMMUNICATION}},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2747789/},
	doi = {10.1089/neu.2008.0615},
	abstract = {Generalized whole brain volume loss has been well documented in moderate-to-severe traumatic brain injury ({TBI}), as has diffuse cerebral atrophy based on magnetic resonance imaging ({MRI}) volumetric methods where white matter may be more selectively affected than gray matter. However, specific regional differences in gray matter thickness of the cortical mantle have not been previously examined. As such, cortical thickness was assessed using {FreeSurfer}® software to identify regions of significant gray matter cortical thinning in {MRI} scans of 16 young {TBI} subjects (age range, 9–16 years) compared to 16 demographically matched controls. Significant cortical thinning was observed globally in the {TBI} group compared to the cohort of typically developing children. Reduced cortical thickness was related to reported deficits in working memory. {TBI}-induced cortical thickness reductions are probably due to a combination of focal and diffuse effects and have implications for the neurobehavioral sequelae of {TBI}.},
	number = {11},
	urldate = {2014-08-23},
	journal = {Journal of Neurotrauma},
	author = {Merkley, Tricia L. and Bigler, Erin D. and Wilde, Elisabeth A. and McCauley, Stephen R. and Hunter, Jill V. and Levin, Harvey S.},
	month = nov,
	year = {2008},
	pmid = {19061377},
	pmcid = {PMC2747789},
	pages = {1343--1345},
	file = {PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/B9HSMDPZ/Merkley et al. - 2008 - SHORT COMMUNICATION Diffuse Changes in Cortical T.pdf:application/pdf}
}

@article{fischl_phase_2007,
	title = {Phase maps reveal cortical architecture},
	volume = {104},
	url = {http://www.pnas.org/content/104/28/11513.short},
	doi = {10.1073/pnas.0704515104},
	number = {28},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Fischl, Bruce and Wald, Lawrence L.},
	month = jul,
	year = {2007},
	keywords = {fs\_Misc-methodology},
	pages = {11513--11514}
}

@article{engvig_effects_2010,
	title = {Effects of memory training on cortical thickness in the elderly},
	volume = {52},
	issn = {1095-9572},
	doi = {10.1016/j.neuroimage.2010.05.041},
	abstract = {The brain's ability to alter its functional and structural architecture in response to experience and learning has been extensively studied. Mental stimulation might serve as a reserve mechanism in brain aging, but macrostructural brain changes in response to cognitive training have been demonstrated in young participants only. We examined the short-term effects of an intensive memory training program on cognition and brain structure in middle-aged and elderly healthy volunteers. The memory trainers completed an 8-week training regimen aimed at improving verbal source memory utilizing the Method of Loci ({MoL}), while control participants did not receive any intervention. Both the memory trainers and the controls underwent magnetic resonance imaging ({MRI}) scans and memory testing pre and post 8 weeks of training or no training, respectively. Cortical thickness was automatically measured across the cortical mantle, and data processing and statistical analyses were optimized for reliable detection of longitudinal changes. The results showed that memory training improved source memory performance. Memory trainers also showed regional increases in cortical thickness compared with controls. Furthermore, thickness change in the right fusiform and lateral orbitofrontal cortex correlated positively with improvement in source memory performance, suggesting a possible functional significance of the structural changes. These findings demonstrate that systematic mental exercise may induce short-term structural changes in the aging human brain, indicating structural brain plasticity in elderly. The present study included short-term assessments, and follow-up studies are needed in order to assess whether such training indeed alters the long-term structural trajectories.},
	language = {eng},
	number = {4},
	journal = {{NeuroImage}},
	author = {Engvig, Andreas and Fjell, Anders M. and Westlye, Lars T. and Moberget, Torgeir and Sundseth, Øyvind and Larsen, Vivi Agnete and Walhovd, Kristine B.},
	month = oct,
	year = {2010},
	pmid = {20580844},
	keywords = {Adult, Aged, Aging, Female, Humans, Magnetic Resonance Imaging, Memory, Middle Aged, Neuronal Plasticity, Temporal Lobe},
	pages = {1667--1676}
}

@article{pardoe_neurodevelopmental_2013,
	title = {A neurodevelopmental basis for {BECTS}: Evidence from structural {MRI}},
	volume = {105},
	issn = {0920-1211},
	shorttitle = {A neurodevelopmental basis for {BECTS}},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3669634/},
	doi = {10.1016/j.eplepsyres.2012.11.008},
	abstract = {Purpose
{BECTS} (benign epilepsy with centro-temporal spikes) is one of the most common childhood-onset epilepsy syndromes. We investigated quantitative evidence for brain morphological variation associated with {BECTS} to provide insights into the neuroanatomical basis of this disorder.

Methods
Three independent {BECTS} groups were imaged at different stages: (a) near onset (n = 16, mean age 9.3 ± 1.6 years), (b) {\textasciitilde}9 years after onset (n = 9, mean age 15.8 ± 2.3 years), and (c) {\textasciitilde}15 years after onset (n = 10, mean age 22.7 ± 2.7 years). Age-matched controls were imaged with each group. Whole brain T1-weighted {MRI} was acquired. Voxel-based morphometry (groups a–c) and cortical thickness analyses (groups b and c) were undertaken within each group and for the groups combined. The relationship between cortical morphology and age was investigated.

Key findings
The voxel-based morphometry analysis indicated increased bilateral grey matter volume in the superior frontal gyrus, insula and right inferior frontal gyrus regions in {BECTS}. The magnitude of the increase lessened with age of the cases. Cortical thickness analysis revealed thicker cortex in {BECTS} along middle and inferior frontal gyri bilaterally, left insula and bilateral supramarginal gyrus in the 9-year-after-onset group, that normalised with age. The rate of cortical thickness changes with age were greater in {BECTS} cases than in controls.

Significance
Increased cortical gray matter associated with {BECTS} was found. The decreasing magnitude of the effect with increasing age parallels the natural history of the disorder. The areas affected are consistent with neurocognitive dysfunction in {BECTS}.},
	number = {0},
	urldate = {2014-08-23},
	journal = {Epilepsy research},
	author = {Pardoe, Heath R. and Berg, Anne T. and Archer, John S. and Fulbright, Robert K. and Jackson, Graeme D.},
	month = jul,
	year = {2013},
	pmid = {23375559},
	pmcid = {PMC3669634},
	keywords = {Adolescent, Brain/*growth \& development, Case-Control Studies, Child, Cross-Sectional Studies, Epilepsy, Rolandic/*diagnosis/metabolism, Female, Humans, Magnetic Resonance Imaging/methods/*trends, Male, Young Adult},
	pages = {133--139},
	annote = {Pardoe, Heath {RBerg}, Anne {TArcher}, John {SFulbright}, Robert {KJackson}, Graeme {DengNS}-R37-31146/{NS}/{NINDS} {NIH} {HHS}/R37 {NS}031146/{NS}/{NINDS} {NIH} {HHS}/Multicenter {StudyResearch} Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov'{tNetherlands}2013/02/05 06:00Epilepsy Res. 2013 Jul;105(1-2):133-9. doi: 10.1016/j.eplepsyres.2012.11.008. Epub 2013 Jan 31.},
	file = {Pardoe-2013-A neurodevelopmental basis for BE1:/autofs/cluster/freesurfer/zotero/storage/FDZVIGCG/Pardoe-2013-A neurodevelopmental basis for BE1.pdf:application/pdf;PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/RH35JTRC/Pardoe et al. - 2013 - A neurodevelopmental basis for BECTS Evidence fro.pdf:application/pdf}
}

@article{shen_comparison_2010,
	title = {Comparison of manual and automated determination of hippocampal volumes in {MCI} and early {AD}},
	volume = {4},
	issn = {1931-7565 (Electronic) 1931-7557 (Linking)},
	shorttitle = {Comparison of manual and automated determination of hippocampal volumes in {MCI} and early {AD}},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/20454594},
	doi = {10.1007/s11682-010-9088-x},
	abstract = {{MRI}-based hippocampal volume analysis has been extensively employed given its potential as a biomarker for brain disorders such as Alzheimer's disease ({AD}), and accurate and efficient determination of hippocampal volumes from brain images is still a challenging issue. We compared an automated method, {FreeSurfer} (V4), with a published manual protocol for the determination of hippocampal volumes from T1-weighted {MRI} scans. Our study included {MRI} data from 125 older adult subjects: healthy controls with no significant cognitive complaints or deficits ({HC}, n=38), euthymic individuals with cognitive complaints ({CC}, n=39) but intact neuropsychological performance, and patients with amnestic mild cognitive impairment ({MCI}, n=37) or a clinical diagnosis of probable {AD} ({AD}, n=11). Pearson correlations and intraclass correlation coefficients ({ICCs}) were calculated to evaluate the relationship between results of the manual tracing and {FreeSurfer} methods and to estimate their agreement. Results indicated that these two methods derived highly correlated results with strong agreement. After controlling for the age, sex and intracranial volume in statistical group analysis, both the manual tracing and {FreeSurfer} methods yield similar patterns: both the {MCI} group and the {AD} group showed hippocampal volume reduction compared to both the {HC} group and the {CC} group, and the {HC} and {CC} groups did not differ. These comparisons suggest that {FreeSurfer} has the potential to be used in automated determination of hippocampal volumes for large-scale {MCI}/{AD}-related {MRI} studies, where manual methods are inefficient or not feasible.},
	language = {en},
	number = {1},
	urldate = {2014-08-21},
	journal = {Brain Imaging Behav},
	author = {Shen, L. and Saykin, A. J. and Kim, S. and Firpi, H. A. and West, J. D. and Risacher, S. L. and McDonald, B. C. and McHugh, T. L. and Wishart, H. A. and Flashman, L. A.},
	month = mar,
	year = {2010},
	keywords = {Aged, Alzheimer Disease/*pathology, *Automation, Cognition Disorders/*pathology, Cohort Studies, Disease Progression, Female, fs\_Validation-Evaluations, Functional Laterality, Hippocampus/*pathology, Humans, Image Processing, Computer-Assisted/*methods, Imaging, Three-Dimensional/methods, Linear Models, Magnetic Resonance Imaging/*methods, Male, Organ Size, Software, Time Factors},
	pages = {86--95},
	annote = {Shen, {LiSaykin}, Andrew {JKim}, {SungeunFirpi}, Hiram {AWest}, John {DRisacher}, Shannon {LMcDonald}, Brenna {CMcHugh}, Tara {LWishart}, Heather {AFlashman}, Laura {AengP}30 {AG}010133-18S1/{AG}/{NIA} {NIH} {HHS}/P30 {AG}10133/{AG}/{NIA} {NIH} {HHS}/R01 {AG}019771-01/{AG}/{NIA} {NIH} {HHS}/R01 {AG}19771/{AG}/{NIA} {NIH} {HHS}/R01 {CA}101318/{CA}/{NCI} {NIH} {HHS}/R01 {CA}101318-01A1/{CA}/{NCI} {NIH} {HHS}/R03 {EB}008674/{EB}/{NIBIB} {NIH} {HHS}/R03 {EB}008674-01/{EB}/{NIBIB} {NIH} {HHS}/R03 {EB}008674-01S1/{EB}/{NIBIB} {NIH} {HHS}/U54 {EB}005149/{EB}/{NIBIB} {NIH} {HHS}/U54 {EB}005149-01/{EB}/{NIBIB} {NIH} {HHS}/Comparative {StudyResearch} Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov't2010/05/11 06:00Brain Imaging Behav. 2010 Mar;4(1):86-95. doi: 10.1007/s11682-010-9088-x.},
	file = {Shen-2010-Comparison of manual and automated 1:/autofs/cluster/freesurfer/zotero/storage/X43JW6B8/Shen-2010-Comparison of manual and automated 1.pdf:application/pdf}
}

@article{salat_hippocampal_2011,
	title = {Hippocampal degeneration is associated with temporal and limbic gray matter/white matter tissue contrast in Alzheimer's disease},
	volume = {54},
	issn = {1095-9572 (Electronic) 1053-8119 (Linking)},
	shorttitle = {Hippocampal degeneration is associated with temporal and limbic gray matter/white matter tissue contrast in Alzheimer's disease},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/20965261},
	doi = {10.1016/j.neuroimage.2010.10.034},
	abstract = {Recent studies have demonstrated alterations in cortical gray to white matter tissue contrast with nondemented aging and in individuals with Alzheimer's disease ({AD}). However, little information exists about the clinical relevance of such changes. It is possible that changes in {MRI} tissue contrast occur via independent mechanisms from those traditionally used in the assessment of {AD} associated degeneration such as hippocampal degeneration measured by more traditional volumetric magnetic resonance imaging ({MRI}). We created cortical surface models of 95 cognitively healthy individuals and 98 individuals with {AD} to characterize changes in regional gray and white matter T1-weighted signal intensities in dementia and to evaluate how such measures related to classically described hippocampal and cortical atrophy. We found a reduction in gray matter to white matter tissue contrast throughout portions of medial and lateral temporal cortical regions as well as in anatomically associated regions including the posterior cingulate, precuneus, and medial frontal cortex. Decreases in tissue contrast were associated with hippocampal volume, however, the regional patterns of these associations differed for demented and nondemented individuals. In nondemented controls, lower hippocampal volume was associated with decreased gray/white matter tissue contrast globally across the cortical mantle. In contrast, in individuals with {AD}, selective associations were found between hippocampal volume and tissue contrast in temporal and limbic tissue. These results demonstrate that there are strong regional changes in neural tissue properties in {AD} which follow a spatial pattern including regions known to be affected from pathology studies. Such changes are associated with traditional imaging metrics of degeneration and may provide a unique biomarker of the tissue loss that occurs as a result of {AD}.},
	number = {3},
	journal = {Neuroimage},
	author = {Salat, D. H. and Chen, J. J. and van der Kouwe, A. J. and Greve, D. N. and Fischl, B. and Rosas, H. D.},
	month = feb,
	year = {2011},
	keywords = {Aged, Aged, 80 and over, Alzheimer Disease/cerebrospinal fluid/*pathology/psychology, Entorhinal Cortex/pathology, Female, Hippocampus/*pathology, Humans, Image Processing, Computer-Assisted, Limbic System/*pathology, Magnetic Resonance Imaging, Male, Middle Aged, Nerve Degeneration/*pathology, Nerve Fibers, Myelinated/pathology, Neuropsychological Tests, Parahippocampal Gyrus/pathology, Reproducibility of Results, Temporal Lobe/*pathology},
	pages = {1795--802},
	annote = {Salat, D {HChen}, J Jvan der Kouwe, A {JGreve}, D {NFischl}, {BRosas}, H {DengBIRN}002/{PHS} {HHS}/K01 {AG}024898-01A1/{AG}/{NIA} {NIH} {HHS}/K01 {AG}024898-02/{AG}/{NIA} {NIH} {HHS}/K01 {AG}024898-03/{AG}/{NIA} {NIH} {HHS}/K01 {AG}024898-03S1/{AG}/{NIA} {NIH} {HHS}/K01 {AG}024898-04/{AG}/{NIA} {NIH} {HHS}/K01 {AG}024898-05/{AG}/{NIA} {NIH} {HHS}/K01AG024898/{AG}/{NIA} {NIH} {HHS}/P01 {AG}003991-16/{AG}/{NIA} {NIH} {HHS}/P01 {AG}03991/{AG}/{NIA} {NIH} {HHS}/P41 {RR}014075-117867/{RR}/{NCRR} {NIH} {HHS}/P41RR14075/{RR}/{NCRR} {NIH} {HHS}/P50 {AG}005681-18/{AG}/{NIA} {NIH} {HHS}/P50 {AG}05681/{AG}/{NIA} {NIH} {HHS}/P50 {MH}071616/{MH}/{NIMH} {NIH} {HHS}/R01 {AG}021910/{AG}/{NIA} {NIH} {HHS}/R01 {EB}006758-02/{EB}/{NIBIB} {NIH} {HHS}/R01 {EB}006758-04/{EB}/{NIBIB} {NIH} {HHS}/R01 {MH}056584-02/{MH}/{NIMH} {NIH} {HHS}/R01 {MH}56584/{MH}/{NIMH} {NIH} {HHS}/R01 {NR}010827-01A1/{NR}/{NINR} {NIH} {HHS}/R01 {NR}010827-02/{NR}/{NINR} {NIH} {HHS}/R01 {NR}010827-03/{NR}/{NINR} {NIH} {HHS}/R01 {NR}010827-04/{NR}/{NINR} {NIH} {HHS}/R01 {NR}010827-04S1/{NR}/{NINR} {NIH} {HHS}/R01 {NR}010827-05/{NR}/{NINR} {NIH} {HHS}/R01 {NS}052585-02/{NS}/{NINDS} {NIH} {HHS}/R01EB001550/{EB}/{NIBIB} {NIH} {HHS}/R01EB006758/{EB}/{NIBIB} {NIH} {HHS}/R01NR010827/{NR}/{NINR} {NIH} {HHS}/R01NS052585/{NS}/{NINDS} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/U24 {RR}021382-01/{RR}/{NCRR} {NIH} {HHS}/U24RR021382/{RR}/{NCRR} {NIH} {HHS}/U54 {EB}005149-02/{EB}/{NIBIB} {NIH} {HHS}/U54 {EB}005149-050002/{EB}/{NIBIB} {NIH} {HHS}/U54EB005149/{EB}/{NIBIB} {NIH} {HHS}/Canadian Institutes of Health Research/{CanadaResearch} Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov't2010/10/23 06:00Neuroimage. 2011 Feb 1;54(3):1795-802. doi: 10.1016/j.neuroimage.2010.10.034. Epub 2010 Oct 18.},
	file = {Salat-2011-Hippocampal degeneration is associa:/autofs/cluster/freesurfer/zotero/storage/S4VR9SZ5/Salat-2011-Hippocampal degeneration is associa.pdf:application/pdf}
}

@article{rohrer_clinical_2011,
	title = {Clinical and neuroanatomical signatures of tissue pathology in frontotemporal lobar degeneration},
	volume = {134},
	issn = {0006-8950},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3170537/},
	doi = {10.1093/brain/awr198},
	abstract = {Relating clinical symptoms to neuroanatomical profiles of brain damage and ultimately to tissue pathology is a key challenge in the field of neurodegenerative disease and particularly relevant to the heterogeneous disorders that comprise the frontotemporal lobar degeneration spectrum. Here we present a retrospective analysis of clinical, neuropsychological and neuroimaging (volumetric and voxel-based morphometric) features in a pathologically ascertained cohort of 95 cases of frontotemporal lobar degeneration classified according to contemporary neuropathological criteria. Forty-eight cases (51\%) had {TDP}-43 pathology, 42 (44\%) had tau pathology and five (5\%) had fused-in-sarcoma pathology. Certain relatively specific clinicopathological associations were identified. Semantic dementia was predominantly associated with {TDP}-43 type C pathology; frontotemporal dementia and motoneuron disease with {TDP}-43 type B pathology; young-onset behavioural variant frontotemporal dementia with {FUS} pathology; and the progressive supranuclear palsy syndrome with progressive supranuclear palsy pathology. Progressive non-fluent aphasia was most commonly associated with tau pathology. However, the most common clinical syndrome (behavioural variant frontotemporal dementia) was pathologically heterogeneous; while pathologically proven Pick's disease and corticobasal degeneration were clinically heterogeneous, and {TDP}-43 type A pathology was associated with similar clinical features in cases with and without progranulin mutations. Volumetric magnetic resonance imaging, voxel-based morphometry and cluster analyses of the pathological groups here suggested a neuroanatomical framework underpinning this clinical and pathological diversity. Frontotemporal lobar degeneration-associated pathologies segregated based on their cerebral atrophy profiles, according to the following scheme: asymmetric, relatively localized (predominantly temporal lobe) atrophy ({TDP}-43 type C); relatively symmetric, relatively localized (predominantly temporal lobe) atrophy (microtubule-associated protein tau mutations); strongly asymmetric, distributed atrophy (Pick's disease); relatively symmetric, predominantly extratemporal atrophy (corticobasal degeneration, fused-in-sarcoma pathology). {TDP}-43 type A pathology was associated with substantial individual variation; however, within this group progranulin mutations were associated with strongly asymmetric, distributed hemispheric atrophy. We interpret the findings in terms of emerging network models of neurodegenerative disease: the neuroanatomical specificity of particular frontotemporal lobar degeneration pathologies may depend on an interaction of disease-specific and network-specific factors.},
	number = {9},
	urldate = {2014-08-25},
	journal = {Brain},
	author = {Rohrer, Jonathan D. and Lashley, Tammaryn and Schott, Jonathan M. and Warren, Jane E. and Mead, Simon and Isaacs, Adrian M. and Beck, Jonathan and Hardy, John and de Silva, Rohan and Warrington, Elizabeth and Troakes, Claire and Al-Sarraj, Safa and King, Andrew and Borroni, Barbara and Clarkson, Matthew J. and Ourselin, Sebastien and Holton, Janice L. and Fox, Nick C. and Revesz, Tamas and Rossor, Martin N. and Warren, Jason D.},
	month = sep,
	year = {2011},
	pmid = {21908872},
	pmcid = {PMC3170537},
	pages = {2565--2581},
	file = {PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/NMNKMGEB/Rohrer et al. - 2011 - Clinical and neuroanatomical signatures of tissue .pdf:application/pdf}
}

@article{bernal-rusiel_detection_2008,
	title = {Detection of focal changes in human cortical thickness: spherical wavelets versus Gaussian smoothing},
	volume = {41},
	issn = {1053-8119},
	shorttitle = {Detection of focal changes in human cortical thickness},
	doi = {10.1016/j.neuroimage.2008.03.022},
	abstract = {Subtle but progressive variations in human cortical thickness have been associated with the initial phases of prevalent neurological and psychiatric conditions. But slight changes in cortical thickness at preclinical stages are typically masked by effects of the Gaussian kernel smoothing on the cortical surface shape descriptors. Here we present the first study aimed at detecting changes in human cortical thickness maps by applying soft-thresholding to multiresolution spherical wavelet coefficients. In order to make Gaussian and wavelet smoothing methods comparable, the trade-off between sensitivity and specificity was optimized to detect simulated thickness changes in various cortical areas of healthy elderly subjects. Results revealed a better sensitivity-specificity trade-off when using wavelet-based methods as compared to Gaussian smoothing in both the whole neocortex (p{\textless}10(-7)) and cortical region-based statistical analyses (p{\textless}10(-9)), which was mainly due to the higher specificity obtained with the wavelet approach. The lower smoothing introduced by wavelets and their adaptive properties may account for the enhanced specificity and sensitivity when compared with Gaussian spatial filters. These results strongly support the use of spherical wavelet methods to detect subtle variations in cortical thickness maps, which may be crucial in better understanding the course of neuronal loss in normal aging and in finding early markers of cortical degeneration.},
	language = {eng},
	number = {4},
	journal = {{NeuroImage}},
	author = {Bernal-Rusiel, Jorge L. and Atienza, Mercedes and Cantero, Jose L.},
	month = jul,
	year = {2008},
	pmid = {18474434},
	keywords = {Aged, Aged, 80 and over, Aging, Algorithms, Analysis of Variance, Atrophy, Data Interpretation, Statistical, False Negative Reactions, False Positive Reactions, Female, Humans, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Male, Middle Aged, Neocortex, Neurons, Neuropsychological Tests, Normal Distribution, Pia Mater},
	pages = {1278--1292}
}

@article{augustinack_detection_2005,
	title = {Detection of entorhinal layer {II} using 7Tesla [corrected] magnetic resonance imaging},
	volume = {57},
	issn = {0364-5134 (Print) 0364-5134 (Linking)},
	shorttitle = {Detection of entorhinal layer {II} using 7Tesla [corrected] magnetic resonance imaging},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3857582/},
	doi = {10.1002/ana.20426},
	abstract = {The entorhinal cortex lies in the mediotemporal lobe and has major functional, structural, and clinical significance. The entorhinal cortex has a unique cytoarchitecture with large stellate neurons in layer {II} that form clusters. The entorhinal cortex receives vast sensory association input, and its major output arises from the layer {II} and {III} neurons that form the perforant pathway. Clinically, the neurons in layer {II} are affected with neurofibrillary tangles, one of the two pathological hallmarks of Alzheimer's disease. We describe detection of the entorhinal layer {II} islands using magnetic resonance imaging. We scanned human autopsied temporal lobe blocks in a 7T human scanner using a solenoid coil. In 70 and 100 microm isotropic data, the entorhinal islands were clearly visible throughout the anterior-posterior extent of entorhinal cortex. Layer {II} islands were prominent in both the magnetic resonance imaging and corresponding histological sections, showing similar size and shape in two types of data. Area borders and island location based on cytoarchitectural features in the mediotemporal lobe were robustly detected using the magnetic resonance images. Our ex vivo results could break ground for high-resolution in vivo scanning that could ultimately benefit early diagnosis and treatment of neurodegenerative disease.},
	language = {eng},
	number = {4},
	journal = {Ann Neurol},
	author = {Augustinack, J. C. and van der Kouwe, A. J. and Blackwell, M. L. and Salat, D. H. and Wiggins, C. J. and Frosch, M. P. and Wiggins, G. C. and Potthast, A. and Wald, L. L. and Fischl, B. R.},
	month = apr,
	year = {2005},
	keywords = {Entorhinal Cortex/*anatomy \& histology/*radiography, Female, Humans, *Magnetic Resonance Imaging/instrumentation, Male, Middle Aged},
	pages = {489--94},
	annote = {Augustinack, Jean Cvan der Kouwe, Andre J {WBlackwell}, Megan {LSalat}, David {HWiggins}, Christopher {JFrosch}, Matthew {PWiggins}, Graham {CPotthast}, {AndreasWald}, Lawrence {LFischl}, Bruce {RengK}01 {AG}028521/{AG}/{NIA} {NIH} {HHS}/P41 {EB}015896/{EB}/{NIBIB} {NIH} {HHS}/P41 {RR}006009/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075/{RR}/{NCRR} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 {EB}006758/{EB}/{NIBIB} {NIH} {HHS}/R01 {NS}052585/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}070963/{NS}/{NINDS} {NIH} {HHS}/R01 {RR}016594/{RR}/{NCRR} {NIH} {HHS}/R01 {RR}16594-01A1/{RR}/{NCRR} {NIH} {HHS}/R21 {NS}072652/{NS}/{NINDS} {NIH} {HHS}/S10 {RR}019307/{RR}/{NCRR} {NIH} {HHS}/S10 {RR}023401/{RR}/{NCRR} {NIH} {HHS}/U54 {EB}005149/{EB}/{NIBIB} {NIH} {HHS}/Comparative {StudyResearch} Support, U.S. Gov't, P.H.S.2005/03/24 09:00Ann Neurol. 2005 Apr;57(4):489-94.},
	file = {Augustinack-2005-Detection of entorhinal layer:/autofs/cluster/freesurfer/zotero/storage/XFFUGWQJ/Augustinack-2005-Detection of entorhinal layer.pdf:application/pdf;PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/I3SRPT6V/Augustinack et al. - 2005 - Detection of Entorhinal Layer II Using Tesla Magne.pdf:application/pdf}
}

@inproceedings{yendiki_anatomical_2009,
	title = {Anatomical Priors for Global Probabilistic Diffusion Tractography},
	shorttitle = {Anatomical Priors for Global Probabilistic Diffusion Tractography},
	author = {Yendiki, A. and Stevens, A. and Jbabdi, S. and Augustinack, J. and Salat, D. and Zollei, L. and Behrens, T. and Fischl, B.},
	year = {2009},
	keywords = {fs\_TRACULA},
	pages = {630--3}
}

@article{vuoksimaa_cognitive_2013,
	title = {Cognitive Reserve Moderates the Association Between Hippocampal Volume and Episodic Memory in Middle Age},
	volume = {51},
	issn = {0028-3932},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3660613/},
	doi = {10.1016/j.neuropsychologia.2013.02.022},
	abstract = {Cognitive reserve is hypothesized to help people withstand greater brain pathology without manifesting clinical symptoms, and may be regarded as a preventive factor of dementia. It is unclear whether the effect of cognitive reserve is evident only among the older adults or after conversion to dementia, or if it can also be seen earlier in life before the prominent effects of cognitive aging become apparent. While finding a main effect of cognitive reserve on cognitive outcome may be consistent with the reserve hypothesis, in our view, it is unnecessary to invoke the idea of reserve if only a main effect is present. Rather, it is the interaction between a measure of reserve and a brain measure on cognitive outcome that is key for confirming that the effects of brain pathology affect people differently according to their cognitive reserve. We studied whether general cognitive ability at an average age of 20 years, as a direct measure of cognitive reserve, moderates the association between hippocampal volume and episodic memory performance in 494 middle-aged men ages 51 to 60. Whereas there was no statistically significant direct relationship between hippocampal volume and episodic memory performance in middle age, we found a statistically significant interaction such that there was a positive association between hippocampal volume and episodic memory only among people with lower general cognitive ability at age 20, i.e., lower levels of cognitive reserve. Our results provide support for the hypothesis that cognitive reserve moderates the relationship between brain structure and cognition in middle age, well before the onset of dementia.},
	number = {6},
	urldate = {2014-08-25},
	journal = {Neuropsychologia},
	author = {Vuoksimaa, Eero and Panizzon, Matthew S. and Chen, Chi-Hua and Eyler, Lisa T. and Fennema-Notestine, Christine and Fiecas, Mark and Fischl, Bruce and Franz, Carol E. and Grant, Michael D. and Jak, Amy and Lyons, Michael J. and Neale, Michael C. and Thompson, Wesley K. and Tsuang, Ming T. and Xian, Hong and Dale, Anders M. and Kremen, William S.},
	month = may,
	year = {2013},
	pmid = {23499725},
	pmcid = {PMC3660613},
	pages = {1124--1131},
	file = {PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/3RGXMHAG/Vuoksimaa et al. - 2013 - Cognitive Reserve Moderates the Association Betwee.pdf:application/pdf}
}

@article{fischl_automatically_2004,
	title = {Automatically parcellating the human cerebral cortex},
	volume = {14},
	issn = {1047-3211 (Print) 1047-3211 (Linking)},
	shorttitle = {Automatically parcellating the human cerebral cortex},
	url = {https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl04-parcellation.pdf},
	abstract = {We present a technique for automatically assigning a neuroanatomical label to each location on a cortical surface model based on probabilistic information estimated from a manually labeled training set. This procedure incorporates both geometric information derived from the cortical model, and neuroanatomical convention, as found in the training set. The result is a complete labeling of cortical sulci and gyri. Examples are given from two different training sets generated using different neuroanatomical conventions, illustrating the flexibility of the algorithm. The technique is shown to be comparable in accuracy to manual labeling.},
	language = {eng},
	number = {1},
	journal = {Cereb Cortex},
	author = {Fischl, B. and van der Kouwe, A. and Destrieux, C. and Halgren, E. and Segonne, F. and Salat, D. H. and Busa, E. and Seidman, L. J. and Goldstein, J. and Kennedy, D. and Caviness, V. and Makris, N. and Rosen, B. and Dale, A. M.},
	month = jan,
	year = {2004},
	keywords = {Algorithms, Anisotropy, Artificial Intelligence, Bayes Theorem, Brain Mapping/*methods, Cerebral Cortex/anatomy \& histology/*physiology, fs\_Cortical-parcellation, Functional Laterality, Humans, Image Processing, Computer-Assisted/*methods, Markov Chains, Models, Neurological, Models, Statistical, Schizophrenia/pathology},
	pages = {11--22},
	annote = {Fischl, Brucevan der Kouwe, {AndreDestrieux}, {ChristopheHalgren}, {EricSegonne}, {FlorentSalat}, David {HBusa}, {EvelinaSeidman}, Larry {JGoldstein}, {JillKennedy}, {DavidCaviness}, {VerneMakris}, {NikosRosen}, {BruceDale}, Anders {MengMH} 56956/{MH}/{NIMH} {NIH} {HHS}/P41 {RR} 14075/{RR}/{NCRR} {NIH} {HHS}/R01 {NS} 34189/{NS}/{NINDS} {NIH} {HHS}/R01 {NS} 39581/{NS}/{NINDS} {NIH} {HHS}/R01 {RR} 13609/{RR}/{NCRR} {NIH} {HHS}/R01 {RR} 16594-01A1/{RR}/{NCRR} {NIH} {HHS}/Research Support, Non-U.S. Gov'{tResearch} Support, U.S. Gov't, P.H.S.New York, N.Y. : 19912003/12/05 05:00Cereb Cortex. 2004 Jan;14(1):11-22.},
	file = {Fischl-2004-Automatically parcellating the hum:/autofs/cluster/freesurfer/zotero/storage/4P2EBSGH/Fischl-2004-Automatically parcellating the hum.pdf:application/pdf}
}

@article{mcdonald_subcortical_2008,
	title = {Subcortical and Cerebellar Atrophy in Mesial Temporal Lobe Epilepsy Revealed by Automatic Segmentation},
	volume = {79},
	issn = {0920-1211},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2412955/},
	doi = {10.1016/j.eplepsyres.2008.01.006},
	abstract = {Purpose
To determine the validity and utility of using automated subcortical segmentation to identify atrophy of the hippocampus and other subcortical and cerebellar structures in patients with mesial temporal lobe epilepsy ({MTLE}).

Methods
Volumetric {MRIs} were obtained on 21 patients with {MTLE} (11 right, 10 left) and 21 age- and gender-matched healthy controls. Labeling of subcortical and cerebellar structures was accomplished using automated reconstruction software ({FreeSurfer}). Multivariate analysis of covariance ({MANCOVA}) was used to explore group differences in intracranial-normalized, age-adjusted volumes and structural asymmetries. Step-wise discriminant function analysis was used to identify the linear combination of volumes that optimized classification of individual subjects.

Results
Results revealed the expected reduction in hippocampal volume on the side ipsilateral to the seizure focus, as well as bilateral reductions in thalamic and cerebellar gray matter volume. Analysis of structural asymmetries revealed significant asymmetry in the hippocampus and putamen in patients compared to controls. Discriminant function analysis revealed that patients with right and left {MTLE} were best distinguished from one another using a combination of subcortical volumes that included the right and left hippocampus and left thalamus (91–100\% correct classification using cross-validation).

Discussion
Volumetric data obtained with automated segmentation of subcortical and cerebellar structures approximate data from previous studies based on manual tracings. Our data suggest that automated segmentation can provide a clinically useful means of evaluating the nature and extent of structural damage in patients with {MTLE} and may increase diagnostic classification of patients, especially when hippocampal atrophy is mild.},
	number = {2-3},
	urldate = {2014-08-25},
	journal = {Epilepsy research},
	author = {McDonald, Carrie R. and Hagler, Donald J. and Ahmadi, Mazyar E. and Tecoma, Evelyn and Iragui, Vicente and Dale, Anders M. and Halgren, Eric},
	month = may,
	year = {2008},
	pmid = {18359198},
	pmcid = {PMC2412955},
	pages = {130--138},
	file = {PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/APTKQK8K/McDonald et al. - 2008 - Subcortical and Cerebellar Atrophy in Mesial Tempo.pdf:application/pdf}
}

@article{fischl_predicting_2009,
	title = {Predicting the location of entorhinal cortex from {MRI}},
	volume = {47},
	issn = {1095-9572 (Electronic) 1053-8119 (Linking)},
	shorttitle = {Predicting the location of entorhinal cortex from {MRI}},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/19376238},
	doi = {10.1016/j.neuroimage.2009.04.033},
	abstract = {Entorhinal cortex ({EC}) is a medial temporal lobe area critical to memory formation and spatial navigation that is among the earliest parts of the brain affected by Alzheimer's disease ({AD}). Accurate localization of {EC} would thus greatly facilitate early detection and diagnosis of {AD}. In this study, we used ultra-high resolution ex vivo {MRI} to directly visualize the architectonic features that define {EC} rostrocaudally and mediolaterally, then applied surface-based registration techniques to quantify the variability of {EC} with respect to cortical geometry, and made predictions of its location on in vivo scans. The results indicate that {EC} can be localized quite accurately based on cortical folding patterns, within 3 mm in vivo, a significant step forward in our ability to detect the earliest effects of {AD} when clinical intervention is most likely to be effective.},
	number = {1},
	journal = {Neuroimage},
	author = {Fischl, B. and Stevens, A. A. and Rajendran, N. and Yeo, B. T. and Greve, D. N. and Van Leemput, K. and Polimeni, J. R. and Kakunoori, S. and Buckner, R. L. and Pacheco, J. and Salat, D. H. and Melcher, J. and Frosch, M. P. and Hyman, B. T. and Grant, P. E. and Rosen, B. R. and van der Kouwe, A. J. and Wiggins, G. C. and Wald, L. L. and Augustinack, J. C.},
	month = aug,
	year = {2009},
	keywords = {Adult, Aged, Aged, 80 and over, Alzheimer Disease/diagnosis/*pathology, Entorhinal Cortex/anatomy \& histology/*pathology, Female, Humans, Image Interpretation, Computer-Assisted/*methods, Magnetic Resonance Imaging/*methods, Male, Middle Aged, Photomicrography},
	pages = {8--17},
	annote = {Fischl, {BruceStevens}, Allison {ARajendran}, {NiranjiniYeo}, B T {ThomasGreve}, Douglas {NVan} Leemput, {KoenPolimeni}, Jonathan {RKakunoori}, {SitaBuckner}, Randy {LPacheco}, {JenniferSalat}, David {HMelcher}, {JenniferFrosch}, Matthew {PHyman}, Bradley {TGrant}, P {EllenRosen}, Bruce Rvan der Kouwe, Andre J {WWiggins}, Graham {CWald}, Lawrence {LAugustinack}, Jean {CengP}41 {RR}014075/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-03S1/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-03S2/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-04S1/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-10/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-105997/{RR}/{NCRR} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 {EB}001550/{EB}/{NIBIB} {NIH} {HHS}/R01 {EB}006758-01A1/{EB}/{NIBIB} {NIH} {HHS}/R01 {NS}052585-01/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}052585-01A1/{NS}/{NINDS} {NIH} {HHS}/R01EB006758/{EB}/{NIBIB} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/U24 {RR}021382-056792/{RR}/{NCRR} {NIH} {HHS}/U54 {EB}005149/{EB}/{NIBIB} {NIH} {HHS}/U54 {EB}005149-04/{EB}/{NIBIB} {NIH} {HHS}/Howard Hughes Medical Institute/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov't2009/04/21 09:00Neuroimage. 2009 Aug 1;47(1):8-17. doi: 10.1016/j.neuroimage.2009.04.033. Epub 2009 Apr 16.},
	file = {Fischl-2009-Predicting the location of entorhi:/autofs/cluster/freesurfer/zotero/storage/3RD8I4HG/Fischl-2009-Predicting the location of entorhi.pdf:application/pdf;PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/39K3RN7M/Fischl et al. - 2009 - Predicting the Location of Entorhinal Cortex from .pdf:application/pdf}
}

@article{tae_validation_2008,
	title = {Validation of hippocampal volumes measured using a manual method and two automated methods ({FreeSurfer} and {IBASPM}) in chronic major depressive disorder},
	volume = {50},
	issn = {1432-1920 (Electronic) 0028-3940 (Linking)},
	shorttitle = {Validation of hippocampal volumes measured using a manual method and two automated methods ({FreeSurfer} and {IBASPM}) in chronic major depressive disorder},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/18414838},
	doi = {10.1007/s00234-008-0383-9},
	abstract = {{INTRODUCTION}: To validate the usefulness of the packages available for automated hippocampal volumetry, we measured hippocampal volumes using one manual and two recently developed automated volumetric methods. {METHODS}: The study included T1-weighted magnetic resonance imaging ({MRI}) of 21 patients with chronic major depressive disorder ({MDD}) and 20 normal controls. Using coronal turbo field echo ({TFE}) {MRI} with a slice thickness of 1.3 mm, the hippocampal volumes were measured using three methods: manual volumetry, surface-based parcellation using {FreeSurfer}, and individual atlas-based volumetry using {IBASPM}. In addition, the intracranial cavity volume ({ICV}) was measured manually. {RESULTS}: The absolute left hippocampal volume of the patients with {MDD} measured using all three methods was significantly smaller than the left hippocampal volume of the normal controls (manual P = 0.029, {FreeSurfer} P = 0.035, {IBASPM} P = 0.018). After controlling for the {ICV}, except for the right hippocampal volume measured using {FreeSurfer}, both measured hippocampal volumes of the patients with {MDD} were significantly smaller than the measured hippocampal volumes of the normal controls (right manual P = 0.019, {IBASPM} P = 0.012; left manual P = 0.003, {FreeSurfer} P = 0.010, {IBASPM} P = 0.002),. In the intrarater reliability test, the intraclass correlation coefficients ({ICCs}) were all excellent (manual right 0.947, left 0.934; {FreeSurfer} right 1.000, left 1.000; {IBASPM} right 1.000, left 1.000). In the test of agreement between the volumetric methods, the {ICCs} were right 0.846 and left 0.848 (manual and {FreeSurfer}), and right 0.654 and left 0.717 (manual and {IBASPM}). {CONCLUSION}: The automated hippocampal volumetric methods showed good agreement with manual hippocampal volumetry, but the volume measured using {FreeSurfer} was 35\% larger and the agreement was questionable with {IBASPM}. Although the automated methods could detect hippocampal atrophy in the patients with {MDD}, the results indicate that manual hippocampal volumetry is still the gold standard, while the automated volumetric methods need to be improved.},
	language = {en},
	number = {7},
	urldate = {2014-08-21},
	journal = {Neuroradiology},
	author = {Tae, W. S. and Kim, S. S. and Lee, K. U. and Nam, E. C. and Kim, K. W.},
	month = jul,
	year = {2008},
	keywords = {Adult, Depressive Disorder, Major/*pathology, Female, fs\_Validation-Evaluations, Hippocampus/*pathology, Humans, *Image Interpretation, Computer-Assisted, *Imaging, Three-Dimensional, *Magnetic Resonance Imaging, Male, Middle Aged, Organ Size, Predictive Value of Tests, Reproducibility of Results, *Software Validation, Young Adult},
	pages = {569--81},
	annote = {Tae, Woo {SukKim}, Sam {SooLee}, Kang {UkNam}, Eui-{CheolKim}, Keun {WooengControlled} Clinical {TrialResearch} Support, Non-U.S. Gov'{tGermany}2008/04/17 09:00Neuroradiology. 2008 Jul;50(7):569-81. doi: 10.1007/s00234-008-0383-9. Epub 2008 Apr 15.}
}

@article{augustinack_entorhinal_2012,
	title = {Entorhinal verrucae correlate with surface geometry},
	volume = {3},
	issn = {2081-3856 2081-6936},
	shorttitle = {Entorhinal verrucae correlate with surface geometry},
	url = {https://surfer.nmr.mgh.harvard.edu/pub/articles/Augustinack_etal_TN_2012.pdf},
	doi = {10.2478/s13380-012-0019-8},
	language = {en},
	number = {2},
	urldate = {2014-08-21},
	journal = {Translational Neuroscience},
	author = {Augustinack, Jean C. and Huber, Kristen E. and Postelnicu, Gheorghe M. and Frosch, Matthew P. and Pienaar, Rudolph and Fischl, Bruce},
	month = jun,
	year = {2012},
	keywords = {fs\_Misc-methodology},
	pages = {123--131}
}

@inproceedings{yeo_spherical_2009,
	title = {Spherical Demons: Fast Surface Registration,},
	volume = {accepted},
	shorttitle = {Spherical Demons: Fast Surface Registration,},
	author = {Yeo, B.T. Thomas and Sabuncu, Mert and Vercauteren, Tom and Ayache, Nicholas and Fischl, Bruce and Golland, Polina},
	year = {2009}
}

@article{pardoe_hippocampal_2009,
	title = {Hippocampal volume assessment in temporal lobe epilepsy: How good is automated segmentation?},
	volume = {50},
	issn = {1528-1167},
	shorttitle = {Hippocampal volume assessment in temporal lobe epilepsy},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3053147/},
	doi = {10.1111/j.1528-1167.2009.02243.x},
	abstract = {{PURPOSE}: Quantitative measurement of hippocampal volume using structural magnetic resonance imaging ({MRI}) is a valuable tool for detection and lateralization of mesial temporal lobe epilepsy with hippocampal sclerosis ({mTLE}). We compare two automated hippocampal volume methodologies and manual hippocampal volumetry to determine which technique is most sensitive for the detection of hippocampal atrophy in {mTLE}.
{METHODS}: We acquired a three-dimensional (3D) volumetric sequence in 10 patients with left-lateralized {mTLE} and 10 age-matched controls. Hippocampal volumes were measured manually, and using the software packages Freesurfer and {FSL}-{FIRST}. The sensitivities of the techniques were compared by determining the effect size for average volume reduction in patients with {mTLE} compared to controls. The volumes and spatial overlap of the automated and manual segmentations were also compared.
{RESULTS}: Significant volume reduction in affected hippocampi in {mTLE} compared to controls was detected by manual hippocampal volume measurement (p {\textless} 0.01, effect size 33.2\%), Freesurfer (p {\textless} 0.01, effect size 20.8\%), and {FSL}-{FIRST} (p {\textless} 0.01, effect size 13.6\%) after correction for brain volume. Freesurfer correlated reasonably (r = 0.74, p {\textless} 0.01) with this manual segmentation and {FSL}-{FIRST} relatively poorly (r = 0.47, p {\textless} 0.01). The spatial overlap between manual and automated segmentation was reduced in affected hippocampi, suggesting the accuracy of automated segmentation is reduced in pathologic brains.
{DISCUSSION}: Expert manual hippocampal volumetry is more sensitive than both automated methods for the detection of hippocampal atrophy associated with {mTLE}. In our study Freesurfer was the most sensitive to hippocampal atrophy in {mTLE} and could be used if expert manual segmentation is not available.},
	language = {eng},
	number = {12},
	journal = {Epilepsia},
	author = {Pardoe, Heath R. and Pell, Gaby S. and Abbott, David F. and Jackson, Graeme D.},
	month = dec,
	year = {2009},
	pmid = {19682030},
	pmcid = {PMC3053147},
	keywords = {Adult, Atrophy, Brain, Brain Mapping, Epilepsy, Temporal Lobe, Female, fs\_Validation-Evaluations, Functional Laterality, Hippocampus, Humans, Image Enhancement, Image Interpretation, Computer-Assisted, Imaging, Three-Dimensional, Magnetic Resonance Imaging, Male, Sclerosis},
	pages = {2586--2592}
}

@article{ehrlich_comt_2010,
	title = {The {COMT} Val108/158Met Polymorphism and Medial Temporal Lobe Volumetry in Patients with Schizophrenia and Healthy Adults},
	volume = {53},
	issn = {1053-8119},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2888809/},
	doi = {10.1016/j.neuroimage.2009.12.046},
	abstract = {Abnormalities of the medial temporal lobe have been consistently demonstrated in schizophrenia. A common functional polymorphism, Val108/158Met, in the putative schizophrenia susceptibility gene, catechol-O-methyltransferase ({COMT}) has been shown to influence medial temporal lobe function. However, the effects of this polymorphism on volumes of medial temporal lobe structures, particularly in patients with schizophrenia, are less clear. Here we measured the effects of {COMT} Val108/158Met genotype on the volume of two regions within the medial temporal lobe, the amygdala and hippocampus, in patients with schizophrenia and healthy control subjects., We obtained {MRI} and genotype data for 98 schizophrenic patients and 114 matched controls. An automated atlas-based segmentation algorithm was used to generate volumetric measures of the amygdala and hippocampus. Regression analyses included {COMT} met allele load as an additive effect, and also controlled for age, intracranial volume, gender and acquisition site., Across patients and controls, each copy of the {COMT} met allele was associated on average with a 2.6\% increase in right amygdala volume, a 3.8\% increase in left amygdala volume and a 2.2\% increase in right hippocampus volume. There were no effects of {COMT} genotype on volumes of the whole brain and prefrontal regions., Therefore, the {COMT} Val108/158Met polymorphism was shown to influence medial temporal lobe volumes in a linear-additive manner, mirroring its effect on dopamine catabolism. Taken together with previous work, our data support a model in which lower {COMT} activity, and a resulting elevation in extracellular dopamine levels, stimulates growth of medial temporal lobe structures.},
	number = {3},
	urldate = {2014-08-25},
	journal = {{NeuroImage}},
	author = {Ehrlich, Stefan and Morrow, Eric M. and Roffman, Joshua L. and Wallace, Stuart R. and Naylor, Melissa and Bockholt, H. Jeremy and Lundquist, Antonia and Yendiki, Anastasia and Ho, Beng-Choon and White, Tonya and Manoach, Dara S. and Clark, Vincent P. and Calhoun, Vince D. and Gollub, Randy L. and Holt, Daphne J.},
	month = nov,
	year = {2010},
	pmid = {20026221},
	pmcid = {PMC2888809},
	pages = {992--1000},
	file = {PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/MBCME342/Ehrlich et al. - 2010 - The COMT Val108158Met Polymorphism and Medial Tem.pdf:application/pdf}
}

@inproceedings{benner_accuracy_2004,
	title = {Accuracy and Repeatability of Automatic Slice Positioning compared with Manual Slice Positioning},
	shorttitle = {Accuracy and Repeatability of Automatic Slice Positioning compared with Manual Slice Positioning},
	author = {Benner, T and Wisco, JJ and Van der Kouwe, A and Fischl, B and Sorensen, AG.},
	year = {2004}
}

@article{schaechter_enhanced_2008,
	title = {Enhanced Cortical Activation in the Contralesional Hemisphere of Chronic Stroke Patients in Response to Motor Skill Challenge},
	volume = {18},
	issn = {1047-3211, 1460-2199},
	url = {http://cercor.oxfordjournals.org/content/18/3/638},
	doi = {10.1093/cercor/bhm096},
	abstract = {The brain processes involved in the restoration of motor skill after hemiparetic stroke are not fully understood. The current study compared cortical activity in chronic stroke patients who successfully recovered hand motor skill and normal control subjects during performance of kinematically matched unskilled and skilled hand movements using functional magnetic resonance imaging. We found that cortical activation during performance of the unskilled movement was increased in the patients relative to controls in the contralesional primary sensorimotor cortex. Performance of the skilled movement elicited increased activation in the patients relative to controls in the contralesional primary sensorimotor cortex, ventral premotor cortex, supplementary motor area/cingulate, and occipitoparietal cortex. Further, the activation change in the contralesional occipitoparietal cortex was greater in the patients relative to controls with the increase in motor skill challenge. Kinematic differences, mirror movements, and residual motor deficits did not account for the enhanced activation in the contralesional cortices in the patients. These results suggest that activation in the contralesional cortical network was enhanced as a function of motor skill challenge in stroke patients with good motor recovery. The findings of the current study suggest that successful recovery of motor skill after hemiparetic stroke involves participation of the contralesional cortical network.},
	language = {en},
	number = {3},
	urldate = {2014-08-25},
	journal = {Cerebral Cortex},
	author = {Schaechter, Judith D. and Perdue, Katherine L.},
	month = mar,
	year = {2008},
	pmid = {17602141},
	keywords = {cerebral ischemia, functional recovery, motor tasks, {MRI}/{fMRI}, neuroplasticity},
	pages = {638--647},
	file = {Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/247JHRP2/Schaechter and Perdue - 2008 - Enhanced Cortical Activation in the Contralesional.pdf:application/pdf;Snapshot:/autofs/cluster/freesurfer/zotero/storage/B5DX8ZMI/638.html:text/html}
}

@article{cardinale_validation_2014,
	title = {Validation of {FreeSurfer}-Estimated Brain Cortical Thickness: Comparison with Histologic Measurements},
	issn = {1559-0089 (Electronic) 1539-2791 (Linking)},
	shorttitle = {Validation of {FreeSurfer}-Estimated Brain Cortical Thickness},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/24789776},
	doi = {10.1007/s12021-014-9229-2},
	abstract = {{FreeSurfer} software package automatically estimates the cerebral cortical thickness. Its use is widely accepted, albeit this tool was validated against histologic measurements in only two post-mortem isolated brain {MR} scans. Indeed, a comparison between histologic measurements and {FreeSurfer} estimation from in vivo data was never performed. At the "Claudio Munari" Center for Epilepsy and Parkinson Surgery we have included {FreeSurfer} in our presurgical workflow since 2008, mainly because the automatic reconstruction of the brain surface is useful for carefully planning the surgical resection. We therefore compared cortical thickness values obtained by the automatic software pipeline with manual histologic measurements performed on 27 histologic specimens resected from the corresponding brain regions of the same epileptic subjects. This method-comparison study, including Passing-Bablok regression and Bland-Altman plot analysis, showed a good agreement between {FreeSurfer} estimation and histologic measurements of cortical thickness. The mean cortical thickness values (+/-Standard Deviation) obtained with {FreeSurfer} and histologic measurements were 3.65 mm +/- 0.44 and 3.72 mm +/- 0.36, respectively (P value = 0.32). Our findings strengthen previous reports on cortical thickness changes as biomarkers of different neurological conditions.},
	language = {en},
	urldate = {2014-08-21},
	journal = {Neuroinformatics},
	author = {Cardinale, F. and Chinnici, G. and Bramerio, M. and Mai, R. and Sartori, I. and Cossu, M. and Lo Russo, G. and Castana, L. and Colombo, N. and Caborni, C. and De Momi, E. and Ferrigno, G.},
	month = may,
	year = {2014},
	keywords = {Bioinformatics, Bland-Altman, Computational Biology/Bioinformatics, Computer Appl. in Life Sciences, Cortical thickness, Epilepsy surgery, {FreeSurfer}, fs\_Validation-Evaluations, Histologic measurement, Neurology, Neurosciences, Passing–Bablok},
	pages = {1--8},
	annote = {Cardinale, {FrancescoChinnici}, {GiuseppaBramerio}, {ManuelaMai}, {RobertoSartori}, {IvanaCossu}, {MassimoLo} Russo, {GiorgioCastana}, {LauraColombo}, {NadiaCaborni}, {ChiaraDe} Momi, {ElenaFerrigno}, {GiancarloENG}2014/05/03 06:00Neuroinformatics. 2014 May 2.}
}

@article{walhovd_functional_2006,
	title = {The functional and structural significance of the frontal shift in the old/new {ERP} effect},
	volume = {1081},
	issn = {0006-8993},
	url = {https://surfer.nmr.mgh.harvard.edu/ftp/articles/walhovd2006a.pdf},
	doi = {10.1016/j.brainres.2006.01.076},
	abstract = {There is a lack of studies mapping electrophysiological event-related potentials ({ERPs}) to structural neuroanatomical characteristics. The aim of the present study was to integrate electrophysiological memory-related activity with cortical and hippocampal volume, as well as psychometric memory performance, in a life-span sample. More specifically, we wanted to investigate the functional significance of the often-observed frontal shift of {ERP} amplitude with increasing age and whether neuroanatomical characteristics can explain this shift. Sixty six healthy participants (20-78 years) went through a neuropsychological examination, {MRI} scans, and a visual recognition {ERP} task with verbal stimuli. The results showed that {ERPs} elicited in the recognition memory task (the old/new effect) correlated significantly with cortical volume, but not with hippocampal volume. Large cortex predicted more differentiated {ERP} activity and not just larger amplitude in general, implying more distinct and efficient retrieval. Furthermore, {ERP} amplitude, cortical volume, and hippocampal volume all predicted scores on a composite memory scale. All these relationship were dependent upon the common influence of age. Finally, the participants with the most anterior distribution of activity showed the poorest recognition memory performance. Neither cortical nor hippocampal volume were related to this frontal shift. It is concluded that the distribution of activity along the anterior-posterior axis in a memory paradigm may have functional but not neuroanatomical volumetric correlates. The functional correlates need not be restricted to the older age groups.},
	language = {eng},
	number = {1},
	journal = {Brain Research},
	author = {Walhovd, Kristine B. and Fjell, Anders M. and Reinvang, Ivar and Lundervold, Arvid and Fischl, Bruce and Quinn, Brian T. and Makris, Nikos and Dale, Anders M.},
	month = apr,
	year = {2006},
	pmid = {16542641},
	keywords = {Adult, Adult, Aged, Aged, Age Factors, Age Factors, *Brain Mapping, Brain Mapping, Evoked Potentials, Evoked Potentials/*physiology, Female, Female, Frontal Lobe, Frontal Lobe/anatomy \& histology/*physiology, Humans, Humans, Magnetic Resonance Imaging, Magnetic Resonance Imaging/methods, Male, Male, Middle Aged, Middle Aged, Models, Biological, Models, Biological, Neuropsychological Tests, Neuropsychological Tests/statistics \& numerical data, Photic Stimulation, Photic Stimulation/methods, Recognition (Psychology), Recognition (Psychology)/*physiology, Regression Analysis, Regression Analysis, Verbal Learning, Verbal Learning/physiology},
	pages = {156--170},
	annote = {Walhovd, Kristine {BFjell}, Anders {MReinvang}, {IvarLundervold}, {ArvidFischl}, {BruceQuinn}, Brian {TMakris}, {NikosDale}, Anders {MengP}41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01-{NS}39581/{NS}/{NINDS} {NIH} {HHS}/R01-{RR}13609/{RR}/{NCRR} {NIH} {HHS}/R01-{RR}16594/{RR}/{NCRR} {NIH} {HHS}/Comparative {StudyResearch} Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov'{tNetherlands}2006/03/18 09:00Brain Res. 2006 Apr 7;1081(1):156-70. Epub 2006 Mar 20.}
}

@article{dale_cortical_1999,
	title = {Cortical surface-based analysis. I. Segmentation and surface reconstruction},
	volume = {9},
	issn = {1053-8119 (Print) 1053-8119 (Linking)},
	shorttitle = {Cortical surface-based analysis. I. Segmentation and surface reconstruction},
	url = {https://surfer.nmr.mgh.harvard.edu/ftp/articles/dale99-recon1.pdf},
	doi = {10.1006/nimg.1998.0395},
	abstract = {Several properties of the cerebral cortex, including its columnar and laminar organization, as well as the topographic organization of cortical areas, can only be properly understood in the context of the intrinsic two-dimensional structure of the cortical surface. In order to study such cortical properties in humans, it is necessary to obtain an accurate and explicit representation of the cortical surface in individual subjects. Here we describe a set of automated procedures for obtaining accurate reconstructions of the cortical surface, which have been applied to data from more than 100 subjects, requiring little or no manual intervention. Automated routines for unfolding and flattening the cortical surface are described in a companion paper. These procedures allow for the routine use of cortical surface-based analysis and visualization methods in functional brain imaging.},
	number = {2},
	journal = {Neuroimage},
	author = {Dale, A. M. and Fischl, B. and Sereno, M. I.},
	month = feb,
	year = {1999},
	keywords = {Brain Mapping/instrumentation, Cerebral Cortex/*anatomy \& histology, fs\_Surface-reconstruction, Humans, Image Processing, Computer-Assisted/*instrumentation, Magnetic Resonance Imaging/*instrumentation, Reference Values, Software},
	pages = {179--94},
	annote = {Dale, A {MFischl}, {BSereno}, M Ieng1999/02/05Neuroimage. 1999 Feb;9(2):179-94.},
	file = {dale99-recon1.pdf:/autofs/cluster/freesurfer/zotero/storage/C93PKFJX/dale99-recon1.pdf:application/pdf}
}

@article{yeo_construction_2008,
	title = {On the construction of invertible filter banks on the 2-sphere.},
	volume = {17},
	url = {http://people.csail.mit.edu/ythomas/publications/2008IFB-TIP.pdf},
	doi = {10.1109/TIP.2007.915550},
	abstract = {The theories of signal sampling, filter banks, wavelets, and "overcomplete wavelets" are well established for the Euclidean spaces and are widely used in the processing and analysis of images. While recent advances have extended some filtering methods to spherical images, many key challenges remain. In this paper, we develop theoretical conditions for the invertibility of filter banks under continuous spherical convolution. Furthermore, we present an analogue of the Papoulis generalized sampling theorem on the 2-Sphere. We use the theoretical results to establish a general framework for the design of invertible filter banks on the sphere and demonstrate the approach with examples of self-invertible spherical wavelets and steerable pyramids. We conclude by examining the use of a  self-invertible spherical steerable pyramid in a denoising experiment and discussing the computational complexity of the filtering framework.},
	language = {eng},
	number = {3},
	journal = {{IEEE} transactions on image processing : a publication of the {IEEE} Signal Processing Society},
	author = {Yeo, Boon Thye Thomas and Ou, Wanmei and Golland, Polina},
	month = mar,
	year = {2008},
	pmid = {18270119},
	pmcid = {PMC2800042},
	keywords = {*Algorithms, fs\_Misc-methodology, Image Enhancement/*methods, Image Interpretation, Computer-Assisted/*methods, Imaging, Three-Dimensional/*methods, Reproducibility of Results, Sensitivity and Specificity, *Signal Processing, Computer-Assisted}
}

@article{jovicich_mri-derived_2009,
	title = {{MRI}-derived measurements of human subcortical, ventricular and intracranial brain volumes: Reliability effects of scan sessions, acquisition sequences, data analyses, scanner upgrade, scanner vendors and field strengths},
	volume = {46},
	issn = {1095-9572 (Electronic) 1053-8119 (Linking)},
	shorttitle = {{MRI}-derived measurements of human subcortical, ventricular and intracranial brain volumes: Reliability effects of scan sessions, acquisition sequences, data analyses, scanner upgrade, scanner vendors and field strengths},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/19233293},
	doi = {10.1016/j.neuroimage.2009.02.010},
	abstract = {Automated {MRI}-derived measurements of in-vivo human brain volumes provide novel insights into normal and abnormal neuroanatomy, but little is known about measurement reliability. Here we assess the impact of image acquisition variables (scan session, {MRI} sequence, scanner upgrade, vendor and field strengths), {FreeSurfer} segmentation pre-processing variables (image averaging, B1 field inhomogeneity correction) and segmentation analysis variables (probabilistic atlas) on resultant image segmentation volumes from older (n=15, mean age 69.5) and younger (both n=5, mean ages 34 and 36.5) healthy subjects. The variability between hippocampal, thalamic, caudate, putamen, lateral ventricular and total intracranial volume measures across sessions on the same scanner on different days is less than 4.3\% for the older group and less than 2.3\% for the younger group. Within-scanner measurements are remarkably reliable across scan sessions, being minimally affected by averaging of multiple acquisitions, B1 correction, acquisition sequence ({MPRAGE} vs. multi-echo-{FLASH}), major scanner upgrades (Sonata-Avanto, Trio-{TrioTIM}), and segmentation atlas ({MPRAGE} or multi-echo-{FLASH}). Volume measurements across platforms (Siemens Sonata vs. {GE} Signa) and field strengths (1.5 T vs. 3 T) result in a volume difference bias but with a comparable variance as that measured within-scanner, implying that multi-site studies may not necessarily require a much larger sample to detect a specific effect. These results suggest that volumes derived from automated segmentation of T1-weighted structural images are reliable measures within the same scanner platform, even after upgrades; however, combining data across platform and across field-strength introduces a bias that should be considered in the design of multi-site studies, such as clinical drug trials. The results derived from the young groups (scanner upgrade effects and B1 inhomogeneity correction effects) should be considered as preliminary and in need for further validation with a larger dataset.},
	number = {1},
	journal = {Neuroimage},
	author = {Jovicich, J. and Czanner, S. and Han, X. and Salat, D. and van der Kouwe, A. and Quinn, B. and Pacheco, J. and Albert, M. and Killiany, R. and Blacker, D. and Maguire, P. and Rosas, D. and Makris, N. and Gollub, R. and Dale, A. and Dickerson, B. C. and Fischl, B.},
	month = may,
	year = {2009},
	keywords = {Adult, Aged, Aged, 80 and over, Brain/*anatomy \& histology, Brain Mapping/instrumentation/methods, fs\_Misc-methodology, Humans, Image Interpretation, Computer-Assisted/*methods, Magnetic Resonance Imaging/*instrumentation/*methods, Multicenter Studies as Topic, Reproducibility of Results},
	pages = {177--92},
	annote = {Jovicich, {JorgeCzanner}, {SilvesterHan}, {XiaoSalat}, Davidvan der Kouwe, {AndreQuinn}, {BrianPacheco}, {JenniAlbert}, {MarilynKilliany}, {RonaldBlacker}, {DeborahMaguire}, {PaulRosas}, {DianaMakris}, {NikosGollub}, {RandyDale}, {AndersDickerson}, Bradford {CFischl}, {BruceengK}23 {AG}022509-01/{AG}/{NIA} {NIH} {HHS}/K23-{AG}22509/{AG}/{NIA} {NIH} {HHS}/P01 {AG}004953/{AG}/{NIA} {NIH} {HHS}/P01 {AG}004953-140004/{AG}/{NIA} {NIH} {HHS}/P01-{AG}04953/{AG}/{NIA} {NIH} {HHS}/P41 {RR}014075/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-04/{RR}/{NCRR} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 {AG}029411-02/{AG}/{NIA} {NIH} {HHS}/R01 {RR}016594-01A1/{RR}/{NCRR} {NIH} {HHS}/R01-{RR}16594-01A1/{RR}/{NCRR} {NIH} {HHS}/R21 {AG}029840-02/{AG}/{NIA} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/U24 {RR}021382-05/{RR}/{NCRR} {NIH} {HHS}/U24RR021382/{RR}/{NCRR} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov't2009/02/24 09:00Neuroimage. 2009 May 15;46(1):177-92. doi: 10.1016/j.neuroimage.2009.02.010. Epub 2009 Feb 20.},
	file = {Jovicich-2009-MRI-derived measurements of huma:/autofs/cluster/freesurfer/zotero/storage/CNIBFE7R/Jovicich-2009-MRI-derived measurements of huma.pdf:application/pdf}
}

@article{martinussen_segmental_2009,
	title = {Segmental brain volumes and cognitive and perceptual correlates in 15-year-old adolescents with low birth weight},
	volume = {155},
	issn = {1097-6833 (Electronic) 0022-3476 (Linking)},
	shorttitle = {Segmental brain volumes and cognitive and perceptual correlates in 15-year-old adolescents with low birth weight},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/19683725},
	doi = {10.1016/j.jpeds.2009.06.015},
	abstract = {{OBJECTIVE}: To determine whether preterm very low birth weight ({VLBW}) or term born small for gestational age ({SGA}) adolescents have reduced regional brain volumes. We also asked which perinatal factors are related to reduced brain volume in {VLBW} adolescents, which regional brain volumes are associated with cognitive and perceptual functioning, and if these differ between the groups. {STUDY} {DESIGN}: Fifty adolescent preterm {VLBW} ({\textless} or =1500 g) births and 49 term {SGA} births (birth weight {\textless}10th percentile) were compared with 57 normal-weight term births. An automated {MRI} segmentation technique was used. Cognitive and perceptual functions were evaluated by {WISC}-{III} and Visual Motor Integration ({VMI}) tests. {RESULTS}: The {VLBW} group had reduced volumes for thalamus and cerebellar white matter (P {\textless} .002). The {SGA} group had smaller total brains, and proportionally smaller regional brain volumes. Cerebellar white matter in the {VLBW}, hippocampus in the {SGA}, and cerebral cortical in the control group were volumes that significantly predicted cognitive and perceptual functions. {CONCLUSIONS}: We speculate that white matter injury may explain the impaired cognitive and perceptual functioning in the prematurely born, whereas hippocampal injury may be related to cognitive dysfunction in term {SGA} adolescents.},
	language = {Eng},
	number = {6},
	journal = {J Pediatr},
	author = {Martinussen, M. and Flanders, D. W. and Fischl, B. and Busa, E. and Lohaugen, G. C. and Skranes, J. and Vangberg, T. R. and Brubakk, A. M. and Haraldseth, O. and Dale, A. M.},
	month = dec,
	year = {2009},
	keywords = {Adolescent, Brain/*pathology, Case-Control Studies, Cognition/*physiology, Female, Humans, Infant, Newborn, Infant, Premature, Infant, Premature, Diseases/*pathology/*psychology, Infant, Small for Gestational Age, Infant, Very Low Birth Weight, Intelligence/*physiology, Magnetic Resonance Imaging, Male, Organ Size, Psychomotor Performance/*physiology, Risk Factors},
	pages = {848--853 e1},
	annote = {Martinussen, {MaritFlanders}, Dana {WFischl}, {BruceBusa}, {EvelinaLohaugen}, Gro {CSkranes}, {JonVangberg}, Torgil {RBrubakk}, Ann-{MariHaraldseth}, {OlavDale}, Anders {MengResearch} Support, Non-U.S. Gov't2009/08/18 09:00J Pediatr. 2009 Dec;155(6):848-853.e1. doi: 10.1016/j.jpeds.2009.06.015. Epub 2009 Aug 15.},
	file = {Martinussen-2009-Segmental brain volumes and c:/autofs/cluster/freesurfer/zotero/storage/C9WWIJ68/Martinussen-2009-Segmental brain volumes and c.pdf:application/pdf}
}

@article{sadananthan_skull_2010,
	title = {Skull stripping using graph cuts.},
	volume = {49},
	url = {https://surfer.nmr.mgh.harvard.edu/pub/articles/graphcuts_NI2010.pdf},
	doi = {10.1016/j.neuroimage.2009.08.050},
	abstract = {Removal of non-brain tissues, particularly dura, is an important step in enabling accurate measurement of brain structures. Many popular methods rely on iterative  surface deformation to fit the brain boundary and tend to leave residual dura. Similar to other approaches, the method proposed here uses intensity thresholding followed by removal of narrow connections to obtain a brain mask. However, instead of using morphological operations to remove narrow connections, a graph theoretic image segmentation technique was used to position cuts that isolate and remove dura. This approach performed well on both the standardized {IBSR} test data sets and empirically derived data. Compared to the Hybrid Watershed Algorithm ({HWA}; (Segonne et al., 2004)) the novel approach achieved an additional 10-30\% of dura removal without incurring further brain tissue erosion. The proposed method  is best used in conjunction with {HWA} as the errors produced by the two approaches often occur at different locations and cancel out when their masks are combined.  Our experiments indicate that this combination can substantially decrease and often fully avoid cortical surface overestimation in subsequent segmentation.},
	language = {eng},
	number = {1},
	journal = {{NeuroImage}},
	author = {Sadananthan, Suresh A. and Zheng, Weili and Chee, Michael W. L. and Zagorodnov, Vitali},
	month = jan,
	year = {2010},
	pmid = {19732839},
	keywords = {Algorithms, Brain/anatomy \& histology, Cerebrospinal Fluid, False Negative Reactions, False Positive Reactions, fs\_Misc-methodology, Functional Laterality/physiology, Humans, Image Processing, Computer-Assisted/*methods, Magnetic Resonance Imaging, Models, Neurological, Reproducibility of Results, Skull/*anatomy \& histology},
	pages = {225--239}
}

@article{fjell_minute_2009,
	title = {Minute effects of sex on the aging brain: a multisample magnetic resonance imaging study of healthy aging and Alzheimer's disease},
	volume = {29},
	issn = {1529-2401 (Electronic) 0270-6474 (Linking)},
	shorttitle = {Minute effects of sex on the aging brain: a multisample magnetic resonance imaging study of healthy aging and Alzheimer's disease},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/19587284},
	doi = {10.1523/JNEUROSCI.0115-09.2009},
	abstract = {Age is associated with substantial macrostructural brain changes. While some recent magnetic resonance imaging studies have reported larger age effects in men than women, others find no sex differences. As brain morphometry is a potentially important tool in diagnosis and monitoring of age-related neurological diseases, e.g., Alzheimer's disease ({AD}), it is important to know whether sex influences brain aging. We analyzed cross-sectional magnetic resonance scans from 1143 healthy participants from seven subsamples provided by four independent research groups. In addition, 96 patients with mild {AD} were included. Estimates of cortical thickness continuously across the brain surface, as well as volume of 17 subcortical structures, were obtained by use of automated segmentation tools ({FreeSurfer}). In the healthy participants, no differences in aging slopes between women and men were found in any part of the cortex. Pallidum corrected for intracranial volume showed slightly higher age correlations for men. The analyses were repeated in each of the seven subsamples, and the lack of age x sex interactions was largely replicated. Analyses of the {AD} sample showed no interactions between sex and age for any brain region. We conclude that sex has negligible effects on the age slope of brain volumes both in healthy participants and in {AD}.},
	language = {eng},
	number = {27},
	journal = {J Neurosci},
	author = {Fjell, A. M. and Westlye, L. T. and Amlien, I. and Espeseth, T. and Reinvang, I. and Raz, N. and Agartz, I. and Salat, D. H. and Greve, D. N. and Fischl, B. and Dale, A. M. and Walhovd, K. B.},
	month = jul,
	year = {2009},
	keywords = {Adolescent, Adult, Aged, Aged, 80 and over, Aging/pathology/*physiology, Alzheimer Disease/*metabolism/pathology, Brain/pathology/*physiology, Female, Humans, Magnetic Resonance Imaging/*methods, Male, Middle Aged, *Sex Characteristics, Young Adult},
	pages = {8774--83},
	annote = {Fjell, Anders {MWestlye}, Lars {TAmlien}, {IngeEspeseth}, {ThomasReinvang}, {IvarRaz}, {NaftaliAgartz}, {IngridSalat}, David {HGreve}, Doug {NFischl}, {BruceDale}, Anders {MWalhovd}, Kristine {BengP}01 {AG}003991-219005/{AG}/{NIA} {NIH} {HHS}/P01 {AG}003991-229005/{AG}/{NIA} {NIH} {HHS}/P01 {AG}003991-239005/{AG}/{NIA} {NIH} {HHS}/P01 {AG}003991-249005/{AG}/{NIA} {NIH} {HHS}/P01 {AG}003991-259005/{AG}/{NIA} {NIH} {HHS}/P01 {AG}03991/{AG}/{NIA} {NIH} {HHS}/P20 {MH}071616/{MH}/{NIMH} {NIH} {HHS}/P41 {RR}014075-075751/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-075752/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-075753/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-086765/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-086766/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-086767/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-098601/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-098602/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-098603/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-105995/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-105996/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-105997/{RR}/{NCRR} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/P50 {AG}005681-170029/{AG}/{NIA} {NIH} {HHS}/P50 {AG}005681-180029/{AG}/{NIA} {NIH} {HHS}/P50 {AG}005681-18S10029/{AG}/{NIA} {NIH} {HHS}/P50 {AG}005681-18S20029/{AG}/{NIA} {NIH} {HHS}/P50 {AG}005681-18S30029/{AG}/{NIA} {NIH} {HHS}/P50 {AG}005681-190029/{AG}/{NIA} {NIH} {HHS}/P50 {AG}005681-19S10029/{AG}/{NIA} {NIH} {HHS}/P50 {AG}005681-19S20029/{AG}/{NIA} {NIH} {HHS}/P50 {AG}05681/{AG}/{NIA} {NIH} {HHS}/R01 {AG}034556-03/{AG}/{NIA} {NIH} {HHS}/R01 {EB}001550/{EB}/{NIBIB} {NIH} {HHS}/R01 {EB}006758-01A1/{EB}/{NIBIB} {NIH} {HHS}/R01 {EB}006758-02/{EB}/{NIBIB} {NIH} {HHS}/R01 {EB}006758-03/{EB}/{NIBIB} {NIH} {HHS}/R01 {EB}006758-03S1/{EB}/{NIBIB} {NIH} {HHS}/R01 {NS}052585-01/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}052585-01A1/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}052585-02/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}052585-02S1/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}052585-03/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}052585-04/{NS}/{NINDS} {NIH} {HHS}/R01 {RR}016594-01A1/{RR}/{NCRR} {NIH} {HHS}/R01 {RR}016594-02/{RR}/{NCRR} {NIH} {HHS}/R01 {RR}016594-03/{RR}/{NCRR} {NIH} {HHS}/R01 {RR}016594-04/{RR}/{NCRR} {NIH} {HHS}/R01 {RR}16594-01A1/{RR}/{NCRR} {NIH} {HHS}/R01-{NS}39581/{NS}/{NINDS} {NIH} {HHS}/R01-{RR}13609/{RR}/{NCRR} {NIH} {HHS}/R01EB006758/{EB}/{NIBIB} {NIH} {HHS}/R37-{AG}11230/{AG}/{NIA} {NIH} {HHS}/{RR} 16594/{RR}/{NCRR} {NIH} {HHS}/{RR}14075/{RR}/{NCRR} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/U54 {EB}005149/{EB}/{NIBIB} {NIH} {HHS}/Howard Hughes Medical Institute/Comparative {StudyResearch} Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov't2009/07/10 09:00J Neurosci. 2009 Jul 8;29(27):8774-83. doi: 10.1523/{JNEUROSCI}.0115-09.2009.},
	file = {Fjell-2009-Minute effects of sex on the aging:/autofs/cluster/freesurfer/zotero/storage/XRN79MBU/Fjell-2009-Minute effects of sex on the aging.pdf:application/pdf}
}

@article{tisdall_volumetric_2011,
	title = {Volumetric Navigators ({vNavs}) for Prospective Motion Correction and Selective Reacquisition in Neuroanatomical {MRI}},
	volume = {in press},
	shorttitle = {Volumetric Navigators ({vNavs}) for Prospective Motion Correction and Selective Reacquisition in Neuroanatomical {MRI}},
	journal = {Magnetic Resonance in Medicine},
	author = {Tisdall, MD and Hess, AT and Reuter, M and Meintjes, EM and Fischl, B and van der Kouwe, AJW},
	year = {2011}
}

@article{zhang_decreased_2009,
	title = {Decreased gyrification in major depressive disorder},
	volume = {20},
	issn = {1473-558X},
	doi = {10.1097/WNR.0b013e3283249b34},
	abstract = {Structural and functional abnormalities have been extensively reported in major depressive disorder, but possible changes in cortical folding have not yet been explored in this disorder. This study investigated this issue in major depressive disorder using the local gyrification index. High-resolution magnetic resonance imaging was performed in 18 patients with first-episode major depressive disorder and 18 age-matched and sex-matched healthy individuals. The local gyrification index was applied to detect brain areas with abnormal cortical folding in major depressive disorder. Compared with healthy participants, patients with major depressive disorder showed significantly decreased local gyrification index in the bilateral mid-posterior cingulate, insula, and orbital frontal cortices, the left anterior cingulate cortex, and the right temporal operculum.},
	language = {eng},
	number = {4},
	journal = {Neuroreport},
	author = {Zhang, Yuanchao and Yu, Chunshui and Zhou, Yuan and Li, Kuncheng and Li, Chong and Jiang, Tianzi},
	month = mar,
	year = {2009},
	pmid = {19218876},
	keywords = {Adult, Cerebral Cortex, Depressive Disorder, Major, Female, Humans, Imaging, Three-Dimensional, Magnetic Resonance Imaging, Male},
	pages = {378--380}
}

@article{zhang_reduced_2010,
	title = {Reduced Cortical Folding in Mental Retardation},
	volume = {31},
	issn = {0195-6108, 1936-959X},
	url = {http://www.ajnr.org/content/31/6/1063},
	doi = {10.3174/ajnr.A1984},
	abstract = {{BACKGROUND} {AND} {PURPOSE}: {MR} is a developmental disorder associated with impaired cognitive functioning and deficits in adaptive behavior. With a 2D region of interest−based {GI}, a preliminary study reported significantly reduced gyrification in the prefrontal lobe in {MR}. The purpose of this study was to further investigate the abnormalities of cortical gyrification in {MR} and to explore the possible causes of these abnormalities.
{MATERIALS} {AND} {METHODS}: Thirteen patients with {MR} and 26 demographically matched healthy controls were included in this study. A 3D surface-based {lGI} was calculated as a measure to quantify gyrification. Then vertex-by-vertex contrasts of {lGI} were performed between patients with {MR} and healthy controls.
{RESULTS}: Statistical analysis showed that patients with {MR} had significantly reduced {lGI} in multiple brain regions compared with healthy controls. These regions include the lateral and medial prefrontal cortices, the right superior temporal gyrus, the left superior parietal lobe, the bilateral insular and adjacent cortices, and the visual and motor cortices.
{CONCLUSIONS}: The observed abnormal pattern of cortical gyrification revealed by significant reduction of {lGI} in multiple brain regions might reflect the developmental disturbance in intracortical organization and cortical connectivities in {MR}.},
	language = {en},
	number = {6},
	urldate = {2014-08-24},
	journal = {American Journal of Neuroradiology},
	author = {Zhang, Y. and Zhou, Y. and Yu, C. and Lin, L. and Li, C. and Jiang, T.},
	month = jun,
	year = {2010},
	pmid = {20075096},
	pages = {1063--1067},
	file = {Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/7MRAKIGJ/Zhang et al. - 2010 - Reduced Cortical Folding in Mental Retardation.pdf:application/pdf;Snapshot:/autofs/cluster/freesurfer/zotero/storage/C4GNGCJP/1063.html:text/html}
}

@article{vuoksimaa_genetic_2014,
	title = {The Genetic Association Between Neocortical Volume and General Cognitive Ability Is Driven by Global Surface Area Rather Than Thickness},
	issn = {1047-3211, 1460-2199},
	url = {http://cercor.oxfordjournals.org/content/early/2014/02/18/cercor.bhu018},
	doi = {10.1093/cercor/bhu018},
	abstract = {Total gray matter volume is associated with general cognitive ability ({GCA}), an association mediated by genetic factors. It is expectable that total neocortical volume should be similarly associated with {GCA}. Neocortical volume is the product of thickness and surface area, but global thickness and surface area are unrelated phenotypically and genetically in humans. The nature of the genetic association between {GCA} and either of these 2 cortical dimensions has not been examined. Humans possess greater cognitive capacity than other species, and surface area increases appear to be the primary driver of the increased size of the human cortex. Thus, we expected neocortical surface area to be more strongly associated with cognition than thickness. Using multivariate genetic analysis in 515 middle-aged twins, we demonstrated that both the phenotypic and genetic associations between neocortical volume and {GCA} are driven primarily by surface area rather than thickness. Results were generally similar for each of 4 specific cognitive abilities that comprised the {GCA} measure. Our results suggest that emphasis on neocortical surface area, rather than thickness, could be more fruitful for elucidating neocortical–{GCA} associations and identifying specific genes underlying those associations.},
	language = {en},
	urldate = {2014-08-24},
	journal = {Cerebral Cortex},
	author = {Vuoksimaa, Eero and Panizzon, Matthew S. and Chen, Chi-Hua and Fiecas, Mark and Eyler, Lisa T. and Fennema-Notestine, Christine and Hagler, Donald J. and Fischl, Bruce and Franz, Carol E. and Jak, Amy and Lyons, Michael J. and Neale, Michael C. and Rinker, Daniel A. and Thompson, Wesley K. and Tsuang, Ming T. and Dale, Anders M. and Kremen, William S.},
	month = feb,
	year = {2014},
	pmid = {24554725},
	keywords = {Cognition, cortex, genetic correlation, heritability, twins},
	pages = {bhu018},
	annote = {Vuoksimaa, {EeroPanizzon}, Matthew {SChen}, Chi-{HuaFiecas}, {MarkEyler}, Lisa {TFennema}-Notestine, {ChristineHagler}, Donald {JFischl}, {BruceFranz}, Carol {EJak}, {AmyLyons}, Michael {JNeale}, Michael {CRinker}, Daniel {AThompson}, Wesley {KTsuang}, Ming {TDale}, Anders {MKremen}, William {SENGNew} York, N.Y. : 19912014/02/21 06:00Cereb Cortex. 2014 Feb 18.},
	file = {Snapshot:/autofs/cluster/freesurfer/zotero/storage/7XHF2B8I/cercor.html:text/html}
}

@article{augustinack_entorhinal_2012-1,
	title = {Entorhinal verrucae geometry is coincident and correlates with Alzheimer's lesions: a combined neuropathology and high-resolution ex vivo {MRI} analysis},
	volume = {123},
	shorttitle = {Entorhinal verrucae geometry is coincident and correlates with Alzheimer's lesions: a combined neuropathology and high-resolution ex vivo {MRI} analysis},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3278990/pdf/nihms-351865.pdf},
	number = {1},
	journal = {Acta Neuropathol},
	author = {Augustinack, JC and Huber, KE and Postelnicu, GM and Kakunoori, S and Wang, R and van der Kouwe, AJ and Wald, LL and Stein, TD and Frosch, MP and Fischl, B.},
	year = {2012},
	keywords = {fs\_Misc-methodology},
	pages = {85--96},
	file = {Augustinack-2012-Entorhinal verrucae geometry:/autofs/cluster/freesurfer/zotero/storage/JHGWARC8/Augustinack-2012-Entorhinal verrucae geometry.pdf:application/pdf}
}

@article{dewey_reliability_2010,
	title = {Reliability and validity of {MRI}-based automated volumetry software relative to auto-assisted manual measurement of subcortical structures in {HIV}-infected patients from a multisite study},
	volume = {51},
	issn = {1095-9572},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2884380/},
	doi = {10.1016/j.neuroimage.2010.03.033},
	abstract = {The automated volumetric output of {FreeSurfer} and Individual Brain Atlases using Statistical Parametric Mapping ({IBASPM}), two widely used and well published software packages, was examined for accuracy and consistency relative to auto-assisted manual ({AAM}) tracings (i.e., manual correction of automated output) when measuring the caudate, putamen, amygdala, and hippocampus in the baseline scans of 120 {HIV}-infected patients (86.7\% male, 47.3+/-6.3y.o., mean {HIV} duration 12.0+/-6.3years) from the {NIH}-funded {HIV} Neuroimaging Consortium ({HIVNC}) cohort. The data was examined for accuracy and consistency relative to auto-assisted manual tracing, and construct validity was assessed by correlating automated and {AAM} volumetric measures with relevant clinical measures of {HIV} progression. When results were averaged across all patients in the eight structures examined, {FreeSurfer} achieved lower absolute volume difference in five, higher sensitivity in seven, and higher spatial overlap in all eight structures. Additionally, {FreeSurfer} results exhibited less variability in all measures. Output from both methods identified discrepant correlations with clinical measures of {HIV} progression relative to {AAM} segmented data. Overall, {FreeSurfer} proved more effective in the context of subcortical volumetry in {HIV}-patients, particularly in a multisite cohort study such as this. These findings emphasize that regardless of the automated method used, visual inspection of segmentation output, along with manual correction if necessary, remains critical to ensuring the validity of reported results.},
	language = {eng},
	number = {4},
	journal = {{NeuroImage}},
	author = {Dewey, Jeffrey and Hana, George and Russell, Troy and Price, Jared and McCaffrey, Daniel and Harezlak, Jaroslaw and Sem, Ekta and Anyanwu, Joy C. and Guttmann, Charles R. and Navia, Bradford and Cohen, Ronald and Tate, David F. and {HIV Neuroimaging Consortium}},
	month = jul,
	year = {2010},
	pmid = {20338250},
	pmcid = {PMC2884380},
	keywords = {Adult, Algorithms, Automatic Data Processing, Brain, Cohort Studies, Data Interpretation, Statistical, Disease Progression, Female, fs\_Validation-Evaluations, {HIV} Infections, Humans, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Male, Middle Aged, Reproducibility of Results, Software},
	pages = {1334--1344}
}

@article{bernal-rusiel_determining_2010,
	title = {Determining the optimal level of smoothing in cortical thickness analysis: a hierarchical approach based on sequential statistical thresholding},
	volume = {52},
	issn = {1095-9572},
	shorttitle = {Determining the optimal level of smoothing in cortical thickness analysis},
	doi = {10.1016/j.neuroimage.2010.03.074},
	abstract = {The extent of smoothing applied to cortical thickness maps critically influences sensitivity, anatomical precision and resolution of statistical change detection. Theoretically, it could be optimized by increasing the trade-off between vertex-wise sensitivity and specificity across several levels of smoothing. But to date neither parametric nor nonparametric methods are able to control the error at the vertex level if the null hypothesis is rejected after smoothing of cortical thickness maps. To overcome these drawbacks, we applied sequential statistical thresholding based on a simple hierarchical model. This methodology aims at controlling erroneous detections; firstly at the level of clusters, over smoothed statistical maps; and secondly at the vertex level, over unsmoothed statistical maps, by applying an adaptive false discovery rate ({FDR}) procedure to clusters previously detected. The superior performance of the proposed methodology over other conventional procedures was demonstrated in simulation studies. As expected, only the hierarchical method yielded a predictable false discovery proportion near the predefined {FDR} q-value for any smoothing level at the same time as being as sensitive as the others at the optimal setting. It was therefore the only method able to approximate the optimal size of spatial smoothing when the true change was assumed unknown. The hierarchical method was further validated in a cross-sectional study comparing moderate Alzheimer's disease ({AD}) patients with healthy elderly subjects. Results suggest that the extent of cortical thinning reported in previous {AD} studies might be artificially inflated by the choice of inadequate smoothing. In these cases, interpretation should be based on the location of local maxima of suprathreshold regions rather than on the spatial extent of the detected signal in the statistical parametric map.},
	language = {eng},
	number = {1},
	journal = {{NeuroImage}},
	author = {Bernal-Rusiel, Jorge L. and Atienza, Mercedes and Cantero, Jose L.},
	month = aug,
	year = {2010},
	pmid = {20362677},
	keywords = {Aged, Aged, 80 and over, Algorithms, Alzheimer Disease, Case-Control Studies, Cerebral Cortex, Cluster Analysis, Computer Simulation, Cross-Sectional Studies, Female, Humans, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Male, Middle Aged, Models, Statistical, Organ Size},
	pages = {158--171}
}

@article{qiu_atlas_2010,
	title = {Atlas generation for subcortical and ventricular structures with its applications in shape analysis},
	volume = {19},
	issn = {1941-0042 (Electronic) 1057-7149 (Linking)},
	shorttitle = {Atlas generation for subcortical and ventricular structures with its applications in shape analysis},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/20129863},
	doi = {10.1109/TIP.2010.2042099},
	abstract = {Atlas-driven morphometric analysis has received great attention for studying anatomical shape variation across clinical populations in neuroimaging research as it provides a local coordinate representation for understanding the family of anatomic observations. We present a procedure for generating atlas of subcortical and ventricular structures, including amygdala, hippocampus, caudate, putamen, globus pallidus, thalamus, and lateral ventricles, using the large deformation diffeomorphic metric atlas generation algorithm. The atlas was built based on manually labeled volumes of 41 subjects randomly selected from the database of Open Access Series of Imaging Studies ({OASIS}, 10 young adults, 10 middle-age adults, 10 healthy elders, and 11 patients with dementia). We show that the estimated atlas is representative of the population in terms of its metric distance to each individual subject in the population. In the application of detecting shape variations, using the estimated atlas may potentially increase statistical power in identifying group shape difference when comparing with using a single subject atlas. In shape-based classification, the metric distances between subjects and each of within-class estimated atlases construct a shape feature space, which allows for performing a variety of classification algorithms to distinguish anatomies.},
	number = {6},
	journal = {{IEEE} Trans Image Process},
	author = {Qiu, A. and Brown, T. and Fischl, B. and Ma, J. and Miller, M. I.},
	month = jun,
	year = {2010},
	keywords = {Adult, Aged, Algorithms, Anatomy, Artistic, Atlases as Topic, Brain/*pathology, Computer Simulation, Dementia/*pathology, Female, Humans, Image Enhancement/methods, Image Interpretation, Computer-Assisted/*methods, Imaging, Three-Dimensional/*methods, Magnetic Resonance Imaging/*methods, Male, Middle Aged, *Models, Anatomic, Pattern Recognition, Automated/*methods, Reproducibility of Results, Sensitivity and Specificity},
	pages = {1539--47},
	annote = {Qiu, {AnqiBrown}, {TimothyFischl}, {BruceMa}, {JunMiller}, Michael {IengP}41 {RR}014075/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-04/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}015241-097563/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}15241/{RR}/{NCRR} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 {EB}000975/{EB}/{NIBIB} {NIH} {HHS}/R01 {EB}001550/{EB}/{NIBIB} {NIH} {HHS}/R01 {EB}001550-04/{EB}/{NIBIB} {NIH} {HHS}/R01 {EB}006758-03/{EB}/{NIBIB} {NIH} {HHS}/R01 {EB}008171/{EB}/{NIBIB} {NIH} {HHS}/R01 {NS}052585-01/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}052585-01A1/{NS}/{NINDS} {NIH} {HHS}/R01 {RR}016594-01A1/{RR}/{NCRR} {NIH} {HHS}/R01 {RR}16594-01A1/{RR}/{NCRR} {NIH} {HHS}/R01EB006758/{EB}/{NIBIB} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/U24 {RR}021382-05/{RR}/{NCRR} {NIH} {HHS}/U54 {EB}005149/{EB}/{NIBIB} {NIH} {HHS}/U54 {EB}005149-04/{EB}/{NIBIB} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov't2010/02/05 06:00IEEE Trans Image Process. 2010 Jun;19(6):1539-47. doi: 10.1109/{TIP}.2010.2042099. Epub 2010 Feb 2.},
	file = {Qiu-2010-Atlas generation for subcortical and:/autofs/cluster/freesurfer/zotero/storage/HSX83RXX/Qiu-2010-Atlas generation for subcortical and.pdf:application/pdf}
}

@book{metten_dreidimensionale_2010,
	address = {Tönning},
	title = {Dreidimensionale zeitauflösende Untersuchung der kortikalen Faltungsstruktur am Beispiel der Schizophrenie / vorgelegt von Burkhard Metten},
	isbn = {978-3-86247-057-0},
	publisher = {Der Andere Verl.},
	author = {Metten, Burkhard},
	year = {2010},
	file = {http\://d-nb.info\:80/1006752226/about/html:/autofs/cluster/freesurfer/zotero/storage/9NWG6RFJ/html.html:text/html}
}

@article{madhavan_superior_2014,
	title = {Superior longitudinal fasciculus and language functioning in healthy aging},
	volume = {1562},
	issn = {1872-6240},
	doi = {10.1016/j.brainres.2014.03.012},
	abstract = {Structural deterioration of brain tissue in older adults is thought to be responsible for the majority of age-related cognitive decline. Disruption of widespread cortical networks due to a loss of axonal integrity may also play an important role. Research examining correlations between structural change and functional decline has focused heavily on working memory, processing speed, and executive processes while other aspects of cognition, such as language functioning, have received less attention. The current study aimed to determine whether age-related changes in the superior longitudinal fasciculus ({SLF}), are responsible for the deterioration in language functioning associated with age. Subjects included 112 right-handed volunteers (ages 19-76). For each subject, the {SLF} of the left hemisphere was reconstructed from diffusion tensor images ({DTI}). Mean fractional anisotropy ({FA}) values were extracted from parietal ({SLFp}) and temporal ({SLFt}) bundles. Language functioning was measured using the Peabody Picture Vocabulary Test ({PPVT}), Boston Naming Test ({BNT}), Controlled Oral Word Association Test ({COWAT}), and Semantic Fluency Test ({SFT}). Regression analyses revealed that males and females showed a different pattern of decline in {FA} across adulthood. For males, greater {SLFt} {FA} was significantly associated with increased {COWAT} performance, and there was a positive relationship between both age and {SLFp} {FA} with {BNT} scores. In females, greater {SLFp} {FA} was related to lower {COWAT} performance. Taken together, the results suggest that white matter integrity of the {SLF} follows a different pattern of decline in adulthood for males and females, and this decline differentially affects language functioning.},
	language = {eng},
	journal = {Brain Research},
	author = {Madhavan, Kiely M. and McQueeny, Tim and Howe, Steven R. and Shear, Paula and Szaflarski, Jerzy},
	month = may,
	year = {2014},
	pmid = {24680744},
	pmcid = {PMC4049076},
	pages = {11--22}
}

@article{van_der_kouwe_-line_2005,
	title = {On-line automatic slice positioning for brain {MR} imaging},
	volume = {27},
	issn = {1053-8119 (Print) 1053-8119 (Linking)},
	shorttitle = {On-line automatic slice positioning for brain {MR} imaging},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/15886023},
	doi = {10.1016/j.neuroimage.2005.03.035},
	abstract = {In clinical brain {MR} imaging protocols, the technician collects a quick localizer and manually positions the subsequent scans using the localizer as a guide. We present a method for automatic slice positioning using a rapidly acquired 3D localizer. The localizer is automatically aligned to a statistical atlas representing 40 healthy subjects. The atlas contains the probability of a given tissue type occurring at a given location in atlas space and the conditional probability distribution of the multi-spectral {MRI} intensity values for a given tissue class. Accurate rigid alignment of each subject to an atlas ensures that all patients' scans are acquired in a consistent manner. A further benefit is that slices are positioned consistently over time, so that scans of patients returning for follow-up imaging can be compared side-by-side to accurately monitor the progression of illness. The procedure also helps ensure that left/right asymmetries reflect true anatomy rather than being the result of oblique slice positioning relative to the underlying anatomy. The use of an atlas-based procedure eliminates the need to refer to a database of previously scanned images of the same patient and ensures corresponding alignment across scanners and sites, without requiring fiducial markers. Since the registration method is probabilistic, the registration error tends to increase smoothly in the presence of increasing noise and unusual anatomy or pathology rather than failing catastrophically. Translations and rotations relative to the atlas can be set so that planning can be done in anatomical space, rather than scanner coordinates, and stored as part of the protocol allowing standardization of slice orientations.},
	number = {1},
	journal = {Neuroimage},
	author = {van der Kouwe, A. J. and Benner, T. and Fischl, B. and Schmitt, F. and Salat, D. H. and Harder, M. and Sorensen, A. G. and Dale, A. M.},
	month = aug,
	year = {2005},
	keywords = {Algorithms, Artifacts, Brain Diseases/pathology, Brain Mapping/*methods, Brain/pathology/*physiology, Databases, Factual, Humans, Image Interpretation, Computer-Assisted, Longitudinal Studies, Magnetic Resonance Angiography, Magnetic Resonance Imaging/*methods, Online Systems, Reproducibility of Results},
	pages = {222--30},
	annote = {van der Kouwe, Andre J {WBenner}, {ThomasFischl}, {BruceSchmitt}, {FranzSalat}, David {HHarder}, {MartinSorensen}, A {GregoryDale}, Anders {MengP}41RR14075/{RR}/{NCRR} {NIH} {HHS}/R01 {RR}16594-01A1/{RR}/{NCRR} {NIH} {HHS}/R01-{EB}1550/{EB}/{NIBIB} {NIH} {HHS}/R21EB02530/{EB}/{NIBIB} {NIH} {HHS}/Research Support, Non-U.S. Gov'{tResearch} Support, U.S. Gov't, P.H.S.2005/05/12 09:00Neuroimage. 2005 Aug 1;27(1):222-30.}
}

@article{reuter_within-subject_2012,
	title = {Within-subject template estimation for unbiased longitudinal image analysis},
	volume = {61},
	issn = {1095-9572 (Electronic) 1053-8119 (Linking)},
	shorttitle = {Within-subject template estimation for unbiased longitudinal image analysis},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/22430496},
	doi = {10.1016/j.neuroimage.2012.02.084},
	abstract = {Longitudinal image analysis has become increasingly important in clinical studies of normal aging and neurodegenerative disorders. Furthermore, there is a growing appreciation of the potential utility of longitudinally acquired structural images and reliable image processing to evaluate disease modifying therapies. Challenges have been related to the variability that is inherent in the available cross-sectional processing tools, to the introduction of bias in longitudinal processing and to potential over-regularization. In this paper we introduce a novel longitudinal image processing framework, based on unbiased, robust, within-subject template creation, for automatic surface reconstruction and segmentation of brain {MRI} of arbitrarily many time points. We demonstrate that it is essential to treat all input images exactly the same as removing only interpolation asymmetries is not sufficient to remove processing bias. We successfully reduce variability and avoid over-regularization by initializing the processing in each time point with common information from the subject template. The presented results show a significant increase in precision and discrimination power while preserving the ability to detect large anatomical deviations; as such they hold great potential in clinical applications, e.g. allowing for smaller sample sizes or shorter trials to establish disease specific biomarkers or to quantify drug effects.},
	number = {4},
	journal = {Neuroimage},
	author = {Reuter, M. and Schmansky, N. J. and Rosas, H. D. and Fischl, B.},
	month = jul,
	year = {2012},
	keywords = {*Algorithms, Brain/*anatomy \& histology/*physiology, Humans, Image Interpretation, Computer-Assisted/*methods, Magnetic Resonance Imaging/*methods},
	pages = {1402--18},
	annote = {Reuter, {MartinSchmansky}, Nicholas {JRosas}, H {DianaFischl}, {BruceengP}01 {AG}003991-25/{AG}/{NIA} {NIH} {HHS}/P01 {NS}058793-05/{NS}/{NINDS} {NIH} {HHS}/P01AG03991/{AG}/{NIA} {NIH} {HHS}/P01NS058793/{NS}/{NINDS} {NIH} {HHS}/P41 {RR}014075/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-13/{RR}/{NCRR} {NIH} {HHS}/P41RR14075/{RR}/{NCRR} {NIH} {HHS}/P50 {MH}071616-05/{MH}/{NIMH} {NIH} {HHS}/P50AG05681/{AG}/{NIA} {NIH} {HHS}/P50MH071616/{MH}/{NIMH} {NIH} {HHS}/R01 {AG}018386/{AG}/{NIA} {NIH} {HHS}/R01 {AG}021910-05/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022381/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022381-10/{AG}/{NIA} {NIH} {HHS}/R01 {EB}006758/{EB}/{NIBIB} {NIH} {HHS}/R01 {EB}006758-04/{EB}/{NIBIB} {NIH} {HHS}/R01 {MH}056584-12/{MH}/{NIMH} {NIH} {HHS}/R01 {NS}042861/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}042861-09/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}052585/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}052585-05/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}070963/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}070963-02/{NS}/{NINDS} {NIH} {HHS}/R01AG021910/{AG}/{NIA} {NIH} {HHS}/R01AG022381/{AG}/{NIA} {NIH} {HHS}/R01EB006758/{EB}/{NIBIB} {NIH} {HHS}/R01MH56584/{MH}/{NIMH} {NIH} {HHS}/R01NS042861/{NS}/{NINDS} {NIH} {HHS}/R01NS052585/{NS}/{NINDS} {NIH} {HHS}/R01NS070963/{NS}/{NINDS} {NIH} {HHS}/R21 {NS}072652/{NS}/{NINDS} {NIH} {HHS}/R21 {NS}072652-02/{NS}/{NINDS} {NIH} {HHS}/R21NS072652/{NS}/{NINDS} {NIH} {HHS}/{RC}1 {AT}005728-02/{AT}/{NCCAM} {NIH} {HHS}/{RC}1AT005728/{AT}/{NCCAM} {NIH} {HHS}/S10 {RR}019307/{RR}/{NCRR} {NIH} {HHS}/S10 {RR}019307-01/{RR}/{NCRR} {NIH} {HHS}/S10 {RR}023043-01/{RR}/{NCRR} {NIH} {HHS}/S10 {RR}023401/{RR}/{NCRR} {NIH} {HHS}/S10 {RR}023401-01A2/{RR}/{NCRR} {NIH} {HHS}/S10RR019307/{RR}/{NCRR} {NIH} {HHS}/S10RR023043/{RR}/{NCRR} {NIH} {HHS}/S10RR023401/{RR}/{NCRR} {NIH} {HHS}/U01 {AG}024904-07/{AG}/{NIA} {NIH} {HHS}/U01AG024904/{AG}/{NIA} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/U24 {RR}021382-05/{RR}/{NCRR} {NIH} {HHS}/U24RR021382/{RR}/{NCRR} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov't2012/03/21 06:00Neuroimage. 2012 Jul 16;61(4):1402-18. doi: 10.1016/j.neuroimage.2012.02.084. Epub 2012 Mar 10.},
	file = {Reuter-2012-Within-subject template estimation:/autofs/cluster/freesurfer/zotero/storage/TKG5EC9T/Reuter-2012-Within-subject template estimation.pdf:application/pdf}
}

@article{katz_prefrontal_2009,
	title = {Prefrontal Plasticity and Stress Inoculation-Induced Resilience},
	volume = {31},
	issn = {0378-5866},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2820579/},
	doi = {10.1159/000216540},
	abstract = {Coping with mild early life stress tends to make subsequent coping efforts more effective and therefore more likely to be used as a means of arousal regulation and resilience. Here we show that this developmental learning-like process of stress inoculation increases ventromedial prefrontal cortical volumes in peripubertal monkeys. Larger volumes do not reflect increased cortical thickness but instead represent surface area expansion of ventromedial prefrontal cortex. Expansion of ventromedial prefrontal cortex coincides with increased white matter myelination inferred from diffusion tensor magnetic resonance imaging. These findings suggest that the process of coping with early life stress increases prefrontal myelination and expands a region of cortex that broadly controls arousal regulation and resilience.},
	number = {4},
	urldate = {2014-08-23},
	journal = {Developmental Neuroscience},
	author = {Katz, Maor and Liu, Chunlei and Schaer, Marie and Parker, Karen J. and Ottet, Marie-Christine and Epps, Averi and Buckmaster, Christine L. and Bammer, Roland and Moseley, Michael E. and Schatzberg, Alan F. and Eliez, Stephan and Lyons, David M.},
	month = jun,
	year = {2009},
	pmid = {19546566},
	pmcid = {PMC2820579},
	pages = {293--299},
	file = {PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/JZ5PCTDD/Katz et al. - 2009 - Prefrontal Plasticity and Stress Inoculation-Induc.pdf:application/pdf}
}

@article{dale_dynamic_2000,
	title = {Dynamic statistical parametric mapping: combining {fMRI} and {MEG} for high-resolution imaging of cortical activity},
	volume = {26},
	issn = {0896-6273 (Print) 0896-6273 (Linking)},
	shorttitle = {Dynamic statistical parametric mapping: combining {fMRI} and {MEG} for high-resolution imaging of cortical activity},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/10798392},
	abstract = {Functional magnetic resonance imaging ({fMRI}) can provide maps of brain activation with millimeter spatial resolution but is limited in its temporal resolution to the order of seconds. Here, we describe a technique that combines structural and functional {MRI} with magnetoencephalography ({MEG}) to obtain spatiotemporal maps of human brain activity with millisecond temporal resolution. This new technique was used to obtain dynamic statistical parametric maps of cortical activity during semantic processing of visually presented words. An initial wave of activity was found to spread rapidly from occipital visual cortex to temporal, parietal, and frontal areas within 185 ms, with a high degree of temporal overlap between different areas. Repetition effects were observed in many of the same areas following this initial wave of activation, providing evidence for the involvement of feedback mechanisms in repetition priming.},
	number = {1},
	journal = {Neuron},
	author = {Dale, A. M. and Liu, A. K. and Fischl, B. R. and Buckner, R. L. and Belliveau, J. W. and Lewine, J. D. and Halgren, E.},
	month = apr,
	year = {2000},
	keywords = {Brain Mapping/*methods, Brain/*physiology, Cerebral Cortex/physiology, Cognition/*physiology, Humans, Magnetic Resonance Imaging/*methods, Magnetoencephalography/*methods},
	pages = {55--67},
	annote = {Dale, A {MLiu}, A {KFischl}, B {RBuckner}, R {LBelliveau}, J {WLewine}, J {DHalgren}, {EengR}01-{NS}18741/{NS}/{NINDS} {NIH} {HHS}/R01-{RR}13609/{RR}/{NCRR} {NIH} {HHS}/Research Support, Non-U.S. Gov'{tResearch} Support, U.S. Gov't, Non-P.H.S.Research Support, U.S. Gov't, P.H.S.2000/05/08 09:00Neuron. 2000 Apr;26(1):55-67.},
	file = {Dale-2000-Dynamic statistical parametric mappi:/autofs/cluster/freesurfer/zotero/storage/TV5UQNUU/Dale-2000-Dynamic statistical parametric mappi.pdf:application/pdf}
}

@article{rimol_sex-dependent_2010,
	title = {Sex-dependent association of common variants of microcephaly genes with brain structure},
	volume = {107},
	issn = {0027-8424},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2806758/},
	doi = {10.1073/pnas.0908454107},
	abstract = {Loss-of-function mutations in the genes associated with primary microcephaly ({MCPH}) reduce human brain size by about two-thirds, without producing gross abnormalities in brain organization or physiology and leaving other organs largely unaffected [Woods {CG}, et al. (2005) Am J Hum Genet 76:717–728]. There is also evidence suggesting that {MCPH} genes have evolved rapidly in primates and humans and have been subjected to selection in recent human evolution [Vallender {EJ}, et al. (2008) Trends Neurosci 31:637–644]. Here, we show that common variants of {MCPH} genes account for some of the common variation in brain structure in humans, independently of disease status. We investigated the correlations of {SNPs} from four {MCPH} genes with brain morphometry phenotypes obtained with {MRI}. We found significant, sex-specific associations between common, nonexonic, {SNPs} of the genes {CDK}5RAP2, {MCPH}1, and {ASPM}, with brain volume or cortical surface area in an ethnically homogenous Norwegian discovery sample (n = 287), including patients with mental illness. The most strongly associated {SNP} findings were replicated in an independent North American sample (n = 656), which included patients with dementia. These results are consistent with the view that common variation in brain structure is associated with genetic variants located in nonexonic, presumably regulatory, regions.},
	number = {1},
	urldate = {2014-08-24},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	author = {Rimol, Lars M. and Agartz, Ingrid and Djurovic, Srdjan and Brown, Andrew A. and Roddey, J. Cooper and Kahler, Anna K. and Mattingsdal, Morten and Athanasiu, Lavinia and Joyner, Alexander H. and Schork, Nicholas J. and Halgren, Eric and Sundet, Kjetil and Melle, Ingrid and Dale, Anders M. and Andreassen, Ole A.},
	month = jan,
	year = {2010},
	pmid = {20080800},
	pmcid = {PMC2806758},
	pages = {384--388},
	file = {PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/DDU38FG9/Rimol et al. - 2010 - Sex-dependent association of common variants of mi.pdf:application/pdf;PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/RW4IIAIM/Rimol et al. - 2010 - Sex-dependent association of common variants of mi.pdf:application/pdf}
}

@article{srivastava_atypical_2012,
	title = {Atypical developmental trajectory of functionally significant cortical areas in children with chromosome 22q11.2 deletion syndrome},
	volume = {33},
	issn = {1097-0193 (Electronic) 1065-9471 (Linking)},
	shorttitle = {Atypical developmental trajectory of functionally significant cortical areas in children with chromosome 22q11.2 deletion syndrome},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/21416559},
	doi = {10.1002/hbm.21206},
	abstract = {Chromosome 22q11.2 deletion syndrome (22q11.2DS) is a neurogenetic disorder associated with neurocognitive impairments. This article focuses on the cortical gyrification changes that are associated with the genetic disorder in 6-15-year-old children with 22q11.2DS, when compared with a group of age-matched typically developing ({TD}) children. Local gyrification index ({lGI}; Schaer et al. [2008]: {IEEE} Trans Med Imaging 27:161-170) was used to characterize the cortical gyrification at each vertex of the pial surface. Vertex-wise statistical analysis of {lGI} differences between the two groups revealed cortical areas of significant reduction in cortical gyrification in children with 22q11.2DS, which were mainly distributed along the medial aspect of each hemisphere. To gain further insight into the developmental trajectory of the cortical gyrification, we examined age as a factor in {lGI} changes over the 6-15 years of development, within and across the two groups of children. Our primary results pertaining to the developmental trajectory of cortical gyrification revealed cortical regions where the change in {lGI} over the 6-15 years of age was significantly modulated by diagnosis, implying an atypical development of cortical gyrification in children with 22q11.2DS, when compared with the {TD} children. Significantly, these cortical areas included parietal structures that are associated, in typical individuals, with visuospatial, attentional, and numerical cognition tasks in which children with 22q11.2DS show impairments.},
	language = {en},
	number = {1},
	urldate = {2014-08-21},
	journal = {Hum Brain Mapp},
	author = {Srivastava, S. and Buonocore, M. H. and Simon, T. J.},
	month = jan,
	year = {2012},
	keywords = {22q11 Deletion Syndrome/*pathology, Adolescent, Cerebral Cortex/growth \& development/*pathology, Child, Female, Humans, Magnetic Resonance Imaging, Male},
	pages = {213--23},
	annote = {Srivastava, {SiddharthBuonocore}, Michael {HSimon}, Tony {JengR}01 {HD}042974/{HD}/{NICHD} {NIH} {HHS}/R01 {HD}042974-01A1/{HD}/{NICHD} {NIH} {HHS}/R01 {HD}042974-02/{HD}/{NICHD} {NIH} {HHS}/R01 {HD}042974-03/{HD}/{NICHD} {NIH} {HHS}/R01 {HD}042974-04/{HD}/{NICHD} {NIH} {HHS}/R01 {HD}042974-05/{HD}/{NICHD} {NIH} {HHS}/R01 {HD}042974-06/{HD}/{NICHD} {NIH} {HHS}/R01 {HD}042974-06S1/{HD}/{NICHD} {NIH} {HHS}/R01 {HD}042974-07A2/{HD}/{NICHD} {NIH} {HHS}/R01HD42974/{HD}/{NICHD} {NIH} {HHS}/{UL}1 {RR}024146/{RR}/{NCRR} {NIH} {HHS}/Research Support, N.I.H., Extramural2011/03/19 06:00Hum Brain Mapp. 2012 Jan;33(1):213-23. doi: 10.1002/hbm.21206. Epub 2011 Mar 17.},
	file = {PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/PQTMWW44/Srivastava et al. - 2012 - Atypical Developmental Trajectory of Functionally .pdf:application/pdf;Srivastava-2012-Atypical developmental trajec1:/autofs/cluster/freesurfer/zotero/storage/869JUHAH/Srivastava-2012-Atypical developmental trajec1.pdf:application/pdf}
}

@article{seiler_vascular_2012,
	series = {Vascular Dementia 2011},
	title = {Vascular cognitive impairment — An ill-defined concept with the need to define its vascular component},
	volume = {322},
	issn = {0022-510X},
	url = {http://www.sciencedirect.com/science/article/pii/S0022510X12002845},
	doi = {10.1016/j.jns.2012.06.001},
	abstract = {New guidelines for the diagnosis of vascular cognitive impairment ({VCI}) represent an important step in the definition of this clinical entity. These guidelines still remain vague in the definition of “vascular” brain lesions causing cognitive decline, because longitudinal correlative imaging studies are still scarce. In this review we explore which abnormalities are likely to contribute to {VCI} based on a proven vascular etiology, fast progression and their incidence or progression being related to cognitive decline. Among focal changes visible on standard {MRI} these features apply for coalescent white matter changes. The evidence for lacunes and microbleeds is much less convincing. Microstructural alterations in normal appearing brain tissue which can be detected by new {MRI} techniques such as magnetization transfer imaging ({MTI}), diffusion tensor imaging ({DTI}) and high resolution {MR} appear to better correlate with cognitive decline, but the etiology of these changes and their histopathological correlates is still incompletely understood as is their evolution over time. New multimodal image processing such as voxel-based lesion-symptom mapping ({VLSM}) or combinations of {DTI} and voxel-based analysis will allow to allocate the lesion patterns that show the greatest covariance with clinical outcome. Such data and more longitudinal correlative data on lacunes and microbleeds will increase our pathophysiologic understanding of {VCI} including the interplay with primary degenerative processes and will lead to refinement of current {VCI} criteria.},
	number = {1–2},
	urldate = {2014-08-25},
	journal = {Journal of the Neurological Sciences},
	author = {Seiler, Stephan and Cavalieri, Margherita and Schmidt, Reinhold},
	month = nov,
	year = {2012},
	keywords = {Lacunes, Magnetic Resonance Imaging, Microbleeds, Normal appearing brain tissue, Vascular cognitive impairment, White matter lesions},
	pages = {11--16},
	file = {ScienceDirect Snapshot:/autofs/cluster/freesurfer/zotero/storage/UUHAC4AU/S0022510X12002845.html:text/html}
}

@article{mccauley_patterns_2010,
	title = {Patterns of Cortical Thinning in Relation to Event-Based Prospective Memory Performance Three Months after Moderate to Severe Traumatic Brain Injury in Children},
	volume = {35},
	issn = {8756-5641},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3061405/},
	doi = {10.1080/87565641003696866},
	abstract = {While event-based prospective memory ({EB}-{PM}) tasks are a familiar part of daily life for children, currently no data exists concerning the relation between {EB}-{PM} performance and brain volumetrics after traumatic brain injury ({TBI}). This study investigated {EB}-{PM} in children (7 to 17 years) with moderate to severe {TBI} or orthopedic injuries. Participants performed an {EB}-{PM} task and concurrently underwent neuroimaging at three months postinjury. Surface reconstruction and cortical thickness analysis were performed using {FreeSurfer} software. Cortical thickness was significantly correlated with {EB}-{PM} (adjusting for age). Significant thinning in the left (dorsolateral and inferior prefrontal cortex, anterior and posterior cingulate, temporal lobe, fusiform and parahippocampal gyri), and right hemispheres (dorsolateral, inferior, and medial prefrontal cortex, cingulate, and temporal lobe) correlated positively and significantly with {EB}-{PM} performance; findings are comparable to those of functional neuroimaging and lesion studies of {EB}-{PM}.},
	number = {3},
	urldate = {2014-08-23},
	journal = {Developmental neuropsychology},
	author = {McCauley, Stephen R. and Wilde, Elisabeth A. and Merkley, Tricia L. and Schnelle, Kathleen P. and Bigler, Erin D. and Hunter, Jill V. and Vasquez, Ana C. and Levin, Harvey S.},
	month = may,
	year = {2010},
	pmid = {20446135},
	pmcid = {PMC3061405},
	pages = {318--332},
	file = {PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/EKB3F85A/McCauley et al. - 2010 - Patterns of Cortical Thinning in Relation to Event.pdf:application/pdf}
}

@article{rohrer_progressive_2010,
	title = {Progressive logopenic/phonological aphasia: Erosion of the language network},
	volume = {49},
	issn = {1053-8119},
	shorttitle = {Progressive logopenic/phonological aphasia},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2943046/},
	doi = {10.1016/j.neuroimage.2009.08.002},
	abstract = {The primary progressive aphasias ({PPA}) are paradigmatic disorders of language network breakdown associated with focal degeneration of the left cerebral hemisphere. Here we addressed brain correlates of {PPA} in a detailed neuroanatomical analysis of the third canonical syndrome of {PPA}, logopenic/phonological aphasia ({LPA}), in relation to the more widely studied clinico-anatomical syndromes of semantic dementia ({SD}) and progressive nonfluent aphasia ({PNFA}). 32 {PPA} patients (9 {SD}, 14 {PNFA}, 9 {LPA}) and 18 cognitively normal controls had volumetric brain {MRI} with regional volumetry, cortical thickness, grey and white matter voxel-based morphometry analyses. Five of nine patients with {LPA} had cerebrospinal fluid biomarkers consistent with Alzheimer ({AD}) pathology ({AD}-{PPA}) and 2/9 patients had progranulin ({GRN}) mutations ({GRN}-{PPA}). The {LPA} group had tissue loss in a widespread left hemisphere network. Compared with {PNFA} and {SD}, the {LPA} group had more extensive involvement of grey matter in posterior temporal and parietal cortices and long association white matter tracts. Overlapping but distinct networks were involved in the {AD}-{PPA} and {GRN}-{PPA} subgroups, with more anterior temporal lobe involvement in {GRN}-{PPA}. The importance of these findings is threefold: firstly, the clinico-anatomical entity of {LPA} has a profile of brain damage that is complementary to the network-based disorders of {SD} and {PNFA}; secondly, the core phonological processing deficit in {LPA} is likely to arise from temporo-parietal junction damage but disease spread occurs through the dorsal language network (and in {GRN}-{PPA}, also the ventral language network); and finally, {GRN} mutations provide a specific molecular substrate for language network dysfunction.},
	number = {1},
	urldate = {2014-08-23},
	journal = {Neuroimage},
	author = {Rohrer, Jonathan D. and Ridgway, Gerard R. and Crutch, Sebastian J. and Hailstone, Julia and Goll, Johanna C. and Clarkson, Matthew J. and Mead, Simon and Beck, Jonathan and Mummery, Cath and Ourselin, Sebastien and Warrington, Elizabeth K. and Rossor, Martin N. and Warren, Jason D.},
	month = jan,
	year = {2010},
	pmid = {19679189},
	pmcid = {PMC2943046},
	pages = {984--993}
}

@article{keller_volume_2012,
	title = {Volume estimation of the thalamus using freesurfer and stereology: consistency between methods},
	volume = {10},
	issn = {1559-0089},
	shorttitle = {Volume estimation of the thalamus using freesurfer and stereology},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3464372/},
	doi = {10.1007/s12021-012-9147-0},
	abstract = {Freely available automated {MR} image analysis techniques are being increasingly used to investigate neuroanatomical abnormalities in patients with neurological disorders. It is important to assess the specificity and validity of automated measurements of structure volumes with respect to reliable manual methods that rely on human anatomical expertise. The thalamus is widely investigated in many neurological and neuropsychiatric disorders using {MRI}, but thalamic volumes are notoriously difficult to quantify given the poor between-tissue contrast at the thalamic gray-white matter interface. In the present study we investigated the reliability of automatically determined thalamic volume measurements obtained using {FreeSurfer} software with respect to a manual stereological technique on 3D T1-weighted {MR} images obtained from a 3 T {MR} system. Further to demonstrating impressive consistency between stereological and {FreeSurfer} volume estimates of the thalamus in healthy subjects and neurological patients, we demonstrate that the extent of agreeability between stereology and {FreeSurfer} is equal to the agreeability between two human anatomists estimating thalamic volume using stereological methods. Using patients with juvenile myoclonic epilepsy as a model for thalamic atrophy, we also show that both automated and manual methods provide very similar ratios of thalamic volume loss in patients. This work promotes the use of {FreeSurfer} for reliable estimation of global volume in healthy and diseased thalami.},
	language = {eng},
	number = {4},
	journal = {Neuroinformatics},
	author = {Keller, Simon S. and Gerdes, Jan S. and Mohammadi, Siawoosh and Kellinghaus, Christoph and Kugel, Harald and Deppe, Katja and Ringelstein, E. Bernd and Evers, Stefan and Schwindt, Wolfram and Deppe, Michael},
	month = oct,
	year = {2012},
	pmid = {22481382},
	pmcid = {PMC3464372},
	keywords = {Adult, Analysis of Variance, Atrophy, Brain Mapping, Female, fs\_Validation-Evaluations, Humans, Imaging, Three-Dimensional, Linear Models, Magnetic Resonance Imaging, Male, Middle Aged, Myoclonic Epilepsy, Juvenile, Nerve Fibers, Myelinated, Software, Stereotaxic Techniques, Thalamus, Young Adult},
	pages = {341--350}
}

@article{chen_hierarchical_2012,
	title = {Hierarchical genetic organization of human cortical surface area},
	volume = {335},
	issn = {1095-9203 (Electronic) 0036-8075 (Linking)},
	shorttitle = {Hierarchical genetic organization of human cortical surface area},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/22461613},
	doi = {10.1126/science.1215330},
	abstract = {Surface area of the cerebral cortex is a highly heritable trait, yet little is known about genetic influences on regional cortical differentiation in humans. Using a data-driven, fuzzy clustering technique with magnetic resonance imaging data from 406 twins, we parceled cortical surface area into genetic subdivisions, creating a human brain atlas based solely on genetically informative data. Boundaries of the genetic divisions corresponded largely to meaningful structural and functional regions; however, the divisions represented previously undescribed phenotypes different from conventional (non-genetically based) parcellation systems. The genetic organization of cortical area was hierarchical, modular, and predominantly bilaterally symmetric across hemispheres. We also found that the results were consistent with human-specific regions being subdivisions of previously described, genetically based lobar regionalization patterns.},
	number = {6076},
	journal = {Science},
	author = {Chen, C. H. and Gutierrez, E. D. and Thompson, W. and Panizzon, M. S. and Jernigan, T. L. and Eyler, L. T. and Fennema-Notestine, C. and Jak, A. J. and Neale, M. C. and Franz, C. E. and Lyons, M. J. and Grant, M. D. and Fischl, B. and Seidman, L. J. and Tsuang, M. T. and Kremen, W. S. and Dale, A. M.},
	month = mar,
	year = {2012},
	keywords = {Brain Mapping, Cerebral Cortex/*anatomy \& histology/*metabolism, Gene Expression, *Genes, Genetic Variation, Humans, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Male, Middle Aged, Phenotype, Twins, Dizygotic/genetics, Twins, Monozygotic/genetics},
	pages = {1634--6},
	annote = {Chen, Chi-{HuaGutierrez}, E {DThompson}, {WesPanizzon}, Matthew {SJernigan}, Terry {LEyler}, Lisa {TFennema}-Notestine, {ChristineJak}, Amy {JNeale}, Michael {CFranz}, Carol {ELyons}, Michael {JGrant}, Michael {DFischl}, {BruceSeidman}, Larry {JTsuang}, Ming {TKremen}, William {SDale}, Anders Meng1R01NS070963/{NS}/{NINDS} {NIH} {HHS}/1R21NS072652-01/{NS}/{NINDS} {NIH} {HHS}/{AG}018384/{AG}/{NIA} {NIH} {HHS}/{AG}018386/{AG}/{NIA} {NIH} {HHS}/{AG}022381/{AG}/{NIA} {NIH} {HHS}/{AG}022982/{AG}/{NIA} {NIH} {HHS}/{AG}031224/{AG}/{NIA} {NIH} {HHS}/{BIRN}002/{PHS} {HHS}/{DA}029475/{DA}/{NIDA} {NIH} {HHS}/{EB}006758/{EB}/{NIBIB} {NIH} {HHS}/{NS}052585-01/{NS}/{NINDS} {NIH} {HHS}/{NS}056883/{NS}/{NINDS} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 {AG}018384/{AG}/{NIA} {NIH} {HHS}/R01 {AG}018386/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022381/{AG}/{NIA} {NIH} {HHS}/{RC}1 {AT}005728-01/{AT}/{NCCAM} {NIH} {HHS}/{RC}2 {DA}029475/{DA}/{NIDA} {NIH} {HHS}/T32DC000041/{DC}/{NIDCD} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov'{tResearch} Support, U.S. Gov't, Non-P.H.S.Twin {StudyNew} York, N.Y.2012/03/31 06:00Science. 2012 Mar 30;335(6076):1634-6. doi: 10.1126/science.1215330.},
	file = {Chen-2012-Hierarchical genetic organization of:/autofs/cluster/freesurfer/zotero/storage/M442UJ7T/Chen-2012-Hierarchical genetic organization of.pdf:application/pdf}
}

@article{cherbuin_vivo_2009,
	title = {In vivo hippocampal measurement and memory: a comparison of manual tracing and automated segmentation in a large community-based sample},
	volume = {4},
	issn = {1932-6203 (Electronic) 1932-6203 (Linking)},
	shorttitle = {In Vivo Hippocampal Measurement and Memory},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/19370155},
	doi = {10.1371/journal.pone.0005265},
	abstract = {While manual tracing is the method of choice in measuring hippocampal volume, its time intensive nature and proneness to human error make automated methods attractive, especially when applied to large samples. Few studies have systematically compared the performance of the two techniques. In this study, we measured hippocampal volumes in a large (N = 403) population-based sample of individuals aged 44-48 years using manual tracing by a trained researcher and automated procedure using Freesurfer (http://surfer.nmr.mgh.harvard.edu) imaging suite. Results showed that absolute hippocampal volumes assessed with these methods were significantly different, with automated measures using the Freesurfer software suite being significantly larger, by 23\% for the left and 29\% for the right hippocampus. The correlation between the two methods varied from 0.61 to 0.80, with lower correlations for hippocampi with visible abnormalities. Inspection of 2D and 3D models suggested that this difference was largely due to greater inclusion of boundary voxels by the automated method and variations in subiculum/entorhinal segmentation. The correlation between left and right hippocampal volumes was very similar by the two methods. The relationship of hippocampal volumes to selected sociodemographic and cognitive variables was not affected by the measurement method, with each measure showing an association with memory performance and suggesting that both were equally valid for this purpose. This study supports the use of automated measures, based on Freesurfer in this instance, as being sufficiently reliable and valid particularly in the context of larger sample sizes when the research question does not rely on 'true' hippocampal volumes.},
	language = {en},
	number = {4},
	urldate = {2014-08-21},
	journal = {{PLoS} One},
	author = {Cherbuin, N. and Anstey, K. J. and Reglade-Meslin, C. and Sachdev, P. S.},
	month = apr,
	year = {2009},
	keywords = {Adult, Female, fs\_Validation-Evaluations, Hippocampus/*anatomy \& histology/physiology, Humans, Image Processing, Computer-Assisted/*methods, Imaging, Three-Dimensional, *Magnetic Resonance Imaging, Male, Memory/*physiology, Middle Aged, Organ Size, Pattern Recognition, Automated/methods, Regression Analysis, Socioeconomic Factors},
	pages = {e5265},
	annote = {Cherbuin, {NicolasAnstey}, Kaarin {JReglade}-Meslin, {ChantalSachdev}, Perminder {SengComparative} {StudyResearch} Support, Non-U.S. Gov't2009/04/17 09:00PLoS One. 2009;4(4):e5265. doi: 10.1371/journal.pone.0005265. Epub 2009 Apr 16.},
	file = {Cherbuin-2009-In vivo hippocampal measurement1:/autofs/cluster/freesurfer/zotero/storage/FJFDHDKX/Cherbuin-2009-In vivo hippocampal measurement1.pdf:application/pdf}
}

@article{gutierrez-galve_patterns_2009,
	title = {Patterns of Cortical Thickness according to {APOE} Genotype in Alzheimer’s Disease},
	volume = {28},
	issn = {1421-9824, 1420-8008},
	url = {http://www.karger.com/Article/FullText/258100},
	doi = {10.1159/000258100},
	language = {en},
	number = {5},
	urldate = {2014-08-23},
	journal = {Dementia and Geriatric Cognitive Disorders},
	author = {Gutiérrez-Galve, Leticia and Lehmann, Manja and Hobbs, Nicola Z. and Clarkson, Matthew J. and Ridgway, Gerard R. and Crutch, Sebastian and Ourselin, Sebastien and Schott, Jonathan M. and Fox, Nick C. and Barnes, Josephine},
	year = {2009},
	keywords = {Aged, Alzheimer Disease, Apolipoprotein E4, Atrophy, Cerebral Cortex, Cognition Disorders, Female, Genotype, Gyrus Cinguli, Hippocampus, Humans, Magnetic Resonance Imaging, Male, Middle Aged, Psychometrics},
	pages = {476--485},
	file = {PayPerView\: Patterns of Cortical Thickness according to APOE Genotype in Alzheimer’s Disease - Karger Publishers:/autofs/cluster/freesurfer/zotero/storage/STMFTHJB/258100.html:text/html}
}

@article{schaer_deviant_2009,
	title = {Deviant trajectories of cortical maturation in 22q11.2 deletion syndrome (22q11DS): a cross-sectional and longitudinal study},
	volume = {115},
	issn = {1573-2509},
	shorttitle = {Deviant trajectories of cortical maturation in 22q11.2 deletion syndrome (22q11DS)},
	doi = {10.1016/j.schres.2009.09.016},
	abstract = {22q11.2 deletion syndrome (22q11DS) is associated with an increased susceptibility to develop schizophrenia. Despite a large body of literature documenting abnormal brain structure in 22q11DS, cerebral changes associated with brain maturation in 22q11DS remained largely unexplored. To map cortical maturation from childhood to adulthood in 22q11.2 deletion syndrome, we used cerebral {MRI} from 59 patients with 22q11DS, aged 6 to 40, and 80 typically developing controls; three year follow-up assessments were also available for 32 patients and 31 matched controls. Cross-sectional cortical thickness trajectories during childhood and adolescence were approximated in age bins. Repeated-measures were also conducted with the longitudinal data. Within the group of patients with 22q11DS, exploratory measures of cortical thickness differences related to {COMT} polymorphism, {IQ}, and schizophrenia were also conducted. We observed deviant trajectories of cortical thickness changes with age in patients with 22q11DS. In affected preadolescents, larger prefrontal thickness was observed compared to age-matched controls. Afterward, we observed greater cortical loss in 22q11DS with a convergence of cortical thickness values by the end of adolescence. No compelling evidence for an effect of {COMT} polymorphism on cortical maturation was observed. Within 22q11DS, significant differences in cortical thickness were related to cognitive level in children and adolescents, and to schizophrenia in adults. Deviant trajectories of cortical thickness from childhood to adulthood provide strong in vivo cues for a defect in the programmed synaptic elimination, which in turn may explain the susceptibility of patients with 22q11DS to develop psychosis.},
	language = {eng},
	number = {2-3},
	journal = {Schizophrenia Research},
	author = {Schaer, Marie and Debbané, Martin and Bach Cuadra, Meritxell and Ottet, Marie-Christine and Glaser, Bronwyn and Thiran, Jean-Philippe and Eliez, Stephan},
	month = dec,
	year = {2009},
	pmid = {19836927},
	keywords = {Adolescent, Age Factors, Analysis of Variance, Brain Mapping, Case-Control Studies, Catechol O-Methyltransferase, Cerebral Cortex, Child, Cross-Sectional Studies, {DiGeorge} Syndrome, Female, Humans, Image Processing, Computer-Assisted, Intelligence, Longitudinal Studies, Magnetic Resonance Imaging, Male, Methionine, Neuropsychological Tests, Polymorphism, Genetic, Schizophrenia, Valine, Young Adult},
	pages = {182--190}
}

@article{walhovd_white_2007,
	title = {White matter volume predicts reaction time instability},
	volume = {45},
	issn = {0028-3932},
	url = {https://surfer.nmr.mgh.harvard.edu/pub/articles/Neuropsychologia(2007).pdf},
	doi = {10.1016/j.neuropsychologia.2007.02.022},
	abstract = {Information processing speed is a central concept in cognitive psychology and neuropsychology. Previous studies have mostly focused on mean reaction time ({RT}), and largely ignored intra-individual differences (the standard deviation of the {RT}: {sdRT}). Still, intra-individual inconsistency across trials has been shown to correlate with age, neurological disorders, intelligence, and performance on cognitive tests. However, {sdRT} has not been correlated with neuroanatomical variables. Such knowledge is important to the understanding of the neurobiological foundation for intra-individual variability. In the present study, white matter ({WM}) and cortical gray matter ({GM}) volume obtained from the average of two {MR} scans of 71 healthy participants (aged 20-88 years) were correlated with {sdRT} and mean {RT} obtained from a 3-stimulus visual oddball task. Negative correlations were hypothesized between {sdRT} and {WM} and between mean {RT} and cortical {GM} volume. These hypotheses were confirmed. The correlation between {sdRT} and {WM} volume was significant also independently of effects of age, gender, and mean {RT}, while there was a trend towards a significant correlation (p=.085) between cortical {GM} volume and mean {RT} independently of age. A path model was constructed, showing that age and {sdRT} gave independent contributions to the variance in performance intelligence, and that {WM} volume predicted performance score through the influence of {sdRT}. Further, {sdRT} was a stronger predictor of performance intelligence than mean {RT}. It is concluded that {sdRT} and mean {RT} may have different neuroanatomical correlates, and that {sdRT} is related to {WM} characteristics of the brain.},
	language = {eng},
	number = {10},
	journal = {Neuropsychologia},
	author = {Walhovd, Kristine B. and Fjell, Anders M.},
	month = jun,
	year = {2007},
	pmid = {17428508},
	keywords = {Adult, Aged, Aged, 80 and over, Brain, Brain Mapping, Cognition, Female, Humans, Intelligence Tests, Magnetic Resonance Imaging, Male, Middle Aged, Models, Psychological, Photic Stimulation, Predictive Value of Tests, Reaction Time},
	pages = {2277--2284}
}

@article{de_crespigny_high_2007,
	title = {High resolution cortical imaging.},
	shorttitle = {High resolution cortical imaging.},
	journal = {Proc. Intl. Soc. Mag. Res. Med.},
	author = {de Crespigny, A. J. and Grant, E. and Wald, L. and Augustinack, J. and Fischl, B. and D’Arceuil, H. E.},
	year = {2007}
}

@article{yeo_task-optimal_2009,
	title = {Task-optimal registration cost functions},
	volume = {12},
	shorttitle = {Task-optimal registration cost functions},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/20426037},
	abstract = {In this paper, we propose a framework for learning the parameters of registration cost functions--such as the tradeoff between the regularization and image similiarity term--with respect to a specific task. Assuming the existence of labeled training data, we specialize the framework for the task of localizing hidden labels via image registration. We learn the parameters of the weighted sum of squared differences ({wSSD}) image similarity term that are optimal for the localization of Brodmann areas ({BAs}) in a new subject based on cortical geometry. We demonstrate state-of-the-art localization of V1, V2, {BA}44 and {BA}45.},
	number = {Pt 1},
	journal = {Med Image Comput Comput Assist Interv},
	author = {Yeo, B. T. and Sabuncu, M. and Golland, P. and Fischl, B.},
	year = {2009},
	keywords = {*Algorithms, *Artificial Intelligence, fs\_Misc-methodology, Image Enhancement/*methods, Image Interpretation, Computer-Assisted/*methods, Pattern Recognition, Automated/*methods, Reproducibility of Results, Sensitivity and Specificity, *Subtraction Technique},
	pages = {598--606},
	annote = {Yeo, B T {ThomasSabuncu}, {MertGolland}, {PolinaFischl}, {BruceengP}41 {RR}013218-11/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-03/{RR}/{NCRR} {NIH} {HHS}/P41-{RR}13218/{RR}/{NCRR} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 {EB}001550/{EB}/{NIBIB} {NIH} {HHS}/R01 {EB}001550-03/{EB}/{NIBIB} {NIH} {HHS}/R01 {EB}006758-02/{EB}/{NIBIB} {NIH} {HHS}/R01 {NS}052585-03/{NS}/{NINDS} {NIH} {HHS}/R01 {RR}016594-01A1/{RR}/{NCRR} {NIH} {HHS}/R01 {RR}16594-01A1/{RR}/{NCRR} {NIH} {HHS}/R01-{NS}051826/{NS}/{NINDS} {NIH} {HHS}/R01EB006758/{EB}/{NIBIB} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/U24 {RR}021382-04/{RR}/{NCRR} {NIH} {HHS}/U24-{RR}021382/{RR}/{NCRR} {NIH} {HHS}/U54 {EB}005149-050001/{EB}/{NIBIB} {NIH} {HHS}/U54-{EB}005149/{EB}/{NIBIB} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov'{tResearch} Support, U.S. Gov't, Non-P.H.S.Germany2009/01/01 00:00Med Image Comput Comput Assist Interv. 2009;12(Pt 1):598-606.},
	file = {Yeo-2009-Task-optimal registration cost functi:/autofs/cluster/freesurfer/zotero/storage/ZD3BJ9DV/Yeo-2009-Task-optimal registration cost functi.pdf:application/pdf}
}

@article{sabuncu_dynamics_2011,
	title = {The Dynamics of Cortical and Hippocampal Atrophy in Alzheimer Disease},
	volume = {68},
	issn = {0003-9942},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3248949/},
	doi = {10.1001/archneurol.2011.167},
	abstract = {Objective
To characterize rates of regional Alzheimer disease ({AD})–specific brain atrophy across the presymptomatic, mild cognitive impairment, and dementia stages.

Design
Multicenter case-control study of neuroimaging, cerebrospinal fluid, and cognitive test score data from the Alzheimer’s Disease Neuroimaging Initiative.

Setting
Research centers across the United States and Canada.

Patients
We examined a total of 317 participants with base-line cerebrospinal fluid biomarker measurements and 3T1-weighted magnetic resonance images obtained within 1 year.

Main Outcome Measures
We used automated tools to compute annual longitudinal atrophy in the hippocampus and cortical regions targeted in {AD}. We used Mini-Mental State Examination scores as a measure of cognitive performance. We performed a cross-subject analysis of atrophy rates and acceleration on individuals with an {AD}-like cerebrospinal fluid molecular profile.

Results
In presymptomatic individuals harboring indicators of {AD}, baseline thickness in {AD}-vulnerable cortical regions was significantly reduced compared with that of healthy control individuals, but baseline hippocampal volume was not. Across the clinical spectrum, rates of {AD}-specific cortical thinning increased with decreasing cognitive performance before peaking at approximately the Mini-Mental State Examination score of 21, beyond which rates of thinning started to decline. Annual rates of hippocampal volume loss showed a continuously increasing pattern with decreasing cognitive performance as low as the Mini-Mental State Examination score of 15. Analysis of the second derivative of imaging measurements revealed that {AD}-specific cortical thinning exhibited early acceleration followed by deceleration. Conversely, hippocampal volume loss exhibited positive acceleration across all study participants.

Conclusions
Alzheimer disease–specific cortical thinning and hippocampal volume loss are consistent with a sigmoidal pattern, with an acceleration phase during the early stages of the disease. Clinical trials should carefully consider the nonlinear behavior of these {AD} biomarkers.},
	number = {8},
	urldate = {2014-08-23},
	journal = {Archives of neurology},
	author = {Sabuncu, Mert R. and Desikan, Rahul S. and Sepulcre, Jorge and Yeo, Boon Thye T. and Liu, Hesheng and Schmansky, Nicholas J. and Reuter, Martin and Weiner, Michael W. and Buckner, Randy L. and Sperling, Reisa A. and Fischl, Bruce},
	month = aug,
	year = {2011},
	pmid = {21825241},
	pmcid = {PMC3248949},
	keywords = {Aged, Aged, 80 and over, Alzheimer Disease/*pathology, Atrophy, Case-Control Studies, Cerebral Cortex/*pathology, Female, Hippocampus/*pathology, Humans, Longitudinal Studies, Male, Middle Aged, Nerve Degeneration/*pathology},
	pages = {1040--1048},
	annote = {Sabuncu, Mert {RDesikan}, Rahul {SSepulcre}, {JorgeYeo}, Boon Thye {TLiu}, {HeshengSchmansky}, Nicholas {JReuter}, {MartinWeiner}, Michael {WBuckner}, Randy {LSperling}, Reisa {AFischl}, Bruceeng1KL2RR025757-01/{RR}/{NCRR} {NIH} {HHS}/{AG}022381/{AG}/{NIA} {NIH} {HHS}/K25 {EB}013649/{EB}/{NIBIB} {NIH} {HHS}/K25 {NS}069805/{NS}/{NINDS} {NIH} {HHS}/K25 {NS}069805-01A1/{NS}/{NINDS} {NIH} {HHS}/K25 {NS}069805-02/{NS}/{NINDS} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 {NS}052585-01/{NS}/{NINDS} {NIH} {HHS}/R01EB006758/{EB}/{NIBIB} {NIH} {HHS}/{RC}1 {AT}005728-01/{AT}/{NCCAM} {NIH} {HHS}/U01AG024904/{AG}/{NIA} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/Multicenter {StudyResearch} Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov't2011/08/10 06:00Arch Neurol. 2011 Aug;68(8):1040-8. doi: 10.1001/archneurol.2011.167.},
	file = {PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/68PXN6RM/Sabuncu et al. - 2011 - The Dynamics of Cortical and Hippocampal Atrophy i.pdf:application/pdf;PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/CCCPIPP9/Sabuncu et al. - 2011 - The Dynamics of Cortical and Hippocampal Atrophy i.pdf:application/pdf;PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/NNSXQSTG/Sabuncu et al. - 2011 - The Dynamics of Cortical and Hippocampal Atrophy i.pdf:application/pdf;Sabuncu-2011-The dynamics of cortical and hipp:/autofs/cluster/freesurfer/zotero/storage/2TUDAX3X/Sabuncu-2011-The dynamics of cortical and hipp.pdf:application/pdf}
}

@inproceedings{van_der_kouwe_-line_2003,
	title = {On-Line Automatic Slice Positioning and Between-Scan Correction for Brain {MR} Protocols},
	shorttitle = {On-Line Automatic Slice Positioning and Between-Scan Correction for Brain {MR} Protocols},
	author = {Van der Kouwe, A and Gicquel, S and Chen, G and Schmitt, F and Harder, M and Salat, D and Sorensen, AG and Fischl, B and Dale, A.},
	year = {2003}
}

@inproceedings{yeo_estimates_2010,
	title = {Estimates of Surface-Based Cortical Networks Using Intrinsic Functional Connectivity From 1000 Subjects},
	shorttitle = {Estimates of Surface-Based Cortical Networks Using Intrinsic Functional Connectivity From 1000 Subjects},
	author = {Yeo, B.T. and Sepulcre, J. and Sabuncu, M.R. and Lashkari, D. and Roffman, J.L. and Smoller, J.W. and Fischl, B. and Liu, H. and Buckner., R.L.},
	year = {2010}
}

@article{benner_comparison_2006,
	title = {Comparison of manual and automatic section positioning of brain {MR} images},
	volume = {239},
	issn = {0033-8419 (Print) 0033-8419 (Linking)},
	shorttitle = {Comparison of manual and automatic section positioning of brain {MR} images},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/16507753},
	doi = {10.1148/radiol.2391050221},
	abstract = {The study protocol was approved by the institutional review board and was in full compliance with {HIPAA} guidelines. Informed consent was obtained from all patients. The purpose of this study was to prospectively compare intra- and intersubject variability of manual versus automatic magnetic resonance ({MR}) imaging section prescription. In two examinations, T2-weighted series were acquired with both methods. All intrasubject and three of six intersubject section prescription variances were significantly higher for manual prescription (P {\textless} .01). Root mean square errors confirmed better coregistration of the automated approach (P {\textless} .001). Automatic section prescription leads to improved reproducibility of imaging orientations for intra- and intersubject series in clinical practice.},
	number = {1},
	journal = {Radiology},
	author = {Benner, T. and Wisco, J. J. and van der Kouwe, A. J. and Fischl, B. and Vangel, M. G. and Hochberg, F. H. and Sorensen, A. G.},
	month = apr,
	year = {2006},
	keywords = {Adult, Aged, Aged, 80 and over, Brain Diseases/*diagnosis, Female, Humans, Magnetic Resonance Imaging/*methods, Male, Middle Aged, Prospective Studies},
	pages = {246--54},
	annote = {Benner, {ThomasWisco}, Jonathan Jvan der Kouwe, Andre J {WFischl}, {BruceVangel}, Mark {GHochberg}, Fred {HSorensen}, A Gregoryeng5T32 {CA} 09502/{CA}/{NCI} {NIH} {HHS}/P41 {RR} 14075/{RR}/{NCRR} {NIH} {HHS}/R01 {EB} 001550/{EB}/{NIBIB} {NIH} {HHS}/R01 {RR} 16594-01A1/{RR}/{NCRR} {NIH} {HHS}/R21 {EB} 02530/{EB}/{NIBIB} {NIH} {HHS}/U24 {RR} 021382/{RR}/{NCRR} {NIH} {HHS}/Comparative {StudyResearch} Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov't2006/03/02 09:00Radiology. 2006 Apr;239(1):246-54. Epub 2006 Feb 28.}
}

@article{yeo_effects_2008,
	title = {Effects of registration regularization and atlas sharpness on segmentation accuracy.},
	volume = {12},
	url = {https://surfer.nmr.mgh.harvard.edu/ftp/articles/2008AtlasSharpness.pdf},
	doi = {10.1016/j.media.2008.06.005},
	abstract = {In non-rigid registration, the tradeoff between warp regularization and image fidelity is typically determined empirically. In atlas-based segmentation, this leads to a probabilistic atlas of arbitrary sharpness: weak regularization results in well-aligned training images and a sharp atlas; strong regularization  yields a "blurry" atlas. In this paper, we employ a generative model for the joint registration and segmentation of images. The atlas construction process arises naturally as estimation of the model parameters. This framework allows the computation of unbiased atlases from manually labeled data at various degrees of  "sharpness", as well as the joint registration and segmentation of a novel brain  in a consistent manner. We study the effects of the tradeoff of atlas sharpness and warp smoothness in the context of cortical surface parcellation. This is an important question because of the increasingly availability of atlases in public  databases, and the development of registration algorithms separate from the atlas construction process. We find that the optimal segmentation (parcellation) corresponds to a unique balance of atlas sharpness and warp regularization, yielding statistically significant improvements over the {FreeSurfer} parcellation  algorithm. Furthermore, we conclude that one can simply use a single atlas computed at an optimal sharpness for the registration-segmentation of a new subject with a pre-determined, fixed, optimal warp constraint. The optimal atlas  sharpness and warp smoothness can be determined by probing the segmentation performance on available training data. Our experiments also suggest that segmentation accuracy is tolerant up to a small mismatch between atlas sharpness  and warp smoothness.},
	language = {eng},
	number = {5},
	journal = {Medical image analysis},
	author = {Yeo, B. T. Thomas and Sabuncu, Mert R. and Desikan, Rahul and Fischl, Bruce and Golland, Polina},
	month = oct,
	year = {2008},
	pmid = {18667352},
	pmcid = {PMC2615799},
	keywords = {Algorithms, Artifacts, Artificial Intelligence, Brain/*anatomy \& histology, fs\_Cortical-parcellation, Humans, Image Enhancement/*methods, Image Interpretation, Computer-Assisted/*methods, Imaging, Three-Dimensional/*methods, Magnetic Resonance Imaging/*methods, Pattern Recognition, Automated/*methods, Reproducibility of Results, Sensitivity and Specificity, *Subtraction Technique},
	pages = {603--615}
}

@inproceedings{yendiki_probabilistic_2008,
	title = {Probabilistic Diffusion Tractography with Spatial Priors},
	shorttitle = {Probabilistic Diffusion Tractography with Spatial Priors},
	author = {Yendiki, A. and Stevens, A. and Jbabdi, S. and Augustinack, J. and Salat, D. and Zollei, L. and Behrens, T. and Fischl, B.},
	year = {2008},
	keywords = {fs\_TRACULA},
	pages = {54--61}
}

@article{kallianpur_regional_2012,
	title = {Regional Cortical Thinning Associated with Detectable Levels of {HIV} {DNA}},
	volume = {22},
	issn = {1047-3211, 1460-2199},
	url = {http://cercor.oxfordjournals.org/content/22/9/2065},
	doi = {10.1093/cercor/bhr285},
	abstract = {High levels of human immunodeficiency virus ({HIV}) {DNA} in peripheral blood mononuclear cells ({PBMCs}), and specifically within {CD}14+ blood monocytes, have been found in {HIV}-infected individuals with neurocognitive impairment and dementia. The failure of highly active antiretroviral therapy ({HAART}) to eliminate cognitive dysfunction in {HIV} may be secondary to persistence of {HIV}-infected {PBMCs} which cross the blood-brain barrier, leading to perivascular inflammation and neuronal injury. This study assessed brain cortical thickness relative to {HIV} {DNA} levels and identified, we believe for the first time, a neuroimaging correlate of detectable {PBMC} {HIV} {DNA} in subjects with undetectable {HIV} {RNA}. Cortical thickness was compared between age- and education-matched groups of older ({\textgreater}40 years) {HIV}-seropositive subjects on {HAART} who had detectable (N = 9) and undetectable (N = 10) {PBMC} {HIV} {DNA}. Statistical testing revealed highly significant (P {\textless} 0.001) cortical thinning associated with detectable {HIV} {DNA}. The largest regions affected were in bilateral insula, orbitofrontal and temporal cortices, right superior frontal cortex, and right caudal anterior cingulate. Cortical thinning correlated significantly with a measure of psychomotor speed. The areas of reduced cortical thickness are key nodes in cognitive and emotional processing networks and may be etiologically important in {HIV}-related neurological deficits.},
	language = {en},
	number = {9},
	urldate = {2014-08-23},
	journal = {Cerebral Cortex},
	author = {Kallianpur, Kalpana J. and Kirk, Gregory R. and Sailasuta, Napapon and Valcour, Victor and Shiramizu, Bruce and Nakamoto, Beau K. and Shikuma, Cecilia},
	month = sep,
	year = {2012},
	pmid = {22016479},
	keywords = {Cortical thickness, insula, Magnetic Resonance Imaging, neurocognitive impairment, {PBMC}},
	pages = {2065--2075},
	file = {Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/2SAPR29Z/Kallianpur et al. - 2012 - Regional Cortical Thinning Associated with Detecta.pdf:application/pdf;Snapshot:/autofs/cluster/freesurfer/zotero/storage/42AA5N5A/2065.html:text/html}
}

@article{fjell_selective_2006,
	title = {Selective increase of cortical thickness in high-performing elderly--structural indices of optimal cognitive aging},
	volume = {29},
	issn = {1053-8119 (Print) 1053-8119 (Linking)},
	shorttitle = {Selective increase of cortical thickness in high-performing elderly--structural indices of optimal cognitive aging},
	url = {https://surfer.nmr.mgh.harvard.edu/pub/articles/fjell2006a.pdf},
	doi = {10.1016/j.neuroimage.2005.08.007},
	abstract = {The aim of this study was to identify cortical areas important for optimal cognitive aging. 74 participants (20-88 years) went through neuropsychological tests and two {MR} sessions. The sample was split into two age groups. In each, every participant was classified as "high" or "average" on fluid ability tests and on neuropsychological tests related to executive function. The groups were compared with regard to thickness on a point-by-point basis across the entire cortical mantle. The old high fluid performers had thicker cortex than the average performers in large areas of cortex, while there was minimal difference between the groups of high vs. average executive function. Furthermore, the old group with high fluid function had thicker cortex than the young participants in the posterior cingulate and adjacent areas. Further analyses showed that the latter was a result of a complex aging pattern, differing between the two performance groups, with decades of cortical thickening and subsequent thinning.},
	language = {eng},
	number = {3},
	journal = {Neuroimage},
	author = {Fjell, A. M. and Walhovd, K. B. and Reinvang, I. and Lundervold, A. and Salat, D. and Quinn, B. T. and Fischl, B. and Dale, A. M.},
	month = feb,
	year = {2006},
	keywords = {Adult, Adult, Aged, Aged, Aged, 80 and over, Aged, 80 and over, Aging, Aging/*physiology/*psychology, Cerebral Cortex, Cerebral Cortex/*anatomy \& histology/growth \& development/*physiology, Cognition, Cognition/*physiology, Female, Female, Humans, Humans, Magnetic Resonance Imaging, Magnetic Resonance Imaging, Male, Male, Middle Aged, Middle Aged, Neuropsychological Tests, Neuropsychological Tests, Nonlinear Dynamics, Nonlinear Dynamics, Psychomotor Performance, Psychomotor Performance/physiology},
	pages = {984--94},
	annote = {Fjell, Anders {MWalhovd}, Kristine {BReinvang}, {IvarLundervold}, {ArvidSalat}, {DavidQuinn}, Brian {TFischl}, {BruceDale}, Anders {MengP}41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01-{NS}39581/{NS}/{NINDS} {NIH} {HHS}/R01-{RR}13609/{RR}/{NCRR} {NIH} {HHS}/R01-{RR}16594/{RR}/{NCRR} {NIH} {HHS}/Clinical {TrialResearch} Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov't2005/09/24 09:00Neuroimage. 2006 Feb 1;29(3):984-94. Epub 2005 Sep 19.}
}

@article{segonne_geometrically_2007,
	title = {Geometrically accurate topology-correction of cortical surfaces using nonseparating loops},
	volume = {26},
	issn = {0278-0062 (Print) 0278-0062 (Linking)},
	shorttitle = {Geometrically accurate topology-correction of cortical surfaces using nonseparating loops},
	url = {https://surfer.nmr.mgh.harvard.edu/ftp/articles/IEEE.TMI.segonne.2007.separating.loops.pdf},
	doi = {10.1109/TMI.2006.887364},
	abstract = {In this paper, we focus on the retrospective topology correction of surfaces. We propose a technique to accurately correct the spherical topology of cortical surfaces. Specifically, we construct a mapping from the original surface onto the sphere to detect topological defects as minimal nonhomeomorphic regions. The topology of each defect is then corrected by opening and sealing the surface along a set of nonseparating loops that are selected in a Bayesian framework. The proposed method is a wholly self-contained topology correction algorithm, which determines geometrically accurate, topologically correct solutions based on the magnetic resonance imaging ({MRI}) intensity profile and the expected local curvature. Applied to real data, our method provides topological corrections similar to those made by a trained operator.},
	number = {4},
	journal = {{IEEE} Trans Med Imaging},
	author = {Segonne, F. and Pacheco, J. and Fischl, B.},
	month = apr,
	year = {2007},
	keywords = {Algorithms, *Artificial Intelligence, Bayes Theorem, Cerebral Cortex/*anatomy \& histology, fs\_Topology-correction, Humans, Image Enhancement/*methods, Image Interpretation, Computer-Assisted/*methods, Imaging, Three-Dimensional/*methods, Magnetic Resonance Imaging/*methods, Pattern Recognition, Automated/*methods, Reproducibility of Results, Sensitivity and Specificity},
	pages = {518--29},
	annote = {Segonne, {FlorentPacheco}, {JenniFischl}, {BruceengBIRN}002/{PHS} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 {EB}001550/{EB}/{NIBIB} {NIH} {HHS}/R01 {NS}052585-01/{NS}/{NINDS} {NIH} {HHS}/R01 {RR}16594-01A1/{RR}/{NCRR} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/U54 {EB}005149/{EB}/{NIBIB} {NIH} {HHS}/Evaluation {StudiesResearch} Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov't2007/04/13 09:00IEEE Trans Med Imaging. 2007 Apr;26(4):518-29.}
}

@article{panizzon_distinct_2009,
	title = {Distinct genetic influences on cortical surface area and cortical thickness},
	volume = {19},
	issn = {1460-2199 (Electronic) 1047-3211 (Linking)},
	shorttitle = {Distinct genetic influences on cortical surface area and cortical thickness},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/19299253},
	doi = {10.1093/cercor/bhp026},
	abstract = {Neuroimaging studies examining the effects of aging and neuropsychiatric disorders on the cerebral cortex have largely been based on measures of cortical volume. Given that cortical volume is a product of thickness and surface area, it is plausible that measures of volume capture at least 2 distinct sets of genetic influences. The present study aims to examine the genetic relationships between measures of cortical surface area and thickness. Participants were men in the Vietnam Era Twin Study of Aging (110 monozygotic pairs and 92 dizygotic pairs). Mean age was 55.8 years (range: 51-59). Bivariate twin analyses were utilized in order to estimate the heritability of cortical surface area and thickness, as well as their degree of genetic overlap. Total cortical surface area and average cortical thickness were both highly heritable (0.89 and 0.81, respectively) but were essentially unrelated genetically (genetic correlation = 0.08). This pattern was similar at the lobar and regional levels of analysis. These results demonstrate that cortical volume measures combine at least 2 distinct sources of genetic influences. We conclude that using volume in a genetically informative study, or as an endophenotype for a disorder, may confound the underlying genetic architecture of brain structure.},
	language = {en},
	number = {11},
	urldate = {2014-08-21},
	journal = {Cereb Cortex},
	author = {Panizzon, M. S. and Fennema-Notestine, C. and Eyler, L. T. and Jernigan, T. L. and Prom-Wormley, E. and Neale, M. and Jacobson, K. and Lyons, M. J. and Grant, M. D. and Franz, C. E. and Xian, H. and Tsuang, M. and Fischl, B. and Seidman, L. and Dale, A. and Kremen, W. S.},
	month = nov,
	year = {2009},
	keywords = {Cerebral Cortex/*anatomy \& histology/*physiology, Humans, Male, Middle Aged, Organ Size/genetics, Twins/*genetics},
	pages = {2728--35},
	annote = {Panizzon, Matthew {SFennema}-Notestine, {ChristineEyler}, Lisa {TJernigan}, Terry {LProm}-Wormley, {ElizabethNeale}, {MichaelJacobson}, {KristenLyons}, Michael {JGrant}, Michael {DFranz}, Carol {EXian}, {HongTsuang}, {MingFischl}, {BruceSeidman}, {LarryDale}, {AndersKremen}, William {SengR}01 {AG} 22982/{AG}/{NIA} {NIH} {HHS}/R01 {AG}018386-09/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022381-09/{AG}/{NIA} {NIH} {HHS}/R01 {AG}18384/{AG}/{NIA} {NIH} {HHS}/R01 {AG}18386/{AG}/{NIA} {NIH} {HHS}/R01 {AG}22381/{AG}/{NIA} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov'{tResearch} Support, U.S. Gov't, Non-P.H.S.Twin {StudyNew} York, N.Y. : 19912009/03/21 09:00Cereb Cortex. 2009 Nov;19(11):2728-35. doi: 10.1093/cercor/bhp026. Epub 2009 Mar 18.},
	file = {Panizzon-2009-Distinct genetic influences on c:/autofs/cluster/freesurfer/zotero/storage/AZQZI4Q9/Panizzon-2009-Distinct genetic influences on c.pdf:application/pdf;PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/NHEZDZXK/Panizzon et al. - 2009 - Distinct Genetic Influences on Cortical Surface Ar.pdf:application/pdf}
}

@article{kremen_genetic_2010,
	title = {Genetic and environmental influences on the size of specific brain regions in midlife: the {VETSA} {MRI} study},
	volume = {49},
	issn = {1095-9572 (Electronic) 1053-8119 (Linking)},
	shorttitle = {Genetic and environmental influences on the size of specific brain regions in midlife: the {VETSA} {MRI} study},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/19786105},
	doi = {10.1016/j.neuroimage.2009.09.043},
	abstract = {The impact of genetic and environmental factors on human brain structure is of great importance for understanding normative cognitive and brain aging as well as neuropsychiatric disorders. However, most studies of genetic and environmental influences on human brain structure have either focused on global measures or have had samples that were too small for reliable estimates. Using the classical twin design, we assessed genetic, shared environmental, and individual-specific environmental influences on individual differences in the size of 96 brain regions of interest ({ROIs}). Participants were 474 middle-aged male twins (202 pairs; 70 unpaired) in the Vietnam Era Twin Study of Aging ({VETSA}). They were 51-59 years old, and were similar to U.S. men in their age range in terms of sociodemographic and health characteristics. We measured thickness of cortical {ROIs} and volume of other {ROIs}. On average, genetic influences accounted for approximately 70\% of the variance in the volume of global, subcortical, and ventricular {ROIs} and approximately 45\% of the variance in the thickness of cortical {ROIs}. There was greater variability in the heritability of cortical {ROIs} (0.00-0.75) as compared with subcortical and ventricular {ROIs} (0.48-0.85). The results did not indicate lateralized heritability differences or greater genetic influences on the size of regions underlying higher cognitive functions. The findings provide key information for imaging genetic studies and other studies of brain phenotypes and endophenotypes. Longitudinal analysis will be needed to determine whether the degree of genetic and environmental influences changes for different {ROIs} from midlife to later life.},
	language = {Eng},
	number = {2},
	journal = {Neuroimage},
	author = {Kremen, W. S. and Prom-Wormley, E. and Panizzon, M. S. and Eyler, L. T. and Fischl, B. and Neale, M. C. and Franz, C. E. and Lyons, M. J. and Pacheco, J. and Perry, M. E. and Stevens, A. and Schmitt, J. E. and Grant, M. D. and Seidman, L. J. and Thermenos, H. W. and Tsuang, M. T. and Eisen, S. A. and Dale, A. M. and Fennema-Notestine, C.},
	month = jan,
	year = {2010},
	keywords = {Aging/*genetics/*pathology, Brain/*pathology, *Environment, Humans, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Male, Middle Aged, Organ Size, Quality Control, Twins, United States},
	pages = {1213--23},
	annote = {Kremen, William {SProm}-Wormley, {ElizabethPanizzon}, Matthew {SEyler}, Lisa {TFischl}, {BruceNeale}, Michael {CFranz}, Carol {ELyons}, Michael {JPacheco}, {JenniferPerry}, Michele {EStevens}, {AllisonSchmitt}, J {EricGrant}, Michael {DSeidman}, Larry {JThermenos}, Heidi {WTsuang}, Ming {TEisen}, Seth {ADale}, Anders {MFennema}-Notestine, {ChristineengAG}018384/{AG}/{NIA} {NIH} {HHS}/{AG}018386/{AG}/{NIA} {NIH} {HHS}/{AG}022381/{AG}/{NIA} {NIH} {HHS}/{AG}022982/{AG}/{NIA} {NIH} {HHS}/{BIRN}002/{PHS} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 {AG}018386-06A2/{AG}/{NIA} {NIH} {HHS}/R01 {AG}018386-07/{AG}/{NIA} {NIH} {HHS}/R01 {AG}018386-07S1/{AG}/{NIA} {NIH} {HHS}/R01 {AG}018386-09/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022381-01/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022381-02/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022381-03/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022381-04/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022381-05/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022381-06/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022381-07/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022381-09/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022982-01A1/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022982-02/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022982-03/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022982-04/{AG}/{NIA} {NIH} {HHS}/R01 {NS}052585-01/{NS}/{NINDS} {NIH} {HHS}/R01EB006758/{EB}/{NIBIB} {NIH} {HHS}/U54 {EB}005149/{EB}/{NIBIB} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov'{tResearch} Support, U.S. Gov't, Non-P.H.S.Twin Study2009/09/30 06:00Neuroimage. 2010 Jan 15;49(2):1213-23. doi: 10.1016/j.neuroimage.2009.09.043. Epub 2009 Sep 26.},
	file = {Kremen-2010-Genetic and environmental influenc:/autofs/cluster/freesurfer/zotero/storage/68AH88AC/Kremen-2010-Genetic and environmental influenc.pdf:application/pdf}
}

@article{zhong_quantitative_2010,
	title = {Quantitative evaluation of {LDDMM}, {FreeSurfer}, and {CARET} for cortical surface mapping},
	volume = {52},
	issn = {1095-9572},
	doi = {10.1016/j.neuroimage.2010.03.085},
	abstract = {Cortical surface mapping has been widely used to compensate for individual variability of cortical shape and topology in anatomical and functional studies. While many surface mapping methods were proposed based on landmarks, curves, spherical or native cortical coordinates, few studies have extensively and quantitatively evaluated surface mapping methods across different methodologies. In this study we compared five cortical surface mapping algorithms, including large deformation diffeomorphic metric mapping ({LDDMM}) for curves ({LDDMM}-curve), for surfaces ({LDDMM}-surface), multi-manifold {LDDMM} ({MM}-{LDDMM}), {FreeSurfer}, and {CARET}, using 40 {MRI} scans and 10 simulated datasets. We computed curve variation errors and surface alignment consistency for assessing the mapping accuracy of local cortical features (e.g., gyral/sulcal curves and sulcal regions) and the curvature correlation for measuring the mapping accuracy in terms of overall cortical shape. In addition, the simulated datasets facilitated the investigation of mapping error distribution over the cortical surface when the {MM}-{LDDMM}, {FreeSurfer}, and {CARET} mapping algorithms were applied. Our results revealed that the {LDDMM}-curve, {MM}-{LDDMM}, and {CARET} approaches best aligned the local curve features with their own curves. The {MM}-{LDDMM} approach was also found to be the best in aligning the local regions and cortical folding patterns (e.g., curvature) as compared to the other mapping approaches. The simulation experiment showed that the {MM}-{LDDMM} mapping yielded less local and global deformation errors than the {CARET} and {FreeSurfer} mappings.},
	language = {eng},
	number = {1},
	journal = {{NeuroImage}},
	author = {Zhong, Jidan and Phua, Desiree Yee Ling and Qiu, Anqi},
	month = aug,
	year = {2010},
	pmid = {20381626},
	keywords = {Aged, Algorithms, Cerebral Cortex, Computer Simulation, Databases as Topic, Female, fs\_Validation-Evaluations, Humans, Image Processing, Computer-Assisted, Imaging, Three-Dimensional, Magnetic Resonance Imaging, Male, Middle Aged, Reproducibility of Results, Software, Young Adult},
	pages = {131--141}
}

@article{van_leemput_automated_2009,
	title = {Automated segmentation of hippocampal subfields from ultra-high resolution in vivo {MRI}},
	volume = {19},
	issn = {1098-1063 (Electronic) 1050-9631 (Linking)},
	shorttitle = {Automated segmentation of hippocampal subfields from ultra-high resolution in vivo {MRI}},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/19405131},
	doi = {10.1002/hipo.20615},
	abstract = {Recent developments in {MRI} data acquisition technology are starting to yield images that show anatomical features of the hippocampal formation at an unprecedented level of detail, providing the basis for hippocampal subfield measurement. However, a fundamental bottleneck in {MRI} studies of the hippocampus at the subfield level is that they currently depend on manual segmentation, a laborious process that severely limits the amount of data that can be analyzed. In this article, we present a computational method for segmenting the hippocampal subfields in ultra-high resolution {MRI} data in a fully automated fashion. Using Bayesian inference, we use a statistical model of image formation around the hippocampal area to obtain automated segmentations. We validate the proposed technique by comparing its segmentations to corresponding manual delineations in ultra-high resolution {MRI} scans of 10 individuals, and show that automated volume measurements of the larger subfields correlate well with manual volume estimates. Unlike manual segmentations, our automated technique is fully reproducible, and fast enough to enable routine analysis of the hippocampal subfields in large imaging studies.},
	number = {6},
	journal = {Hippocampus},
	author = {Van Leemput, K. and Bakkour, A. and Benner, T. and Wiggins, G. and Wald, L. L. and Augustinack, J. and Dickerson, B. C. and Golland, P. and Fischl, B.},
	month = jun,
	year = {2009},
	keywords = {Adult, Aged, Aged, 80 and over, Aging/pathology, Algorithms, Alzheimer Disease/pathology, Automation, Bayes Theorem, fs\_Misc-methodology, fs\_Subcortical-segmentation, Hippocampus/*anatomy \& histology/pathology, Humans, Magnetic Resonance Imaging/*methods, Middle Aged, Organ Size, Young Adult},
	pages = {549--57},
	annote = {Van Leemput, {KoenBakkour}, {AkramBenner}, {ThomasWiggins}, {GrahamWald}, Lawrence {LAugustinack}, {JeanDickerson}, Bradford {CGolland}, {PolinaFischl}, {BruceengP}41 {RR}013218-08/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-02/{RR}/{NCRR} {NIH} {HHS}/P41-{RR}13218/{RR}/{NCRR} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 {AG}029411-02/{AG}/{NIA} {NIH} {HHS}/R01 {EB}001550/{EB}/{NIBIB} {NIH} {HHS}/R01 {EB}001550-03/{EB}/{NIBIB} {NIH} {HHS}/R01 {EB}006758-03/{EB}/{NIBIB} {NIH} {HHS}/R01 {NS}051826/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}051826-02/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}052585-01/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}052585-01A1/{NS}/{NINDS} {NIH} {HHS}/R01 {RR}016594-01A1/{RR}/{NCRR} {NIH} {HHS}/R01 {RR}16594-01A1/{RR}/{NCRR} {NIH} {HHS}/R01EB006758/{EB}/{NIBIB} {NIH} {HHS}/R21 {AG}029840-02/{AG}/{NIA} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/U24 {RR}021382-03/{RR}/{NCRR} {NIH} {HHS}/U54 {EB}005149-010014/{EB}/{NIBIB} {NIH} {HHS}/U54-{EB}005149/{EB}/{NIBIB} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov't2009/05/01 09:00Hippocampus. 2009 Jun;19(6):549-57. doi: 10.1002/hipo.20615.},
	file = {Van Leemput-2009-Automated segmentation of hip:/autofs/cluster/freesurfer/zotero/storage/5ZC7D8UP/Van Leemput-2009-Automated segmentation of hip.pdf:application/pdf}
}

@article{espeseth_apolipoprotein_2012,
	title = {Apolipoprotein E ε4-related thickening of the cerebral cortex modulates selective attention},
	volume = {33},
	issn = {1558-1497},
	doi = {10.1016/j.neurobiolaging.2009.12.027},
	abstract = {{APOE} ε4 carriers have thicker cortex in several neocortical areas than ε4 noncarriers (Espeseth T., Westlye L.T., Fjell A.M., Walhovd K.B., Rootwelt H., Reinvang I., 2008. Accelerated age-related cortical thinning in healthy carriers of apolipoprotein E ε4. Neurobiol. Aging 29, 329-340). To investigate potential physiological and cognitive correlates of these anatomical effects structural magnetic resonance imaging ({MRI}) data were obtained from 20 {APOE} ε3 homozygotes and 20 ε4 hetero- and homozygotes, and event-related potentials ({ERPs}) were recorded during a selective attention task (i.e. three-stimulus oddball). Several areas in both hemispheres were thicker in ε4 carriers than in noncarriers. ε4 carriers also had lower amplitudes to distractors (P3a) and lower target detection accuracy than noncarriers. Mean thickness in cortical areas were correlated with P3a amplitudes, which in turn correlated with accuracy. Path analyses showed that {APOE}-related difference in accuracy was mediated by {APOE}-related differences in cortical thickness and P3a amplitudes. The results suggest that {APOE} ε4 modulates the structural integrity of critical nodes in brain attentional networks.},
	language = {eng},
	number = {2},
	journal = {Neurobiology of Aging},
	author = {Espeseth, Thomas and Westlye, Lars T. and Walhovd, Kristine B. and Fjell, Anders M. and Endestad, Tor and Rootwelt, Helge and Reinvang, Ivar},
	month = feb,
	year = {2012},
	pmid = {20382449},
	keywords = {Apolipoprotein E4, Attention, Cerebral Cortex, Female, Heterozygote, Humans, Male, Middle Aged, Statistics as Topic, Tissue Distribution},
	pages = {304--322.e1}
}

@inproceedings{sabuncu_supervised_2009,
	title = {Supervised Nonparametric Image Parcellation.},
	volume = {12(1)},
	shorttitle = {Supervised Nonparametric Image Parcellation.},
	author = {Sabuncu, M.R. and Yeo, B.T. and Van Leemput, K. and Fischl, B. and Golland, P.},
	year = {2009},
	pages = {1075--1083}
}

@article{gronenschild_effects_2012,
	title = {The effects of {FreeSurfer} version, workstation type, and Macintosh operating system version on anatomical volume and cortical thickness measurements},
	volume = {7},
	issn = {1932-6203 (Electronic) 1932-6203 (Linking)},
	shorttitle = {The effects of {FreeSurfer} version, workstation type, and Macintosh operating system version on anatomical volume and cortical thickness measurements},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/22675527 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3365894/pdf/pone.0038234.pdf},
	doi = {10.1371/journal.pone.0038234},
	abstract = {{FreeSurfer} is a popular software package to measure cortical thickness and volume of neuroanatomical structures. However, little if any is known about measurement reliability across various data processing conditions. Using a set of 30 anatomical T1-weighted 3T {MRI} scans, we investigated the effects of data processing variables such as {FreeSurfer} version (v4.3.1, v4.5.0, and v5.0.0), workstation (Macintosh and Hewlett-Packard), and Macintosh operating system version ({OSX} 10.5 and {OSX} 10.6). Significant differences were revealed between {FreeSurfer} version v5.0.0 and the two earlier versions. These differences were on average 8.8 +/- 6.6\% (range 1.3-64.0\%) (volume) and 2.8 +/- 1.3\% (1.1-7.7\%) (cortical thickness). About a factor two smaller differences were detected between Macintosh and Hewlett-Packard workstations and between {OSX} 10.5 and {OSX} 10.6. The observed differences are similar in magnitude as effect sizes reported in accuracy evaluations and neurodegenerative studies.The main conclusion is that in the context of an ongoing study, users are discouraged to update to a new major release of either {FreeSurfer} or operating system or to switch to a different type of workstation without repeating the analysis; results thus give a quantitative support to successive recommendations stated by {FreeSurfer} developers over the years. Moreover, in view of the large and significant cross-version differences, it is concluded that formal assessment of the accuracy of {FreeSurfer} is desirable.},
	language = {en},
	number = {6},
	urldate = {2014-08-21},
	journal = {{PLoS} One},
	author = {Gronenschild, E. H. and Habets, P. and Jacobs, H. I. and Mengelers, R. and Rozendaal, N. and van Os, J. and Marcelis, M.},
	month = jun,
	year = {2012},
	keywords = {Adolescent, Adult, Cerebral Cortex/*anatomy \& histology, *Computers, fs\_Validation-Evaluations, Humans, Magnetic Resonance Imaging/methods, Middle Aged, Organ Size, *Software, Young Adult},
	pages = {e38234},
	annote = {Gronenschild, Ed H B {MHabets}, {PetraJacobs}, Heidi I {LMengelers}, {RonRozendaal}, Nicovan Os, {JimMarcelis}, {MachteldengResearch} Support, Non-U.S. Gov't2012/06/08 06:00PLoS One. 2012;7(6):e38234. doi: 10.1371/journal.pone.0038234. Epub 2012 Jun 1.},
	file = {Gronenschild-2012-The effects of FreeSurfer v1:/autofs/cluster/freesurfer/zotero/storage/F5ZDU752/Gronenschild-2012-The effects of FreeSurfer v1.pdf:application/pdf}
}

@article{alner_distinct_2012,
	title = {Distinct neuropsychological profiles correspond to distribution of cortical thinning in inherited prion disease caused by insertional mutation},
	volume = {83},
	issn = {1468-330X},
	doi = {10.1136/jnnp-2011-300167},
	abstract = {{BACKGROUND}: The human prion diseases are a group of universally fatal neurodegenerative disorders associated with the auto-catalytic misfolding of the normal cell surface prion protein ({PrP}). Mutations causative of inherited human prion disease ({IPD}) include an insertion of six additional octapeptide repeats (6-{OPRI}) and a missense mutation (P102L) with large families segregating for each mutation residing in southern England. Here we report for the first time the neuropsychological and clinical assessments in these two groups.
{METHOD}: The cognitive profiles addressing all major domains were obtained for 26 patients (18 6-{OPRI}, 8 P102L) and the cortical thickness determined using 1.5T {MRI} in a subset of 10 (six 6-{OPRI}, four P102L).
{RESULTS}: The cognitive profiles were different in patients with the two mutations in the symptomatic phase of the disease. The 6-{OPRI} group had lower premorbid optimal levels of functioning (assessed on the {NART}) than the P102L group. In the symptomatic phase of the disease the 6-{OPRI} patients had significantly more executive dysfunction than the P102L group and were more impaired on tests of perception and nominal functions. There was anecdotal evidence of low premorbid social performance in the 6-{OPRI} but not P102L patients. Cortical thinning distribution correlated with the neuropsychological profile in the 6-{OPRI} group principally involving the parietal, occipital and posterior frontal regions. The small number of patients in the P102L group precluded statistical comparison between the groups.
{CONCLUSIONS}: The 6-{OPRI} patients had more widespread and severe cognitive dysfunction than the P102L group and this correlated with cortical thinning distribution.},
	language = {eng},
	number = {1},
	journal = {Journal of Neurology, Neurosurgery, and Psychiatry},
	author = {Alner, K. and Hyare, H. and Mead, S. and Rudge, P. and Wroe, S. and Rohrer, J. D. and Ridgway, G. R. and Ourselin, S. and Clarkson, M. and Hunt, H. and Fox, N. C. and Webb, T. and Collinge, J. and Cipolotti, L.},
	month = jan,
	year = {2012},
	pmid = {21849340},
	keywords = {Adult, Brain, Cognition Disorders, Executive Function, Female, Great Britain, Humans, Magnetic Resonance Imaging, Male, Memory Disorders, Middle Aged, Mutagenesis, Insertional, Neuroimaging, Neuropsychological Tests, Prion Diseases, Prions, Young Adult},
	pages = {109--114}
}

@article{lusebrink_cortical_2013,
	title = {Cortical thickness determination of the human brain using high resolution 3T and 7T {MRI} data},
	volume = {70},
	issn = {1095-9572 (Electronic) 1053-8119 (Linking)},
	shorttitle = {Cortical thickness determination of the human brain using high resolution 3T and 7T {MRI} data},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/23261638},
	doi = {10.1016/j.neuroimage.2012.12.016},
	abstract = {{PURPOSE}: The analysis of the human cerebral cortex and the measurement of its thickness based on {MRI} data can provide insight into normal brain development and neurodegenerative disorders. Accurate and reproducible results of the cortical thickness measurement are desired for sensitive detection. This study compares ultra-high resolution data acquired at 7T with 3T data for determination of the cortical thickness of the human brain. The impact of field strength, resolution, and processing method is evaluated systematically. {METHODS}: Five subjects were scanned at 3T (1 mm isotropic resolution) and 7T (1 mm and 0.5 mm isotropic resolution) with 3D {MP}-{RAGE} and 3D gradient echo methods. The inhomogeneous signal and contrast of the 7T data due to the B1 field was corrected by division of the {MP}-{RAGE} with the {GE}. {ARCTIC}, utilizing a voxel-based approach, and {FreeSurfer}, utilizing a surface-based approach, have been used to compute the cortical thickness of the high resolution 3T and 7T data and of the ultra-high resolution 7T data. {FreeSurfer} is not designed to process data with a spatial resolution other than 1mm and was modified to avoid this limitation. Additionally {SPM} and {FSL} have been used to generate segmentations which were further processed with {ARCTIC} to determine the cortical thickness. {RESULTS} {AND} {CONCLUSION}: At identical resolution, the cortical thickness determination yielded consistent results between 3T and 7T confirming the robustness of the acquisition and processing against potential field strength related effects. However, the ultra-high resolution 7T data resulted in significantly reduced values for the cortical thickness estimation compared to the lower resolution data. The reduction in thickness amounts approximately one sixth to one third, depending on the processing algorithm and software used. This suggests a bias in the gray matter segmentation due to partial volume effects and indicates that true cortical thickness is overestimated by most current {MR} studies using both a voxel-based or surface-based method and can be more accurately determined with high resolution imaging at 7T.},
	language = {en},
	urldate = {2014-08-21},
	journal = {Neuroimage},
	author = {Lusebrink, F. and Wollrab, A. and Speck, O.},
	month = apr,
	year = {2013},
	keywords = {Adult, Adult, Brain Mapping, Brain Mapping/methods, Cerebral Cortex, Cerebral Cortex/*anatomy \& histology, fs\_Validation-Evaluations, Humans, Humans, Magnetic Resonance Imaging, *Magnetic Resonance Imaging/methods, Male, Male, Middle Aged, Middle Aged},
	pages = {122--31},
	annote = {Lusebrink, {FalkWollrab}, {AstridSpeck}, {OliverengResearch} Support, Non-U.S. Gov't2012/12/25 06:00Neuroimage. 2013 Apr 15;70:122-31. doi: 10.1016/j.neuroimage.2012.12.016. Epub 2012 Dec 20.}
}

@article{kremen_finding_2009,
	title = {Finding converging evidence in inconsistent results: The case for the heritability of brain ventricle size},
	volume = {39},
	issn = {0001-8244},
	shorttitle = {Finding converging evidence in inconsistent results: The case for the heritability of brain ventricle size},
	url = {://WOS:000272027300095},
	number = {6},
	journal = {Behavior Genetics},
	author = {Kremen, W. and Panizzon, M. and Neale, M. and Fennema-Notestine, C. and Prom-Wormley, E. and Eyler, L. and Pacheco, J. and Stevens, A. and Franz, C. and Lyons, M. and Grant, M. and Jak, A. and Jernigan, T. and Fischl, B. and Seidman, L. and Dale, A.},
	month = nov,
	year = {2009},
	pages = {664--664},
	annote = {Times Cited: 0Kremen, William Panizzon, Matthew Neale, Michael Fennema-Notestine, Christine Prom-Wormley, Elizabeth Eyler, Lisa Pacheco, Jenni Stevens, Allison Franz, Carol Lyons, Michael Grant, Michael Jak, Amy Jernigan, Terry Fischl, Bruce Seidman, Larry Dale, Anders39th Annual Meeting of the Behavior-Genetics-{AssociationJun} 17-20, 2009Mineapolis, {MN}}
}

@article{morey_scan-rescan_2010,
	title = {Scan-rescan reliability of subcortical brain volumes derived from automated segmentation},
	volume = {31},
	issn = {1097-0193},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3782252/},
	doi = {10.1002/hbm.20973},
	abstract = {Large-scale longitudinal studies of regional brain volume require reliable quantification using automated segmentation and labeling. However, repeated {MR} scanning of the same subject, even if using the same scanner and acquisition parameters, does not result in identical images due to small changes in image orientation, changes in prescan parameters, and magnetic field instability. These differences may lead to appreciable changes in estimates of volume for different structures. This study examined scan-rescan reliability of automated segmentation algorithms for measuring several subcortical regions, using both within-day and across-day comparison sessions in a group of 23 normal participants. We found that the reliability of volume measures including percent volume difference, percent volume overlap (Dice's coefficient), and intraclass correlation coefficient ({ICC}), varied substantially across brain regions. Low reliability was observed in some structures such as the amygdala ({ICC} = 0.6), with higher reliability ({ICC} = 0.9) for other structures such as the thalamus and caudate. Patterns of reliability across regions were similar for automated segmentation with {FSL}/{FIRST} and {FreeSurfer} (longitudinal stream). Reliability was associated with the volume of the structure, the ratio of volume to surface area for the structure, the magnitude of the interscan interval, and the method of segmentation. Sample size estimates for detecting changes in brain volume for a range of likely effect sizes also differed by region. Thus, longitudinal research requires a careful analysis of sample size and choice of segmentation method combined with a consideration of the brain structure(s) of interest and the magnitude of the anticipated effects.},
	language = {eng},
	number = {11},
	journal = {Human Brain Mapping},
	author = {Morey, Rajendra A. and Selgrade, Elizabeth S. and Wagner, Henry Ryan and Huettel, Scott A. and Wang, Lihong and McCarthy, Gregory},
	month = nov,
	year = {2010},
	pmid = {20162602},
	pmcid = {PMC3782252},
	keywords = {Adult, Analysis of Variance, Brain, Female, fs\_Validation-Evaluations, Humans, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Male, Organ Size, Reproducibility of Results},
	pages = {1751--1762}
}

@article{fischl_measuring_2000,
	title = {Measuring the thickness of the human cerebral cortex from magnetic resonance images},
	volume = {97},
	issn = {0027-8424 (Print) 0027-8424 (Linking)},
	shorttitle = {Measuring the thickness of the human cerebral cortex from magnetic resonance images},
	url = {https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl00-cortical-thickness.pdf},
	doi = {10.1073/pnas.200033797},
	abstract = {Accurate and automated methods for measuring the thickness of human cerebral cortex could provide powerful tools for diagnosing and studying a variety of neurodegenerative and psychiatric disorders. Manual methods for estimating cortical thickness from neuroimaging data are labor intensive, requiring several days of effort by a trained anatomist. Furthermore, the highly folded nature of the cortex is problematic for manual techniques, frequently resulting in measurement errors in regions in which the cortical surface is not perpendicular to any of the cardinal axes. As a consequence, it has been impractical to obtain accurate thickness estimates for the entire cortex in individual subjects, or group statistics for patient or control populations. Here, we present an automated method for accurately measuring the thickness of the cerebral cortex across the entire brain and for generating cross-subject statistics in a coordinate system based on cortical anatomy. The intersubject standard deviation of the thickness measures is shown to be less than 0.5 mm, implying the ability to detect focal atrophy in small populations or even individual subjects. The reliability and accuracy of this new method are assessed by within-subject test-retest studies, as well as by comparison of cross-subject regional thickness measures with published values.},
	number = {20},
	journal = {Proc Natl Acad Sci U S A},
	author = {Fischl, B. and Dale, A. M.},
	month = sep,
	year = {2000},
	keywords = {Cerebral Cortex/*cytology/*radiography, fs\_Thickness-measurement, Humans, Image Processing, Computer-Assisted, Magnetic Resonance Imaging},
	pages = {11050--5},
	annote = {Fischl, {BDale}, A {MengP}41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01-{NS}39581/{NS}/{NINDS} {NIH} {HHS}/R01-{RR}13609/{RR}/{NCRR} {NIH} {HHS}/Research Support, U.S. Gov't, P.H.S.2000/09/14 11:00Proc Natl Acad Sci U S A. 2000 Sep 26;97(20):11050-5.},
	file = {Fischl-2000-Measuring the thickness of the hum:/autofs/cluster/freesurfer/zotero/storage/IXF88IQE/Fischl-2000-Measuring the thickness of the hum.pdf:application/pdf}
}

@article{walhovd_regional_2006,
	title = {Regional cortical thickness matters in recall after months more than minutes},
	volume = {31},
	shorttitle = {Regional cortical thickness matters in recall after months more than minutes},
	url = {http://www.sciencedirect.com/science/article/pii/S1053811906000462},
	number = {3},
	journal = {{NeuroImage}},
	author = {Walhovd, Kristine B and Fjell, Anders Martin and Dale, Anders M and Fischl, Bruce and Quinn, Brian T and Makris, Nikos and Salat, David and Reinvang, Ivar.},
	year = {2006},
	keywords = {Adult, Aged, Aging, Cerebral Cortex, Dominance, Cerebral, Female, Hippocampus, Humans, Image Processing, Computer-Assisted, Imaging, Three-Dimensional, Magnetic Resonance Imaging, Male, Mathematical Computing, Memory, Short-Term, Mental Recall, Middle Aged, Parahippocampal Gyrus, Retention (Psychology), Statistics as Topic, Verbal Learning},
	pages = {1343--1351}
}

@article{fjell_relationship_2008,
	title = {The relationship between diffusion tensor imaging and volumetry as measures of white matter properties},
	volume = {42},
	issn = {1053-8119},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808804/},
	doi = {10.1016/j.neuroimage.2008.06.005},
	abstract = {There is still limited knowledge about the relationship between different structural brain parameters, despite huge progress in analysis of neuroimaging data. The aim of the present study was to test the relationship between fractional anisotropy ({FA}) from diffusion tensor imaging ({DTI}) and regional white matter ({WM}) volume. As {WM} volume has been shown to develop until middle age, the focus was on changes in {WM} properties in the age range of 40 to 60 years. 100 participants were scanned with magnetic resonance imaging ({MRI}). Each hemisphere was parcellated into 35 {WM} regions, and volume, {FA}, axial, and radial diffusion in each region were calculated. The relationships between age and the regional measures of {FA} and {WM} volume were tested, and then {FA} and {WM} volume were correlated, corrected for intracranial volume, age, and sex. {WM} volume was weakly related to age, while {FA} correlated negatively with age in 26 of 70 regions, caused by a mix of reduced axial and increased radial diffusion with age. 23 relationships between {FA} and {WM} volume were found, with seven being positive and sixteen negative. The positive correlations were mainly caused by increased radial diffusion. It is concluded that {FA} is more sensitive than volume to changes in {WM} integrity during middle age, and that {FA}-age correlations probably are related to reduced amount of myelin with increasing age. Further, {FA} and {WM} volume are moderately to weakly related and to a large extent sensitive to different characteristics of {WM} integrity.},
	number = {4},
	urldate = {2014-08-25},
	journal = {{NeuroImage}},
	author = {Fjell, Anders M. and Westlye, Lars T. and Greve, Doug N. and Fischl, Bruce and Benner, Thomas and van der Kouwe, Andre J.W. and Salat, David and Bj?rnerud, Atle and Due-T?nnessen, Paulina and Walhovd, Kristine B.},
	month = oct,
	year = {2008},
	pmid = {18620064},
	pmcid = {PMC2808804},
	keywords = {Aging/*pathology, *Algorithms, Brain/*anatomy \& histology, Diffusion Magnetic Resonance Imaging/*methods, Female, Humans, Image Enhancement/methods, Image Interpretation, Computer-Assisted/*methods, Imaging, Three-Dimensional/*methods, Male, Nerve Fibers, Myelinated/*ultrastructure, Reproducibility of Results, Sensitivity and Specificity, Statistics as Topic},
	pages = {1654--1668},
	annote = {Fjell, Anders {MWestlye}, Lars {TGreve}, Doug {NFischl}, {BruceBenner}, Thomasvan der Kouwe, Andre J {WSalat}, {DavidBjornerud}, {AtleDue}-Tonnessen, {PaulinaWalhovd}, Kristine {BengP}41 {RR}014075/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-075751/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-075752/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-075753/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-086765/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-086766/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-086767/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-098601/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-098602/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-098603/{RR}/{NCRR} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 {EB}001550/{EB}/{NIBIB} {NIH} {HHS}/R01 {EB}006758/{EB}/{NIBIB} {NIH} {HHS}/R01 {EB}006758-01A1/{EB}/{NIBIB} {NIH} {HHS}/R01 {EB}006758-02/{EB}/{NIBIB} {NIH} {HHS}/R01 {NS}052585/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}052585-01A1/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}052585-02/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}052585-02S1/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}052585-03/{NS}/{NINDS} {NIH} {HHS}/R01 {RR}016594/{RR}/{NCRR} {NIH} {HHS}/R01 {RR}016594-01A1/{RR}/{NCRR} {NIH} {HHS}/R01 {RR}016594-02/{RR}/{NCRR} {NIH} {HHS}/R01 {RR}016594-03/{RR}/{NCRR} {NIH} {HHS}/R01 {RR}016594-04/{RR}/{NCRR} {NIH} {HHS}/R01-{NS}39581/{NS}/{NINDS} {NIH} {HHS}/R01-{RR}13609/{RR}/{NCRR} {NIH} {HHS}/R01-{RR}16594/{RR}/{NCRR} {NIH} {HHS}/R01EB006758/{EB}/{NIBIB} {NIH} {HHS}/R01NS052585-01/{NS}/{NINDS} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov't2008/07/16 09:00Neuroimage. 2008 Oct 1;42(4):1654-68. doi: 10.1016/j.neuroimage.2008.06.005. Epub 2008 Jun 17.},
	file = {Fjell-2008-The relationship between diffusion:/autofs/cluster/freesurfer/zotero/storage/BWVNIU2J/Fjell-2008-The relationship between diffusion.pdf:application/pdf;PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/WUDUTWTF/Fjell et al. - 2008 - The relationship between diffusion tensor imaging .pdf:application/pdf}
}

@inproceedings{yu_cortical_2007,
	title = {Cortical Folding Development Study based on Over-Complete Spherical Wavelets},
	url = {https://surfer.nmr.mgh.harvard.edu/ftp/articles/yu_MMBIA_2007.pdf},
	doi = {10.1109/ICCV.2007.4409137},
	abstract = {We introduce the use of over-complete spherical wavelets for shape analysis of 2D closed surfaces. Bi-orthogonal spherical wavelets have been shown to be powerful tools in the segmentation and shape analysis of 2D closed surfaces, but unfortunately they suffer from aliasing problems and are therefore not invariant under rotations of the underlying surface parameterization. In this paper, we demonstrate the theoretical advantage of over-complete wavelets over bi-orthogonal wavelets and illustrate their utility on both synthetic and real data. In particular, we show that over-complete spherical wavelets allow us to build more stable cortical folding development models, and detect a wider array of regions of folding development in a newborn dataset.},
	booktitle = {{IEEE} 11th International Conference on Computer Vision, 2007. {ICCV} 2007},
	author = {Yu, Peng and Yeo, B.T.T. and Grant, P.E. and Fischl, B. and Golland, P.},
	month = oct,
	year = {2007},
	keywords = {2D closed surface, Biomedical imaging, biorthogonal spherical wavelets, cortical folding development, Frequency, Image analysis, image segmentation, medical image processing, over-complete spherical wavelets, Shape, shape analysis, Signal processing, surface parameterization, surface segmentation, Surface waves, Wavelet analysis, Wavelet coefficients, wavelet transforms},
	pages = {1--8},
	file = {IEEE Xplore Abstract Record:/autofs/cluster/freesurfer/zotero/storage/376TEQ2M/login.html:text/html}
}

@article{bar_cortical_2001,
	title = {Cortical mechanisms specific to explicit visual object recognition},
	volume = {29},
	shorttitle = {Cortical mechanisms specific to explicit visual object recognition},
	abstract = {The cortical mechanisms associated with conscious object recognition were studied using functional magnetic resonance imaging ({fMRI}). Participants were required to recognize pictures of masked objects that were presented very briefly, randomly and repeatedly. This design yielded a gradual accomplishment of successful recognition. Cortical activity in a ventrotemporal visual region was linearly correlated with perception of object identity. Therefore, although object recognition is rapid, awareness of an object's identity is not a discrete phenomenon but rather associated with gradually increasing cortical activity. Furthermore, the focus of the activity in the temporal cortex shifted anteriorly as subjects reported an increased knowledge regarding identity. The results presented here provide new insights into the processes underlying explicit object recognition, as well as the analysis that takes place immediately before and after recognition is possible},
	number = {2},
	journal = {Neuron},
	author = {Bar, M. and Tootell, R. B. and Schacter, D. L. and Greve, D. N. and Fischl, B. and Mendola, J. D. and Rosen, B. R. and Dale, A. M.},
	year = {2001},
	pmid = {11239441 http://ac.els-cdn.com/S0896627301002240/1-s2.0-S0896627301002240-main.pdf?_tid=638fd578-2a27-11e4-a152-00000aacb35d&acdnat=1408731119_0135454044615bae5412f4029b36d3ec},
	keywords = {Adult, Awareness, Cerebral Cortex, cortex, Female, human, Magnetic Resonance Imaging, methods, Perception, Photic Stimulation, physiology, Reaction Time, Recognition (Psychology), Support,Non-U.S.Gov't, Support,U.S.Gov't,P.H.S., temporal cortex, United States},
	pages = {529--535},
	annote = {{UI} - 21134733NOT {IN} {FILE}},
	file = {Bar-2001-Cortical mechanisms specific to expli:/autofs/cluster/freesurfer/zotero/storage/4EGUCSB6/Bar-2001-Cortical mechanisms specific to expli.pdf:application/pdf}
}

@article{salat_regional_2009,
	title = {Regional white matter volume differences in nondemented aging and Alzheimer's disease},
	volume = {44},
	issn = {1095-9572},
	url = {https://surfer.nmr.mgh.harvard.edu/pub/articles/salat_2008.pdf},
	doi = {10.1016/j.neuroimage.2008.10.030},
	abstract = {Accumulating evidence suggests that altered cerebral white matter ({WM}) influences normal aging, and further that {WM} degeneration may modulate the clinical expression of Alzheimer's disease ({AD}). Here we conducted a study of differences in {WM} volume across the adult age span and in {AD} employing a newly developed, automated method for regional parcellation of the subcortical {WM} that uses curvature landmarks and gray matter ({GM})/{WM} surface boundary information. This procedure measures the volume of gyral {WM}, utilizing a distance constraint to limit the measurements from extending into the centrum semiovale. Regional estimates were first established to be reliable across two scan sessions in 20 young healthy individuals. Next, the method was applied to a large clinically-characterized sample of 299 individuals including 73 normal older adults and 91 age-matched participants with very mild to mild {AD}. The majority of measured regions showed a decline in volume with increasing age, with strong effects found in bilateral fusiform, lateral orbitofrontal, superior frontal, medial orbital frontal, inferior temporal, and middle temporal {WM}. The association between {WM} volume and age was quadratic in many regions suggesting that {WM} volume loss accelerates in advanced aging. A number of {WM} regions were further reduced in {AD} with parahippocampal, entorhinal, inferior parietal and rostral middle frontal {WM} showing the strongest {AD}-associated reductions. There were minimal sex effects after correction for intracranial volume, and there were associations between ventricular volume and regional {WM} volumes in the older adults and {AD} that were not apparent in the younger adults. Certain results, such as the loss of {WM} in the fusiform region with aging, were unexpected and provide novel insight into patterns of age associated neural and cognitive decline. Overall, these results demonstrate the utility of automated regional {WM} measures in revealing the distinct patterns of age and {AD} associated volume loss that may contribute to cognitive decline.},
	language = {eng},
	number = {4},
	journal = {{NeuroImage}},
	author = {Salat, David H. and Greve, Douglas N. and Pacheco, Jennifer L. and Quinn, Brian T. and Helmer, Karl G. and Buckner, Randy L. and Fischl, Bruce},
	month = feb,
	year = {2009},
	pmid = {19027860},
	pmcid = {PMC2810540},
	keywords = {Aged, Aged, Aging, Aging/*pathology, Alzheimer Disease, Alzheimer Disease/*pathology, Brain, Brain/*pathology, Dementia, Dementia/*pathology, Female, Female, Humans, Humans, Imaging, Three-Dimensional, Imaging, Three-Dimensional/*methods, Magnetic Resonance Imaging, Magnetic Resonance Imaging/*methods, Male, Male, Nerve Fibers, Myelinated, Nerve Fibers, Myelinated/*pathology, Young Adult, Young Adult},
	pages = {1247--1258},
	annote = {Salat, David {HGreve}, Douglas {NPacheco}, Jennifer {LQuinn}, Brian {THelmer}, Karl {GBuckner}, Randy {LFischl}, {BruceengAG}024898/{AG}/{NIA} {NIH} {HHS}/{AG}05681/{AG}/{NIA} {NIH} {HHS}/{AG}05886/{AG}/{NIA} {NIH} {HHS}/F32 {AG}005886-01/{AG}/{NIA} {NIH} {HHS}/K01 {AG}024898-01A1/{AG}/{NIA} {NIH} {HHS}/{NR}010827/{NR}/{NINR} {NIH} {HHS}/{NS}39581/{NS}/{NINDS} {NIH} {HHS}/P41 {RR}014075/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-01A1/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-06/{RR}/{NCRR} {NIH} {HHS}/P41RR14075/{RR}/{NCRR} {NIH} {HHS}/P50 {AG}005681-19S20029/{AG}/{NIA} {NIH} {HHS}/P50 {AG}005681-25/{AG}/{NIA} {NIH} {HHS}/R01 {AG}034556-02/{AG}/{NIA} {NIH} {HHS}/R01 {AG}034556-03/{AG}/{NIA} {NIH} {HHS}/R01 {NR}010827-02/{NR}/{NINR} {NIH} {HHS}/R01 {NR}010827-05/{NR}/{NINR} {NIH} {HHS}/R01 {NS}039581/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}039581-01/{NS}/{NINDS} {NIH} {HHS}/{RR}14075/{RR}/{NCRR} {NIH} {HHS}/Howard Hughes Medical Institute/Research Support, N.I.H., Extramural2008/11/26 09:00Neuroimage. 2009 Feb 15;44(4):1247-58. doi: 10.1016/j.neuroimage.2008.10.030. Epub 2008 Nov 5.},
	file = {PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/54QBBD2F/Salat et al. - 2009 - REGIONAL WHITE MATTER VOLUME DIFFERENCES IN NONDEM.pdf:application/pdf;Salat-2009-Regional white matter volume differ:/autofs/cluster/freesurfer/zotero/storage/2KIR382R/Salat-2009-Regional white matter volume differ.pdf:application/pdf}
}

@article{wright_neuroanatomical_2006,
	title = {Neuroanatomical correlates of extraversion and neuroticism},
	volume = {16},
	issn = {1047-3211},
	doi = {10.1093/cercor/bhj118},
	abstract = {Introversion/extraversion and neuroticism are 2 important and frequently studied dimensions of human personality. These dimensions describe individual differences in emotional responding across a range of situations and may contribute to a predisposition for psychiatric disorders. Recent neuroimaging research has begun to provide evidence that neuroticism and introversion/extraversion have specific functional and structural neural correlates. Previous studies in healthy adults have reported an association between neuroticism, introversion/extraversion, and the activity of the prefrontal cortex and amygdala. Studies of individuals with psychopathological states have also indicated that anatomic variations in these brain areas may relate to extraversion and neuroticism. The purpose of the present study was to examine selected structural correlates of neuroticism and extraversion in healthy subjects (n = 28) using neuroanatomic measures of the cerebral cortex and amygdala. We observed that the thickness of specific prefrontal cortex regions correlates with measures of extraversion and neuroticism. In contrast, no such correlations were observed for the volume of the amygdala. The results suggest that specific aspects of regional prefrontal anatomy are associated with specific personality traits.},
	language = {eng},
	number = {12},
	journal = {Cerebral Cortex (New York, N.Y.: 1991)},
	author = {Wright, Christopher I. and Williams, Danielle and Feczko, Eric and Barrett, Lisa Feldman and Dickerson, Bradford C. and Schwartz, Carl E. and Wedig, Michelle M.},
	month = dec,
	year = {2006},
	pmid = {16421327},
	keywords = {Adult, Amygdala, Brain Mapping, Cerebral Cortex, Extraversion (Psychology), Female, Humans, Magnetic Resonance Imaging, Male, Neurotic Disorders, Personality Inventory, Sex Factors},
	pages = {1809--1819}
}

@article{fischl_sequence-independent_2004,
	title = {Sequence-independent segmentation of magnetic resonance images},
	volume = {23 Suppl 1},
	issn = {1053-8119 (Print) 1053-8119 (Linking)},
	shorttitle = {Sequence-independent segmentation of magnetic resonance images},
	url = {http://www.nmr.mgh.harvard.edu/~fischl/reprints/sequence_independent_segmentation_reprint.pdf},
	doi = {10.1016/j.neuroimage.2004.07.016},
	abstract = {We present a set of techniques for embedding the physics of the imaging process that generates a class of magnetic resonance images ({MRIs}) into a segmentation or registration algorithm. This results in substantial invariance to acquisition parameters, as the effect of these parameters on the contrast properties of various brain structures is explicitly modeled in the segmentation. In addition, the integration of image acquisition with tissue classification allows the derivation of sequences that are optimal for segmentation purposes. Another benefit of these procedures is the generation of probabilistic models of the intrinsic tissue parameters that cause {MR} contrast (e.g., T1, proton density, T2*), allowing access to these physiologically relevant parameters that may change with disease or demographic, resulting in nonmorphometric alterations in {MR} images that are otherwise difficult to detect. Finally, we also present a high band width multiecho {FLASH} pulse sequence that results in high signal-to-noise ratio with minimal image distortion due to B0 effects. This sequence has the added benefit of allowing the explicit estimation of T2* and of reducing test-retest intensity variability.},
	language = {eng},
	journal = {Neuroimage},
	author = {Fischl, B. and Salat, D. H. and van der Kouwe, A. J. and Makris, N. and Segonne, F. and Quinn, B. T. and Dale, A. M.},
	year = {2004},
	keywords = {Algorithms, Brain/*anatomy \& histology/*pathology, Cerebral Cortex/anatomy \& histology/pathology, Echo-Planar Imaging, fs\_Subcortical-segmentation, Functional Laterality/physiology, Humans, Image Processing, Computer-Assisted/*statistics \& numerical data, Magnetic Resonance Imaging/*statistics \& numerical data, Models, Statistical, Nonlinear Dynamics},
	pages = {S69--84},
	annote = {Fischl, {BruceSalat}, David Hvan der Kouwe, Andre J {WMakris}, {NikosSegonne}, {FlorentQuinn}, Brian {TDale}, Anders {MengP}41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 {RR}16594-01A1/{RR}/{NCRR} {NIH} {HHS}/Research Support, Non-U.S. Gov'{tResearch} Support, U.S. Gov't, P.H.S.2004/10/27 09:00Neuroimage. 2004;23 Suppl 1:S69-84.}
}

@article{custo_anatomical_2010,
	title = {Anatomical atlas-guided diffuse optical tomography of brain activation},
	volume = {49},
	issn = {1095-9572 (Electronic) 1053-8119 (Linking)},
	shorttitle = {Anatomical atlas-guided diffuse optical tomography of brain activation},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/19643185},
	doi = {10.1016/j.neuroimage.2009.07.033},
	abstract = {We describe a neuroimaging protocol that utilizes an anatomical atlas of the human head to guide diffuse optical tomography of human brain activation. The protocol is demonstrated by imaging the hemodynamic response to median-nerve stimulation in three healthy subjects, and comparing the images obtained using a head atlas with the images obtained using the subject-specific head anatomy. The results indicate that using the head atlas anatomy it is possible to reconstruct the location of the brain activation to the expected gyrus of the brain, in agreement with the results obtained with the subject-specific head anatomy. The benefits of this novel method derive from eliminating the need for subject-specific head anatomy and thus obviating the need for a subject-specific {MRI} to improve the anatomical interpretation of diffuse optical tomography images of brain activation.},
	number = {1},
	journal = {Neuroimage},
	author = {Custo, A. and Boas, D. A. and Tsuzuki, D. and Dan, I. and Mesquita, R. and Fischl, B. and Grimson, W. E. and Wells, 3rd, W.},
	month = jan,
	year = {2010},
	keywords = {Adult, Aged, Aging/physiology, Algorithms, Atlases as Topic, Brain/*physiology, Cerebrospinal Fluid/physiology, Cerebrovascular Circulation/physiology, Female, Functional Laterality/physiology, Head/anatomy \& histology, Humans, Image Processing, Computer-Assisted/methods, Imaging, Three-Dimensional, Linear Models, Male, Median Nerve/physiology, Middle Aged, Monte Carlo Method, Somatosensory Cortex/anatomy \& histology/physiology, Tomography, Optical, Young Adult},
	pages = {561--7},
	annote = {Custo, {AnnaBoas}, David {ATsuzuki}, {DaisukeDan}, {IppeitaMesquita}, {RicksonFischl}, {BruceGrimson}, W Eric {LWells}, Williams 3rdengP41 {RR}013218-12/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-10/{RR}/{NCRR} {NIH} {HHS}/P41-{RR}13218/{RR}/{NCRR} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/U54 {EB}005149-02/{EB}/{NIBIB} {NIH} {HHS}/U54-{EB}-005149/{EB}/{NIBIB} {NIH} {HHS}/Research Support, N.I.H., Extramural2009/08/01 09:00Neuroimage. 2010 Jan 1;49(1):561-7. doi: 10.1016/j.neuroimage.2009.07.033. Epub 2009 Jul 28.},
	file = {Custo-2010-Anatomical atlas-guided diffuse opt:/autofs/cluster/freesurfer/zotero/storage/EIPG8ASX/Custo-2010-Anatomical atlas-guided diffuse opt.pdf:application/pdf;PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/GGVUA74H/Custo et al. - 2010 - Anatomical Atlas-Guided Diffuse Optical Tomography.pdf:application/pdf}
}

@article{fennema-notestine_quantitative_2006,
	title = {Quantitative evaluation of automated skull-stripping methods applied to contemporary and legacy images: effects of diagnosis, bias correction, and slice location},
	volume = {27},
	issn = {1065-9471 (Print) 1065-9471 (Linking)},
	shorttitle = {Quantitative evaluation of automated skull-stripping methods applied to contemporary and legacy images: effects of diagnosis, bias correction, and slice location},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2408865/},
	doi = {10.1002/hbm.20161},
	abstract = {Performance of automated methods to isolate brain from nonbrain tissues in magnetic resonance ({MR}) structural images may be influenced by {MR} signal inhomogeneities, type of {MR} image set, regional anatomy, and age and diagnosis of subjects studied. The present study compared the performance of four methods: Brain Extraction Tool ({BET}; Smith [2002]: Hum Brain Mapp 17:143-155); 3dIntracranial (Ward [1999] Milwaukee: Biophysics Research Institute, Medical College of Wisconsin; in {AFNI}); a Hybrid Watershed algorithm ({HWA}, Segonne et al. [2004] Neuroimage 22:1060-1075; in {FreeSurfer}); and Brain Surface Extractor ({BSE}, Sandor and Leahy [1997] {IEEE} Trans Med Imag 16:41-54; Shattuck et al. [2001] Neuroimage 13:856-876) to manually stripped images. The methods were applied to uncorrected and bias-corrected datasets; Legacy and Contemporary T1-weighted image sets; and four diagnostic groups (depressed, Alzheimer's, young and elderly control). To provide a criterion for outcome assessment, two experts manually stripped six sagittal sections for each dataset in locations where brain and nonbrain tissue are difficult to distinguish. Methods were compared on Jaccard similarity coefficients, Hausdorff distances, and an Expectation-Maximization algorithm. Methods tended to perform better on contemporary datasets; bias correction did not significantly improve method performance. Mesial sections were most difficult for all methods. Although {AD} image sets were most difficult to strip, {HWA} and {BSE} were more robust across diagnostic groups compared with 3dIntracranial and {BET}. With respect to specificity, {BSE} tended to perform best across all groups, whereas {HWA} was more sensitive than other methods. The results of this study may direct users towards a method appropriate to their T1-weighted datasets and improve the efficiency of processing for large, multisite neuroimaging studies.},
	number = {2},
	journal = {Hum Brain Mapp},
	author = {Fennema-Notestine, C. and Ozyurt, I. B. and Clark, C. P. and Morris, S. and Bischoff-Grethe, A. and Bondi, M. W. and Jernigan, T. L. and Fischl, B. and Segonne, F. and Shattuck, D. W. and Leahy, R. M. and Rex, D. E. and Toga, A. W. and Zou, K. H. and Brown, G. G.},
	month = feb,
	year = {2006},
	keywords = {Adult, Aged, Age Factors, Algorithms, Brain Diseases/radiography, Brain/*radiography, fs\_Validation-Evaluations, Humans, Image Processing, Computer-Assisted/*methods, *Magnetic Resonance Imaging, Middle Aged, Sensitivity and Specificity, Software},
	pages = {99--113},
	annote = {Fennema-Notestine, {ChristineOzyurt}, I {BurakClark}, Camellia {PMorris}, {ShaunnaBischoff}-Grethe, {AmandaBondi}, Mark {WJernigan}, Terry {LFischl}, {BruceSegonne}, {FlorentShattuck}, David {WLeahy}, Richard {MRex}, David {EToga}, Arthur {WZou}, Kelly {HBrown}, Gregory Geng5K08MH01642/{MH}/{NIMH} {NIH} {HHS}/{AG}04085/{AG}/{NIA} {NIH} {HHS}/K08 {MH}001642-05/{MH}/{NIMH} {NIH} {HHS}/M01 {RR}000827-328412/{RR}/{NCRR} {NIH} {HHS}/M01RR00827/{RR}/{NCRR} {NIH} {HHS}/{MH}45294/{MH}/{NIMH} {NIH} {HHS}/P41-{RR}13642/{RR}/{NCRR} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/P50AGO5131/{PHS} {HHS}/R01 {AG}12674/{AG}/{NIA} {NIH} {HHS}/R01 {EB}002010/{EB}/{NIBIB} {NIH} {HHS}/R01 {RR}16594-01A1/{RR}/{NCRR} {NIH} {HHS}/R01MH42575/{MH}/{NIMH} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/Comparative {StudyResearch} Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov'{tResearch} Support, U.S. Gov't, Non-P.H.S.2005/06/30 09:00Hum Brain Mapp. 2006 Feb;27(2):99-113.},
	file = {Fennema-Notesti-2006-Quantitative evaluation o:/autofs/cluster/freesurfer/zotero/storage/DQ9HERIC/Fennema-Notesti-2006-Quantitative evaluation o.pdf:application/pdf}
}

@article{kremen_salivary_2010,
	title = {Salivary cortisol and prefrontal cortical thickness in middle-aged men: A twin study},
	volume = {53},
	issn = {1095-9572 (Electronic) 1053-8119 (Linking)},
	shorttitle = {Salivary cortisol and prefrontal cortical thickness in middle-aged men: A twin study},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/20156572},
	doi = {10.1016/j.neuroimage.2010.02.026},
	abstract = {Although glucocorticoid receptors are highly expressed in the prefrontal cortex, the hippocampus remains the predominant focus in the literature examining relationships between cortisol and brain. We examined phenotypic and genetic associations of cortisol levels with the thickness of prefrontal and anterior cingulate cortex regions, and with hippocampal volume in a sample of 388 middle-aged male twins who were 51-59 years old. Small but significant negative phenotypic associations were found between cortisol levels and the thickness of left dorsolateral (superior frontal gyrus, left rostral middle frontal gyrus) and ventrolateral (pars opercularis, pars triangularis, pars orbitalis) prefrontal regions, and right dorsolateral (superior frontal gyrus) and medial orbital frontal cortex. Most of the associations remained significant after adjusting for general cognitive ability, cardiovascular risk factors, and depression. Bivariate genetic analyses suggested that some of the associations were primarily accounted for by shared genetic influences; that is, some of the genes that tend to result in increased cortisol levels also tend to result in reduced prefrontal cortical thickness. Aging has been associated with reduced efficiency of hypothalamic-pituitary-adrenal function, frontal lobe shrinkage, and increases in health problems, but our present data do not allow us to determine the direction of effects. Moreover, the degree or the direction of the observed associations and the extent of their shared genetic underpinnings may well change as these individuals age. Longitudinal assessments are underway to elucidate the direction of the associations and the genetic underpinnings of longitudinal phenotypes for changes in cortisol and brain morphology.},
	number = {3},
	journal = {Neuroimage},
	author = {Kremen, W. S. and O'Brien, R. C. and Panizzon, M. S. and Prom-Wormley, E. and Eaves, L. J. and Eisen, S. A. and Eyler, L. T. and Hauger, R. L. and Fennema-Notestine, C. and Fischl, B. and Grant, M. D. and Hellhammer, D. H. and Jak, A. J. and Jacobson, K. C. and Jernigan, T. L. and Lupien, S. J. and Lyons, M. J. and Mendoza, S. P. and Neale, M. C. and Seidman, L. J. and Thermenos, H. W. and Tsuang, M. T. and Dale, A. M. and Franz, C. E.},
	month = nov,
	year = {2010},
	keywords = {*Brain Mapping, Humans, Hydrocortisone/*analysis, Image Interpretation, Computer-Assisted, Magnetic Resonance Imaging, Male, Middle Aged, Phenotype, Prefrontal Cortex/*anatomy \& histology/*physiology, Quantitative Trait, Heritable, Radioimmunoassay, Saliva/chemistry, Twins/genetics/metabolism},
	pages = {1093--102},
	annote = {Kremen, William {SO}'Brien, Robert {CPanizzon}, Matthew {SProm}-Wormley, {ElizabethEaves}, Lindon {JEisen}, Seth {AEyler}, Lisa {THauger}, Richard {LFennema}-Notestine, {ChristineFischl}, {BruceGrant}, Michael {DHellhammer}, Dirk {HJak}, Amy {JJacobson}, Kristen {CJernigan}, Terry {LLupien}, Sonia {JLyons}, Michael {JMendoza}, Sally {PNeale}, Michael {CSeidman}, Larry {JThermenos}, Heidi {WTsuang}, Ming {TDale}, Anders {MFranz}, Carol {EengAG}018384/{AG}/{NIA} {NIH} {HHS}/{AG}018386/{AG}/{NIA} {NIH} {HHS}/{AG}022381/{AG}/{NIA} {NIH} {HHS}/{AG}022982/{AG}/{NIA} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 {AG}018384/{AG}/{NIA} {NIH} {HHS}/R01 {AG}018386/{AG}/{NIA} {NIH} {HHS}/R01 {AG}018386-09/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022381/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022381-09/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022982/{AG}/{NIA} {NIH} {HHS}/R01 {NS}052585-01/{NS}/{NINDS} {NIH} {HHS}/R01EB006758/{EB}/{NIBIB} {NIH} {HHS}/U54 {EB}005149/{EB}/{NIBIB} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov'{tResearch} Support, U.S. Gov't, Non-P.H.S.Twin Study2010/02/17 06:00Neuroimage. 2010 Nov 15;53(3):1093-102. doi: 10.1016/j.neuroimage.2010.02.026. Epub 2010 Feb 13.},
	file = {Kremen-2010-Salivary cortisol and prefrontal c:/autofs/cluster/freesurfer/zotero/storage/RMXMEE55/Kremen-2010-Salivary cortisol and prefrontal c.pdf:application/pdf}
}

@inproceedings{polimeni_resting-state_2011,
	title = {Resting-state correlations between depths within columns of voxels radial to the cortical surface},
	shorttitle = {Resting-state correlations between depths within columns of voxels radial to the cortical surface},
	author = {Polimeni, J. R. and Fujimoto, K. and Keil, B. and Greve, D. N. and Fischl, B. and Wald, L. L.},
	year = {2011}
}

@article{schaer_regional_2010,
	title = {Regional cortical volumes and congenital heart disease: a {MRI} study in 22q11.2 deletion syndrome},
	volume = {2},
	issn = {1866-1947},
	shorttitle = {Regional cortical volumes and congenital heart disease},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2974935/},
	doi = {10.1007/s11689-010-9061-4},
	abstract = {Children with congenital heart disease ({CHD}) who survive surgery often present impaired neurodevelopment and qualitative brain anomalies. However, the impact of {CHD} on total or regional brain volumes only received little attention. We address this question in a sample of patients with 22q11.2 deletion syndrome (22q11DS), a neurogenetic condition frequently associated with {CHD}. Sixty-one children, adolescents, and young adults with confirmed 22q11.2 deletion were included, as well as 80 healthy participants matched for age and gender. Subsequent subdivision of the patients group according to {CHD} yielded a subgroup of 27 patients with normal cardiac status and a subgroup of 26 patients who underwent cardiac surgery during their first years of life (eight patients with unclear status were excluded). Regional cortical volumes were extracted using an automated method and the association between regional cortical volumes, and {CHD} was examined within a three-condition fixed factor. Robust protection against type I error used Bonferroni correction. Smaller total cerebral volumes were observed in patients with {CHD} compared to both patients without {CHD} and controls. The pattern of bilateral regional reductions associated with {CHD} encompassed the superior parietal region, the precuneus, the fusiform gyrus, and the anterior cingulate cortex. Within patients, a significant reduction in the left parahippocampal, the right middle temporal, and the left superior frontal gyri was associated with {CHD}. The present results of global and regional volumetric reductions suggest a role for disturbed hemodynamic in the pathophysiology of brain alterations in patients with neurodevelopmental disease and cardiac malformations.},
	number = {4},
	urldate = {2014-08-25},
	journal = {Journal of neurodevelopmental disorders},
	author = {Schaer, Marie and Glaser, Bronwyn and Ottet, Marie-Christine and Schneider, Maude and Bach Cuadra, Meritxell and Debbane, Martin and Thiran, Jean-Philippe and Eliez, Stephan},
	month = dec,
	year = {2010},
	pmid = {21125003},
	pmcid = {PMC2974935},
	pages = {224--234},
	file = {PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/492ZNV8F/Schaer et al. - 2010 - Regional cortical volumes and congenital heart dis.pdf:application/pdf}
}

@article{augustinack_direct_2010,
	title = {Direct visualization of the perforant pathway in the human brain with ex vivo diffusion tensor imaging},
	volume = {4},
	issn = {1662-5161 (Electronic) 1662-5161 (Linking)},
	shorttitle = {Direct visualization of the perforant pathway in the human brain with ex vivo diffusion tensor imaging},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/20577631},
	doi = {10.3389/fnhum.2010.00042},
	abstract = {Ex vivo magnetic resonance imaging yields high resolution images that reveal detailed cerebral anatomy and explicit cytoarchitecture in the cerebral cortex, subcortical structures, and white matter in the human brain. Our data illustrate neuroanatomical correlates of limbic circuitry with high resolution images at high field. In this report, we have studied ex vivo medial temporal lobe samples in high resolution structural {MRI} and high resolution diffusion {MRI}. Structural and diffusion {MRIs} were registered to each other and to histological sections stained for myelin for validation of the perforant pathway. We demonstrate probability maps and fiber tracking from diffusion tensor data that allows the direct visualization of the perforant pathway. Although it is not possible to validate the {DTI} data with invasive measures, results described here provide an additional line of evidence of the perforant pathway trajectory in the human brain and that the perforant pathway may cross the hippocampal sulcus.},
	journal = {Front Hum Neurosci},
	author = {Augustinack, J. C. and Helmer, K. and Huber, K. E. and Kakunoori, S. and Zollei, L. and Fischl, B.},
	year = {2010},
	pages = {42},
	annote = {Augustinack, Jean {CHelmer}, {KarlHuber}, Kristen {EKakunoori}, {SitaZollei}, {LillaFischl}, {BruceengK}01 {AG}028521-04/{AG}/{NIA} {NIH} {HHS}/Switzerland2010/06/26 06:00Front Hum Neurosci. 2010 May 28;4:42. doi: 10.3389/fnhum.2010.00042. {eCollection} 2010.},
	file = {Augustinack-2010-Direct visualization of the p:/autofs/cluster/freesurfer/zotero/storage/DVV5IS76/Augustinack-2010-Direct visualization of the p.pdf:application/pdf;PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/T25XISWC/Augustinack et al. - 2010 - Direct Visualization of the Perforant Pathway in t.pdf:application/pdf}
}

@article{morey_comparison_2009,
	title = {A comparison of automated segmentation and manual tracing for quantifying hippocampal and amygdala volumes},
	volume = {45},
	issn = {1095-9572},
	url = {https://surfer.nmr.mgh.harvard.edu/ftp/articles/2009_NeuroImage_Morey.pdf},
	doi = {10.1016/j.neuroimage.2008.12.033},
	abstract = {Large databases of high-resolution structural {MR} images are being assembled to quantitatively examine the relationships between brain anatomy, disease progression, treatment regimens, and genetic influences upon brain structure. Quantifying brain structures in such large databases cannot be practically accomplished by expert neuroanatomists using hand-tracing. Rather, this research will depend upon automated methods that reliably and accurately segment and quantify dozens of brain regions. At present, there is little guidance available to help clinical research groups in choosing such tools. Thus, our goal was to compare the performance of two popular and fully automated tools, {FSL}/{FIRST} and {FreeSurfer}, to expert hand tracing in the measurement of the hippocampus and amygdala. Volumes derived from each automated measurement were compared to hand tracing for percent volume overlap, percent volume difference, across-sample correlation, and 3-D group-level shape analysis. In addition, sample size estimates for conducting between-group studies were computed for a range of effect sizes. Compared to hand tracing, hippocampal measurements with {FreeSurfer} exhibited greater volume overlap, smaller volume difference, and higher correlation than {FIRST}, and sample size estimates with {FreeSurfer} were closer to hand tracing. Amygdala measurement with {FreeSurfer} was also more highly correlated to hand tracing than {FIRST}, but exhibited a greater volume difference than {FIRST}. Both techniques had comparable volume overlap and similar sample size estimates. Compared to hand tracing, a 3-D shape analysis of the hippocampus showed {FreeSurfer} was more accurate than {FIRST}, particularly in the head and tail. However, {FIRST} more accurately represented the amygdala shape than {FreeSurfer}, which inflated its anterior and posterior surfaces.},
	language = {eng},
	number = {3},
	journal = {{NeuroImage}},
	author = {Morey, Rajendra A. and Petty, Christopher M. and Xu, Yuan and Hayes, Jasmeet Pannu and Wagner, H. Ryan and Lewis, Darrell V. and LaBar, Kevin S. and Styner, Martin and McCarthy, Gregory},
	month = apr,
	year = {2009},
	pmid = {19162198},
	pmcid = {PMC2714773},
	keywords = {Amygdala, Automation, fs\_Validation-Evaluations, Hippocampus, Humans, Image Processing, Computer-Assisted, Magnetic Resonance Imaging},
	pages = {855--866}
}

@article{fischl_cortical_1999,
	title = {Cortical surface-based analysis. {II}: Inflation, flattening, and a surface-based coordinate system},
	volume = {9},
	issn = {1053-8119 (Print) 1053-8119 (Linking)},
	shorttitle = {Cortical surface-based analysis. {II}: Inflation, flattening, and a surface-based coordinate system},
	url = {https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl99b-recon2.pdf},
	doi = {10.1006/nimg.1998.0396},
	abstract = {The surface of the human cerebral cortex is a highly folded sheet with the majority of its surface area buried within folds. As such, it is a difficult domain for computational as well as visualization purposes. We have therefore designed a set of procedures for modifying the representation of the cortical surface to (i) inflate it so that activity buried inside sulci may be visualized, (ii) cut and flatten an entire hemisphere, and (iii) transform a hemisphere into a simple parameterizable surface such as a sphere for the purpose of establishing a surface-based coordinate system.},
	number = {2},
	journal = {Neuroimage},
	author = {Fischl, B. and Sereno, M. I. and Dale, A. M.},
	month = feb,
	year = {1999},
	keywords = {Artifacts, Brain Mapping/instrumentation, Cerebral Cortex/*anatomy \& histology, Dominance, Cerebral/physiology, fs\_Surface-reconstruction, Humans, Image Processing, Computer-Assisted/*instrumentation, Magnetic Resonance Imaging/*instrumentation, Software},
	pages = {195--207},
	annote = {Fischl, {BSereno}, M {IDale}, A Meng1999/02/05Neuroimage. 1999 Feb;9(2):195-207.}
}

@article{salat_age-related_2005-1,
	title = {Age-related changes in prefrontal white matter measured by diffusion tensor imaging},
	volume = {1064},
	issn = {0077-8923 (Print) 0077-8923 (Linking)},
	shorttitle = {Age-related changes in prefrontal white matter measured by diffusion tensor imaging},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/16394146},
	doi = {10.1196/annals.1340.009},
	abstract = {Age-related degeneration of brain white matter ({WM}) has received a great deal of attention, with recent studies demonstrating that such changes are correlated with cognitive decline and increased risk for the development of age-related neurodegenerative disease. Past studies have used magnetic resonance imaging ({MRI}) to measure the volume of normal and abnormal tissue signal as an index of tissue pathology. More recently, diffusion tensor {MRI} ({DTI}) has been employed to obtain regional measures of tissue microstructure, such as fractional anisotropy ({FA}), providing better spatial resolution and potentially more sensitive metrics of tissue damage than traditional volumetric measures. We used {DTI} to examine the regional basis of age-related alterations in prefrontal {WM}. As expected from prior volumetric and {DTI} studies, prefrontal {FA} was reduced in older adults ({OA}) compared to young adults ({YA}). Although {WM} volume has been reported to be relatively preserved until late aging, {FA} was significantly reduced by middle age. Much of prefrontal {WM} showed reduced {FA} with increasing age. Ventromedial and deep prefrontal regions showed a somewhat greater reduction compared to other prefrontal areas. Prefrontal {WM} anisotropy correlated with prefrontal {WM} volume, but the correlation was significant only when the analysis was limited to participants over age 40. This evidence of widespread and regionally accelerated alterations in prefrontal {WM} with aging illustrates {FA}'s potential as a microstructural index of volumetric measures.},
	journal = {Ann N Y Acad Sci},
	author = {Salat, D. H. and Tuch, D. S. and Hevelone, N. D. and Fischl, B. and Corkin, S. and Rosas, H. D. and Dale, A. M.},
	month = dec,
	year = {2005},
	keywords = {Adult, Aged, Aged, 80 and over, Aging/*pathology, Atrophy/*diagnosis/physiopathology, Brain Mapping/*methods, Dementia/*diagnosis/physiopathology, Diagnosis, Differential, Diffusion Magnetic Resonance Imaging/*methods/trends, Humans, Middle Aged, Nerve Fibers, Myelinated/*pathology, Predictive Value of Tests, Prefrontal Cortex/*pathology/physiopathology},
	pages = {37--49},
	annote = {Salat, D {HTuch}, D {SHevelone}, N {DFischl}, {BCorkin}, {SRosas}, H {DDale}, A {MengReview}2006/01/06 09:00Ann N Y Acad Sci. 2005 Dec;1064:37-49.}
}

@inproceedings{van_der_kouwe_functional_2007,
	title = {Functional single voxel spectroscopy with automatic voxel positioning},
	shorttitle = {Functional single voxel spectroscopy with automatic voxel positioning},
	author = {van der Kouwe, A.J.W. and Balasubramanian, M. and Salat, D.H. and Wastiaux, L. and Fischl, B.},
	year = {2007}
}

@article{dasilva_thickening_2007,
	title = {Thickening in the somatosensory cortex of patients with migraine},
	volume = {69},
	issn = {0028-3878},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3757544/},
	doi = {10.1212/01.wnl.0000291618.32247.2d},
	abstract = {Objective
To examine morphologic changes in the somatosensory cortex ({SSC}) of patients with migraine.

Methods
Cortical thickness of the {SSC} of patients with migraine was measured in vivo and compared with age- and sex-matched healthy subjects. The cohort was composed of 24 patients with migraine, subdivided into 12 patients who had migraine with aura, 12 patients who had migraine without aura, and 12 controls. Group and individual analyses were performed in the {SSC} and shown as average maps of significant changes in cortical thickness.

Results
Migraineurs had on average thicker {SSCs} than the control group. The most significant thickness changes were noticed in the caudal {SSC}, where the trigeminal area, including head and face, is somatotopically represented.

Conclusions
Our findings indicate the presence of interictal structural changes in the somatosensory cortex ({SSC}) of migraineurs. The {SSC} plays a crucial role in the noxious and nonnoxious somatosensory processing. Thickening in the {SSC} is in line with diffusional abnormalities observed in the subcortical trigeminal somatosensory pathway of the same migraine cohort in a previous study. Repetitive migraine attacks may lead to, or be the result of, neuroplastic changes in cortical and subcortical structures of the trigeminal somatosensory system.},
	number = {21},
	urldate = {2014-08-23},
	journal = {Neurology},
	author = {DaSilva, Alexandre F.M. and Granziera, Cristina and Nouchine Hadjikhani, Josh Snyder},
	month = nov,
	year = {2007},
	pmid = {18025393},
	pmcid = {PMC3757544},
	pages = {1990--1995},
	file = {PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/NSGMIZMX/DaSilva et al. - 2007 - Thickening in the somatosensory cortex of patients.pdf:application/pdf}
}

@article{isaacs_impact_2010,
	title = {Impact of breast milk on {IQ}, brain size and white matter development},
	volume = {67},
	issn = {0031-3998},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2939272/},
	doi = {10.1203/PDR.0b013e3181d026da},
	abstract = {Although observational findings linking breast milk to higher scores on cognitive tests may be confounded by factors associated with mothers’ choice to breastfeed, it has been suggested that one or more constituents of breast milk facilitate cognitive development, particularly in preterms. Because cognitive scores are related to head size, we hypothesised that breast milk mediates cognitive effects by affecting brain growth. We used detailed data from a randomized feeding trial to calculate percentage of breast milk (\%{EBM}) in the infant diet of 50 adolescents. {MRI} scans were obtained (mean age=15y9m), allowing volumes of total brain ({TBV}), white and grey matter ({WMV}, {GMV}) to be calculated. In the total group \%{EBM} correlated significantly with Verbal {IQ} ({VIQ}); in boys, with all {IQ} scores, {TBV} and {WMV}. {VIQ} was, in turn, correlated with {WMV} and, in boys only, additionally with {TBV}. No significant relationships were seen in girls or with grey matter. These data support the hypothesis that breast milk promotes brain development, particularly white matter growth. The selective effect in males accords with animal and human evidence regarding gender effects of early diet. Our data have important neurobiological and public health implications and identify areas for future mechanistic study.},
	number = {4},
	urldate = {2014-08-25},
	journal = {Pediatric research},
	author = {Isaacs, Elizabeth B. and Fischl, Bruce R. and Quinn, Brian T. and Chong, Wui K. and Gadian, David G. and Lucas, Alan},
	month = apr,
	year = {2010},
	pmid = {20035247},
	pmcid = {PMC2939272},
	keywords = {Adolescent, Brain/*anatomy \& histology/*growth \& development, *Breast Feeding, Cognition/physiology, Female, Humans, Infant, Newborn, Infant, Premature, *Intelligence, Intelligence Tests, Magnetic Resonance Imaging, Male, *Milk, Human, *Nerve Fibers, Myelinated, Randomized Controlled Trials as Topic},
	pages = {357--362},
	annote = {Isaacs, Elizabeth {BFischl}, Bruce {RQuinn}, Brian {TChong}, Wui {KGadian}, David {GLucas}, {AlanengBIRN}002/{PHS} {HHS}/P41 {RR}014075-075751/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-075752/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-075753/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-086765/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-086766/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-086767/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-098601/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-098602/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-098603/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-105995/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-105996/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-105997/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-117865/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-117866/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-117867/{RR}/{NCRR} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 {AG}018386-09/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022381-01/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022381-02/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022381-03/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022381-04/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022381-05/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022381-06/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022381-07/{AG}/{NIA} {NIH} {HHS}/R01 {EB}001550/{EB}/{NIBIB} {NIH} {HHS}/R01 {EB}006758-01A1/{EB}/{NIBIB} {NIH} {HHS}/R01 {EB}006758-02/{EB}/{NIBIB} {NIH} {HHS}/R01 {EB}006758-03/{EB}/{NIBIB} {NIH} {HHS}/R01 {EB}006758-03S1/{EB}/{NIBIB} {NIH} {HHS}/R01 {NS}052585-01/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}052585-01A1/{NS}/{NINDS} {NIH} {HHS}/R01 {RR}16594-01A1/{RR}/{NCRR} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/U54 {EB}005149/{EB}/{NIBIB} {NIH} {HHS}/U54 {EB}005149-050002/{EB}/{NIBIB} {NIH} {HHS}/Medical Research Council/United {KingdomWellcome} Trust/United {KingdomResearch} Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov't2009/12/26 06:00Pediatr Res. 2010 Apr;67(4):357-62. doi: 10.1203/{PDR}.0b013e3181d026da.},
	file = {Isaacs-2010-Impact of breast milk on intellige:/autofs/cluster/freesurfer/zotero/storage/6BKWJJWR/Isaacs-2010-Impact of breast milk on intellige.pdf:application/pdf;PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/483JZRKT/Isaacs et al. - 2010 - Impact of breast milk on IQ, brain size and white .pdf:application/pdf}
}

@article{desikan_temporoparietal_2009,
	title = {Temporoparietal {MRI} Measures of Atrophy in Subjects with Mild Cognitive Impairment that Predict Subsequent Diagnosis of Alzheimer's Disease},
	volume = {30},
	issn = {0195-6108},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2656417/},
	doi = {10.3174/ajnr.A1397},
	abstract = {Background and Purpose
Mild cognitive impairment ({MCI}) represents a transitional state between normal aging and Alzheimer’s disease ({AD}). Our goal was to determine if specific temporoparietal regions can predict the time to progress from {MCI} to {AD}.

Methods
{MRI} scans from 129 individuals with {MCI} were analyzed to identify the volume of 14 neocortical and 2 non-neocortical brain regions, comprising the temporal and parietal lobes. In addition, three neuropsychological test scores were included to determine whether they would provide independent information. After a mean follow-up time of 5 years, 44 of these individuals had progressed to a diagnosis of {AD}.

Results
Cox proportional hazards models demonstrated significant effects for six {MRI} regions with the greatest differences being: entorhinal cortex ({HR}=0.54, p {\textless} 0.001), inferior parietal lobule ({HR}=0.64, p {\textless}0.005), and middle temporal gyrus ({HR}=0.64, p {\textless} 0.004), indicating decreased risk with larger volumes. A multivariable model showed that a combination of the entorhinal cortex ({HR} = 0.60, p {\textless} 0.001) and inferior parietal lobule ({HR} = 0.62, p {\textless} 0.01) was the ‘best’ predictor of time to progress to {AD}. A multivariable model re-iterated the importance of included both {MRI} and neuropsychological variables in the final model.

Conclusion
These findings reaffirm the importance of the entorhinal cortex and present evidence for the importance of the inferior parietal lobule as a predictor of time to progress from {MCI} to {AD}. The inclusion of neuropsychological performance in the final model continues to highlight the importance of using these measures in a complementary fashion.},
	number = {3},
	urldate = {2014-08-25},
	journal = {{AJNR}. American journal of neuroradiology},
	author = {Desikan, Rahul S. and Cabral, Howard J. and Fischl, Bruce and Guttmann, Charles R. G. and Blacker, Deborah and Hyman, Bradley T. and Albert, Marilyn S. and Killiany, Ronald J.},
	month = mar,
	year = {2009},
	pmid = {19112067},
	pmcid = {PMC2656417},
	pages = {532--538},
	file = {PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/XC9KPMEK/Desikan et al. - 2009 - Temporoparietal MRI Measures of Atrophy in Subject.pdf:application/pdf}
}

@article{yeo_organization_2011,
	title = {The organization of the human cerebral cortex estimated by intrinsic functional connectivity},
	volume = {106},
	issn = {1522-1598 (Electronic) 0022-3077 (Linking)},
	shorttitle = {The organization of the human cerebral cortex estimated by intrinsic functional connectivity},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/21653723},
	doi = {10.1152/jn.00338.2011},
	abstract = {Information processing in the cerebral cortex involves interactions among distributed areas. Anatomical connectivity suggests that certain areas form local hierarchical relations such as within the visual system. Other connectivity patterns, particularly among association areas, suggest the presence of large-scale circuits without clear hierarchical relations. In this study the organization of networks in the human cerebrum was explored using resting-state functional connectivity {MRI}. Data from 1,000 subjects were registered using surface-based alignment. A clustering approach was employed to identify and replicate networks of functionally coupled regions across the cerebral cortex. The results revealed local networks confined to sensory and motor cortices as well as distributed networks of association regions. Within the sensory and motor cortices, functional connectivity followed topographic representations across adjacent areas. In association cortex, the connectivity patterns often showed abrupt transitions between network boundaries. Focused analyses were performed to better understand properties of network connectivity. A canonical sensory-motor pathway involving primary visual area, putative middle temporal area complex ({MT}+), lateral intraparietal area, and frontal eye field was analyzed to explore how interactions might arise within and between networks. Results showed that adjacent regions of the {MT}+ complex demonstrate differential connectivity consistent with a hierarchical pathway that spans networks. The functional connectivity of parietal and prefrontal association cortices was next explored. Distinct connectivity profiles of neighboring regions suggest they participate in distributed networks that, while showing evidence for interactions, are embedded within largely parallel, interdigitated circuits. We conclude by discussing the organization of these large-scale cerebral networks in relation to monkey anatomy and their potential evolutionary expansion in humans to support cognition.},
	number = {3},
	journal = {J Neurophysiol},
	author = {Yeo, B. T. and Krienen, F. M. and Sepulcre, J. and Sabuncu, M. R. and Lashkari, D. and Hollinshead, M. and Roffman, J. L. and Smoller, J. W. and Zollei, L. and Polimeni, J. R. and Fischl, B. and Liu, H. and Buckner, R. L.},
	month = sep,
	year = {2011},
	keywords = {Adolescent, Adult, Brain Mapping/*methods, Cerebral Cortex/*physiology, Female, Humans, Magnetic Resonance Imaging/methods, Male, Nerve Net/*physiology, Young Adult},
	pages = {1125--65},
	annote = {Yeo, B T {ThomasKrienen}, Fenna {MSepulcre}, {JorgeSabuncu}, Mert {RLashkari}, {DanialHollinshead}, {MarisaRoffman}, Joshua {LSmoller}, Jordan {WZollei}, {LillaPolimeni}, Jonathan {RFischl}, {BruceLiu}, {HeshengBuckner}, Randy Leng1R01NS070963/{NS}/{NINDS} {NIH} {HHS}/1R21NS072652/{NS}/{NINDS} {NIH} {HHS}/1S10RR019/{RR}/{NCRR} {NIH} {HHS}/1S10RR023043/{RR}/{NCRR} {NIH} {HHS}/1S10RR023401/{RR}/{NCRR} {NIH} {HHS}/{AG}021910/{AG}/{NIA} {NIH} {HHS}/{AG}022381/{AG}/{NIA} {NIH} {HHS}/K01 {EB}011498-02/{EB}/{NIBIB} {NIH} {HHS}/K08MH067966/{MH}/{NIMH} {NIH} {HHS}/K25 {EB}013649/{EB}/{NIBIB} {NIH} {HHS}/K25 {NS}069805/{NS}/{NINDS} {NIH} {HHS}/K25 {NS}069805-01A1/{NS}/{NINDS} {NIH} {HHS}/K25 {NS}069805-02/{NS}/{NINDS} {NIH} {HHS}/P41RR14074/{RR}/{NCRR} {NIH} {HHS}/P41RR14075/{RR}/{NCRR} {NIH} {HHS}/R01NS052585/{NS}/{NINDS} {NIH} {HHS}/{RC}1AT005728/{AT}/{NCCAM} {NIH} {HHS}/U24RR021382/{RR}/{NCRR} {NIH} {HHS}/U54MH091665/{MH}/{NIMH} {NIH} {HHS}/Howard Hughes Medical Institute/Comparative {StudyResearch} Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov't2011/06/10 06:00J Neurophysiol. 2011 Sep;106(3):1125-65. doi: 10.1152/jn.00338.2011. Epub 2011 Jun 8.},
	file = {Yeo-2011-The organization of the human cerebra:/autofs/cluster/freesurfer/zotero/storage/6B3F8EQZ/Yeo-2011-The organization of the human cerebra.pdf:application/pdf}
}

@article{cha_circuit-wide_2014,
	title = {Circuit-Wide Structural and Functional Measures Predict Ventromedial Prefrontal Cortex Fear Generalization: Implications for Generalized Anxiety Disorder},
	volume = {34},
	issn = {0270-6474, 1529-2401},
	shorttitle = {Circuit-Wide Structural and Functional Measures Predict Ventromedial Prefrontal Cortex Fear Generalization},
	url = {http://www.jneurosci.org/content/34/11/4043},
	doi = {10.1523/JNEUROSCI.3372-13.2014},
	abstract = {The ventromedial prefrontal cortex ({vmPFC}) plays a critical role in a number of evaluative processes, including risk assessment. Impaired discrimination between threat and safety is considered a hallmark of clinical anxiety. Here, we investigated the circuit-wide structural and functional mechanisms underlying {vmPFC} threat–safety assessment in humans. We tested patients with generalized anxiety disorder ({GAD}; n = 32, female) and healthy controls (n = 25, age-matched female) on a task that assessed the generalization of conditioned threat during {fMRI} scanning. The task consisted of seven rectangles of graded widths presented on a screen; only the midsize one was paired with mild electric shock [conditioned stimulus ({CS})], while the others, safety cues, systematically varied in width by ±20, 40, and 60\% [generalization stimuli ({GS})] compared with the {CS}. We derived an index reflecting {vmPFC} functioning from the {BOLD} reactivity on a continuum of threat ({CS}) to safety ({GS} least similar to {CS}); patients with {GAD} showed less discrimination between threat and safety cues, compared with healthy controls (Greenberg et al., 2013b). Using structural, functional (i.e., resting-state), and diffusion {MRI}, we measured {vmPFC} thickness, {vmPFC} functional connectivity, and {vmPFC} structural connectivity within the corticolimbic systems. The results demonstrate that all three factors predict individual variability of {vmPFC} threat assessment in an independent fashion. Moreover, these neural features are also linked to {GAD}, most likely via an {vmPFC} fear generalization. Our results strongly suggest that {vmPFC} threat processing is closely associated with broader corticolimbic circuit anomalies, which may synergistically contribute to clinical anxiety.},
	language = {en},
	number = {11},
	urldate = {2014-08-25},
	journal = {The Journal of Neuroscience},
	author = {Cha, Jiook and Greenberg, Tsafrir and Carlson, Joshua M. and DeDora, Daniel J. and Hajcak, Greg and Mujica-Parodi, Lilianne R.},
	month = mar,
	year = {2014},
	pmid = {24623781},
	keywords = {anxiety, connectivity, fear conditioning, fear generalizaton, resting-state, Tractography},
	pages = {4043--4053},
	file = {Snapshot:/autofs/cluster/freesurfer/zotero/storage/C4K33FSZ/4043.html:text/html}
}

@article{tsao_faces_2003,
	title = {Faces and objects in macaque cerebral cortex},
	volume = {6},
	copyright = {© 2003 Nature Publishing Group},
	issn = {1097-6256},
	url = {http://www.nature.com/neuro/journal/v6/n9/abs/nn1111.html},
	doi = {10.1038/nn1111},
	abstract = {How are different object categories organized by the visual system? Current evidence indicates that monkeys and humans process object categories in fundamentally different ways. Functional magnetic resonance imaging ({fMRI}) studies suggest that humans have a ventral temporal face area, but such evidence is lacking in macaques. Instead, face-responsive neurons in macaques seem to be scattered throughout temporal cortex, with some relative concentration in the superior temporal sulcus ({STS}). Here, using {fMRI} in alert fixating macaque monkeys and humans, we found that macaques do have discrete face-selective patches, similar in relative size and number to face patches in humans. The face patches were embedded within a large swath of object-selective cortex extending from V4 to rostral {TE}. This large region responded better to pictures of intact objects compared to scrambled objects, with different object categories eliciting different patterns of activity, as in the human. Overall, our results suggest that humans and macaques share a similar brain architecture for visual object processing.},
	language = {en},
	number = {9},
	urldate = {2014-08-25},
	journal = {Nature Neuroscience},
	author = {Tsao, Doris Y. and Freiwald, Winrich A. and Knutsen, Tamara A. and Mandeville, Joseph B. and Tootell, Roger B. H.},
	month = sep,
	year = {2003},
	pages = {989--995},
	file = {Snapshot:/autofs/cluster/freesurfer/zotero/storage/T65D7SM3/nn1111.html:text/html}
}

@article{chee_brain_2011,
	title = {Brain Structure in Young and Old East Asians and Westerners: Comparisons of Structural Volume and Cortical Thickness},
	volume = {23},
	issn = {0898-929X},
	shorttitle = {Brain Structure in Young and Old East Asians and Westerners},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3361742/},
	doi = {10.1162/jocn.2010.21513},
	abstract = {There is an emergent literature suggesting that East Asians and Westerners differ in cognitive processes because of cultural biases to process information holistically (East Asians) or analytically (Westerners). To evaluate the possibility that such differences are accompanied by differences in brain structure, we conducted a large comparative study on cognitively matched young and old adults from two cultural/ethnic groups—Chinese Singaporeans and non-Asian Americans—that involved a total of 140 persons. Young predominantly White American adults were found to have higher cortical thickness in frontal, parietal, and medial-temporal polymodal association areas in both hemispheres. These findings were replicated using voxel-based morphometry applied to the same data set. Differences in cortical thickness observed between young volunteers were not significant in older subjects as a whole. However, group differences were evident when high-performing old were compared. Although the observed differences in gray matter may be rooted in strategic differences in cognition arising from ethnic/cultural differences, alternative explanations involving genetic heritage and environmental factors are also considered.},
	number = {5},
	urldate = {2014-08-23},
	journal = {Journal of Cognitive Neuroscience},
	author = {Chee, Michael Wei Liang and Zheng, Hui and Goh, Joshua Oon Soo and Park, Denise and Sutton, Bradley P.},
	month = may,
	year = {2011},
	pmid = {20433238},
	pmcid = {PMC3361742},
	pages = {1065--1079},
	file = {PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/7UHZQVSJ/Chee et al. - 2011 - Brain Structure in Young and Old East Asians and W.pdf:application/pdf;PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/UXWR88RC/Chee et al. - 2011 - Brain Structure in Young and Old East Asians and W.pdf:application/pdf}
}

@article{reuter_highly_2010,
	title = {Highly accurate inverse consistent registration: a robust approach},
	volume = {53},
	issn = {1095-9572 (Electronic) 1053-8119 (Linking)},
	shorttitle = {Highly accurate inverse consistent registration: a robust approach},
	url = {http://reuter.mit.edu/papers/reuter-robreg10.pdf},
	doi = {10.1016/j.neuroimage.2010.07.020},
	abstract = {The registration of images is a task that is at the core of many applications in computer vision. In computational neuroimaging where the automated segmentation of brain structures is frequently used to quantify change, a highly accurate registration is necessary for motion correction of images taken in the same session, or across time in longitudinal studies where changes in the images can be expected. This paper, inspired by Nestares and Heeger (2000), presents a method based on robust statistics to register images in the presence of differences, such as jaw movement, differential {MR} distortions and true anatomical change. The approach we present guarantees inverse consistency (symmetry), can deal with different intensity scales and automatically estimates a sensitivity parameter to detect outlier regions in the images. The resulting registrations are highly accurate due to their ability to ignore outlier regions and show superior robustness with respect to noise, to intensity scaling and outliers when compared to state-of-the-art registration tools such as {FLIRT} (in {FSL}) or the coregistration tool in {SPM}.},
	number = {4},
	journal = {Neuroimage},
	author = {Reuter, M. and Rosas, H. D. and Fischl, B.},
	month = dec,
	year = {2010},
	keywords = {Algorithms, Brain/*anatomy \& histology, fs\_Longitudinal-processing, Humans, Image Interpretation, Computer-Assisted/*methods, longitudinal processing, *Models, Theoretical},
	pages = {1181--96},
	annote = {Reuter, {MartinRosas}, H {DianaFischl}, {BruceengP}01 {NS}058793/{NS}/{NINDS} {NIH} {HHS}/P01 {NS}058793-01A10001/{NS}/{NINDS} {NIH} {HHS}/P41 {RR}014075-117867/{RR}/{NCRR} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 {AG}018386-09/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022381/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022381-07/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022381-09/{AG}/{NIA} {NIH} {HHS}/R01 {EB}006758/{EB}/{NIBIB} {NIH} {HHS}/R01 {EB}006758-04/{EB}/{NIBIB} {NIH} {HHS}/R01 {NS}042861/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}042861-08/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}052585-01/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}052585-05/{NS}/{NINDS} {NIH} {HHS}/U01 {AG}024904-05/{AG}/{NIA} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/U24 {RR}021382-056792/{RR}/{NCRR} {NIH} {HHS}/U54 {AG}024904/{AG}/{NIA} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov't2010/07/20 06:00Neuroimage. 2010 Dec;53(4):1181-96. doi: 10.1016/j.neuroimage.2010.07.020. Epub 2010 Jul 14.},
	file = {Reuter-2010-Highly accurate inverse consistent:/autofs/cluster/freesurfer/zotero/storage/6S85WBRW/Reuter-2010-Highly accurate inverse consistent.pdf:application/pdf}
}

@inproceedings{polimeni_laminar-specific_2010-1,
	title = {Laminar-specific functional connectivity: distinguishing directionality in cortical networks},
	shorttitle = {Laminar-specific functional connectivity: distinguishing directionality in cortical networks},
	author = {Polimeni, J. R. and Fischl, D., B. Greve and Wald, L. L.},
	year = {2010}
}

@article{segonne_genetic_2005,
	title = {A genetic algorithm for the topology correction of cortical surfaces},
	volume = {19},
	issn = {1011-2499 (Print) 1011-2499 (Linking)},
	shorttitle = {A genetic algorithm for the topology correction of cortical surfaces},
	url = {http://www.nmr.mgh.harvard.edu/~fischl/reprints/segonne_ga_ipmi2005.pdf},
	abstract = {We propose a technique to accurately correct the spherical topology of cortical surfaces. We construct a mapping from the original surface onto the sphere to detect topological defects as minimal non-homeomorphic regions. A genetic algorithm corrects each defect by finding the maximum-a-posteriori retessellation in a Bayesian framework. During the genetic search, incorrect vertices are iteratively identified and eliminated, while the optimal retessellation is constructed. Applied to synthetic and real data, our method generates optimal topological corrections with only a few iterations.},
	number = {393-405},
	journal = {Inf Process Med Imaging},
	author = {Segonne, F. and Grimson, E. and Fischl, B.},
	year = {2005},
	keywords = {*Algorithms, *Artifacts, Artificial Intelligence, Cerebral Cortex/*anatomy \& histology, Computer Simulation, fs\_Surface-reconstruction, fs\_Topology-correction, Image Enhancement/*methods, Image Interpretation, Computer-Assisted/*methods, Imaging, Three-Dimensional/*methods, Models, Genetic, Models, Neurological, Pattern Recognition, Automated/*methods, Reproducibility of Results, Sensitivity and Specificity},
	pages = {393--405},
	annote = {Segonne, {FlorentGrimson}, {EricFischl}, {BruceengEvaluation} {StudiesGermany}2007/03/16 09:00Inf Process Med Imaging. 2005;19:393-405.}
}

@article{versace_elevated_2014,
	title = {Elevated serum measures of lipid peroxidation and abnormal prefrontal white matter in euthymic bipolar adults: toward peripheral biomarkers of bipolar disorder},
	volume = {19},
	copyright = {© 2013 Nature Publishing Group},
	issn = {1359-4184},
	shorttitle = {Elevated serum measures of lipid peroxidation and abnormal prefrontal white matter in euthymic bipolar adults},
	url = {http://www.nature.com/mp/journal/v19/n2/full/mp2012188a.html},
	doi = {10.1038/mp.2012.188},
	abstract = {Diffusion tensor imaging ({DTI}) studies consistently reported abnormalities in fractional anisotropy ({FA}) and radial diffusivity ({RD}), measures of the integrity of white matter ({WM}), in bipolar disorder ({BD}), that may reflect underlying pathophysiologic processes. There is, however, a pressing need to identify peripheral measures that are related to these {WM} measures, to help identify easily obtainable peripheral biomarkers of {BD}. Given the high lipid content of axonal membranes and myelin sheaths, and that elevated serum levels of lipid peroxidation are reported in {BD}, these serum measures may be promising peripheral biomarkers of underlying {WM} abnormalities in {BD}. We used {DTI} and probabilistic tractography to compare {FA} and {RD} in ten prefrontal-centered {WM} tracts, 8 of which are consistently shown to have abnormal {FA} (and/or {RD}) in {BD}, and also examined serum lipid peroxidation (lipid hydroperoxides, {LPH} and 4-hydroxy-2-nonenal, 4-{HNE}), in 24 currently euthymic {BD} adults ({BDE}) and 19 age- and gender-matched healthy adults ({CONT}). There was a significant effect of group upon {FA} in these a priori {WM} tracts ({BDE}{\textless}{CONT}: F[1,41]=6.8; P=0.013) and {RD} ({BDE}{\textgreater}{CONT}: F[1,41]=10.3; P=0.003), and a significant between-group difference in {LPH} ({BDE}{\textgreater}{CONT}: t[40]=2.4; P=0.022), but not in 4-{HNE}. Multivariate multiple regression analyses revealed that {LPH} variance explained, respectively, 59 and 51\% of the variance of {FA} and {RD} across all study participants. This is the first study to examine relationships between measures of {WM} integrity and peripheral measures of lipid peroxidation. Our findings suggest that serum {LPH} may be useful in the development of a clinically relevant, yet easily obtainable and inexpensive, peripheral biomarkers of {BD}.},
	language = {en},
	number = {2},
	urldate = {2014-08-25},
	journal = {Molecular Psychiatry},
	author = {Versace, A. and Andreazza, A. C. and Young, L. T. and Fournier, J. C. and Almeida, J. R. C. and Stiffler, R. S. and Lockovich, J. C. and Aslam, H. A. and Pollock, M. H. and Park, H. and Nimgaonkar, V. L. and Kupfer, D. J. and Phillips, M. L.},
	month = feb,
	year = {2014},
	keywords = {Bipolar Disorder, fractional anisotropy, global probabilistic tractography, lipid peroxidation, oxidative stress, radial diffusivity},
	pages = {200--208},
	file = {Snapshot:/autofs/cluster/freesurfer/zotero/storage/P22828SW/mp2012188a.html:text/html}
}

@article{greve_cortical_2014,
	title = {Cortical surface-based analysis reduces bias and variance in kinetic modeling of brain {PET} data},
	volume = {92},
	issn = {1095-9572 (Electronic) 1053-8119 (Linking)},
	shorttitle = {Cortical surface-based analysis reduces bias and variance in kinetic modeling of brain {PET} data},
	url = {https://surfer.nmr.mgh.harvard.edu/pub/articles/2014/greve.2014.ni.surface-km.pdf},
	doi = {10.1016/j.neuroimage.2013.12.021},
	abstract = {Exploratory (i.e., voxelwise) spatial methods are commonly used in neuroimaging to identify areas that show an effect when a region-of-interest ({ROI}) analysis cannot be performed because no strong a priori anatomical hypothesis exists. However, noise at a single voxel is much higher than noise in a {ROI} making noise management critical to successful exploratory analysis. This work explores how preprocessing choices affect the bias and variability of voxelwise kinetic modeling analysis of brain positron emission tomography ({PET}) data. These choices include the use of volume- or cortical surface-based smoothing, level of smoothing, use of voxelwise partial volume correction ({PVC}), and {PVC} masking threshold. {PVC} was implemented using the Muller-Gartner method with the masking out of voxels with low gray matter ({GM}) partial volume fraction. Dynamic {PET} scans of an antagonist serotonin-4 receptor radioligand ([(11)C]{SB}207145) were collected on sixteen healthy subjects using a Siemens {HRRT} {PET} scanner. Kinetic modeling was used to compute maps of non-displaceable binding potential ({BPND}) after preprocessing. The results showed a complicated interaction between smoothing, {PVC}, and masking on {BPND} estimates. Volume-based smoothing resulted in large bias and intersubject variance because it smears signal across tissue types. In some cases, {PVC} with volume smoothing paradoxically caused the estimated {BPND} to be less than when no {PVC} was used at all. When applied in the absence of {PVC}, cortical surface-based smoothing resulted in dramatically less bias and the least variance of the methods tested for smoothing levels 5mm and higher. When used in combination with {PVC}, surface-based smoothing minimized the bias without significantly increasing the variance. Surface-based smoothing resulted in 2-4 times less intersubject variance than when volume smoothing was used. This translates into more than 4 times fewer subjects needed in a group analysis to achieve similarly powered statistical tests. Surface-based smoothing has less bias and variance because it respects cortical geometry by smoothing the {PET} data only along the cortical ribbon and so does not contaminate the {GM} signal with that of white matter and cerebrospinal fluid. The use of surface-based analysis in {PET} should result in substantial improvements in the reliability and detectability of effects in exploratory {PET} analysis, with or without {PVC}.},
	language = {en},
	urldate = {2014-08-21},
	journal = {Neuroimage},
	author = {Greve, D. N. and Svarer, C. and Fisher, P. M. and Feng, L. and Hansen, A. E. and Baare, W. and Rosen, B. and Fischl, B. and Knudsen, G. M.},
	month = may,
	year = {2014},
	keywords = {fs\_PET},
	pages = {225--36},
	annote = {Greve, Douglas {NSvarer}, {ClausFisher}, Patrick {MFeng}, {LingHansen}, Adam {EBaare}, {WilliamRosen}, {BruceFischl}, {BruceKnudsen}, Gitte Meng5R01EB006758-04/{EB}/{NIBIB} {NIH} {HHS}/5R01NS052585-05/{NS}/{NINDS} {NIH} {HHS}/5R21NS072652-02/{NS}/{NINDS} {NIH} {HHS}/P41 {RR}014075/{RR}/{NCRR} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01RR16594-01A1/{RR}/{NCRR} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov't2013/12/24 06:00Neuroimage. 2014 May 15;92:225-36. doi: 10.1016/j.neuroimage.2013.12.021. Epub 2013 Dec 19.}
}

@article{panizzon_testosterone_2010,
	title = {Testosterone modifies the effect of {APOE} genotype on hippocampal volume in middle-aged men},
	volume = {75},
	issn = {0028-3878},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2938973/},
	doi = {10.1212/WNL.0b013e3181f11deb},
	abstract = {Background:
The {APOE} ε4 allele is an established risk factor for Alzheimer disease ({AD}), yet findings are mixed for how early its effects are manifest. One reason for the mixed results could be the presence of interaction effects with other {AD} risk factors. Increasing evidence indicates that testosterone may play a significant role in the development of {AD}. The aim of the present study was to examine the potential interaction of testosterone and {APOE} genotype with respect to hippocampal volume in middle age.

Methods:
Participants were men from the Vietnam Era Twin Study of Aging (n = 375). The mean age was 55.9 years (range 51–59). Between-group comparisons were performed utilizing a hierarchical linear mixed model that adjusted for the nonindependence of twin data.

Results:
A significant interaction was observed between testosterone and {APOE} genotype (ε4-negative vs ε4-positive). Those with both low testosterone (≥1 {SD} below the mean) and an ε4-positive status had the smallest hippocampal volumes, although comparisons with normal testosterone groups were not significant. However, individuals with low testosterone and ε4-negative status had significantly larger hippocampal volumes relative to all other groups. A main effect of {APOE} genotype on hippocampal volume was observed, but only when the {APOE}-by-testosterone interaction was present.

Conclusions:
These findings demonstrate an interaction effect between testosterone and the {APOE} ε4 allele on hippocampal volume in middle-aged men, and they may suggest 2 low testosterone subgroups. Furthermore, these results allude to potential gene–gene interactions between {APOE} and either androgen receptor polymorphisms or genes associated with testosterone production.

{GLOSSARY}
null},
	number = {10},
	urldate = {2014-08-25},
	journal = {Neurology},
	author = {Panizzon, M.S. and Hauger, R. and Dale, A.M. and Eaves, L.J. and Eyler, L.T. and Fischl, B. and Fennema-Notestine, C. and Franz, C.E. and Grant, M.D. and Jak, A.J. and Jacobson, K.C. and Lyons, M.J. and Mendoza, S.P. and Neale, M.C. and Prom-Wormley, E.C. and Seidman, L.J. and Tsuang, M.T. and Xian, H. and Kremen, W.S.},
	month = sep,
	year = {2010},
	pmid = {20819998},
	pmcid = {PMC2938973},
	keywords = {Aging/genetics, Alleles, Apolipoproteins E/*genetics/metabolism, Genotype, Hippocampus/*anatomy \& histology/metabolism, Humans, Magnetic Resonance Imaging, Male, Middle Aged, Organ Size, Polymorphism, Genetic, Testosterone/*blood, United States, Veterans, Vietnam Conflict},
	pages = {874--880},
	annote = {Panizzon, M {SHauger}, {RDale}, A {MEaves}, L {JEyler}, L {TFischl}, {BFennema}-Notestine, {CFranz}, C {EGrant}, M {DJak}, A {JJacobson}, K {CLyons}, M {JMendoza}, S {PNeale}, M {CProm}-Wormley, E {CSeidman}, L {JTsuang}, M {TXian}, {HKremen}, W {SengR}01 {AG}018384/{AG}/{NIA} {NIH} {HHS}/R01 {AG}018386/{AG}/{NIA} {NIH} {HHS}/R01 {AG}018386-09/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022381/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022381-09/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022982/{AG}/{NIA} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov'{tTwin} Study2010/09/08 06:00Neurology. 2010 Sep 7;75(10):874-80. doi: 10.1212/{WNL}.0b013e3181f11deb.},
	file = {Panizzon-2010-Testosterone modifies the effect:/autofs/cluster/freesurfer/zotero/storage/6CB39Q4X/Panizzon-2010-Testosterone modifies the effect.pdf:application/pdf;PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/KEWFTGRM/Panizzon et al. - 2010 - Testosterone modifies the effect of APOE genotype .pdf:application/pdf}
}

@article{salat_age-associated_2009,
	title = {Age-Associated Alterations in Cortical Gray and White Matter Signal Intensity and Gray to White Matter Contrast},
	volume = {48},
	issn = {1053-8119},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2750073/},
	doi = {10.1016/j.neuroimage.2009.06.074},
	abstract = {Prior studies have focused on patterns of brain atrophy with aging and age-associated cognitive decline. It is possible that changes in neural tissue properties could provide an important marker of more subtle changes compared to gross morphometry. However, little is known about how {MRI} tissue parameters are altered in aging. We created cortical surface models of 148 individuals and mapped regional gray and white matter T1-weighted signal intensities from 3D {MPRAGE} images to examine patterns of age-associated signal alterations. Gray matter intensity was decreased with aging with strongest effects in medial frontal, anterior cingulate, and inferior temporal regions. White matter signal intensity decreased with aging in superior and medial frontal, cingulum, and medial and lateral temporal regions. The gray/white ratio ({GWR}) was altered throughout a large potion of the cortical mantle, with strong changes in superior and inferior frontal, lateral parietal, and superior temporal and precuneus regions demonstrating decreased overall contrast. Statistical effects of contrast changes were stronger than those of cortical thinning. These results demonstrate that there are strong regional changes in neural tissue properties with aging and tissue intensity measures may serve as an important biomarker of degeneration.},
	number = {1},
	urldate = {2014-08-23},
	journal = {{NeuroImage}},
	author = {Salat, DH and Lee, SY and van der Kouwe, AJ and Greve, DN and Fischl, B and Rosas, HD},
	month = oct,
	year = {2009},
	pmid = {19580876},
	pmcid = {PMC2750073},
	keywords = {Adult, Aged, Aged, 80 and over, *Aging, Cerebral Cortex/*anatomy \& histology/*physiology, Female, Humans, Magnetic Resonance Imaging, Male, Middle Aged, Myelin Sheath/*physiology, Organ Size, Reproducibility of Results, Sex Characteristics, Young Adult},
	pages = {21--28},
	annote = {Salat, D {HLee}, S Yvan der Kouwe, A {JGreve}, D {NFischl}, {BRosas}, H {DengBIRN}002/{PHS} {HHS}/K01 {AG}024898-01A1/{AG}/{NIA} {NIH} {HHS}/K01 {AG}024898-02/{AG}/{NIA} {NIH} {HHS}/K01 {AG}024898-03/{AG}/{NIA} {NIH} {HHS}/K01 {AG}024898-04/{AG}/{NIA} {NIH} {HHS}/K01 {AG}024898-05/{AG}/{NIA} {NIH} {HHS}/K01AG024898/{AG}/{NIA} {NIH} {HHS}/P41RR14075/{RR}/{NCRR} {NIH} {HHS}/R01 {NR}010827-01A1/{NR}/{NINR} {NIH} {HHS}/R01 {NR}010827-02/{NR}/{NINR} {NIH} {HHS}/R01 {NR}010827-05/{NR}/{NINR} {NIH} {HHS}/R01EB001550/{EB}/{NIBIB} {NIH} {HHS}/R01EB006758/{EB}/{NIBIB} {NIH} {HHS}/R01NR010827/{NR}/{NINR} {NIH} {HHS}/R01NS052585/{NS}/{NINDS} {NIH} {HHS}/U24RR021382/{RR}/{NCRR} {NIH} {HHS}/U54EB005149/{EB}/{NIBIB} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov't2009/07/08 09:00Neuroimage. 2009 Oct 15;48(1):21-8. doi: 10.1016/j.neuroimage.2009.06.074. Epub 2009 Jul 4.},
	file = {PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/S2UJ3F3W/Salat et al. - 2009 - Age-Associated Alterations in Cortical Gray and Wh.pdf:application/pdf;Salat-2009-Age-associated alterations in corti:/autofs/cluster/freesurfer/zotero/storage/P8TAQCXS/Salat-2009-Age-associated alterations in corti.pdf:application/pdf}
}

@article{han_reliability_2006,
	title = {Reliability of {MRI}-derived measurements of human cerebral cortical thickness: the effects of field strength, scanner upgrade and manufacturer},
	volume = {32},
	issn = {1053-8119 (Print) 1053-8119 (Linking)},
	shorttitle = {Reliability of {MRI}-derived measurements of human cerebral cortical thickness: the effects of field strength, scanner upgrade and manufacturer},
	url = {http://www.nmr.mgh.harvard.edu/~fischl/reprints/Han_NeuroImage_2006_thickness_reliability.pdf},
	doi = {10.1016/j.neuroimage.2006.02.051},
	abstract = {In vivo {MRI}-derived measurements of human cerebral cortex thickness are providing novel insights into normal and abnormal neuroanatomy, but little is known about their reliability. We investigated how the reliability of cortical thickness measurements is affected by {MRI} instrument-related factors, including scanner field strength, manufacturer, upgrade and pulse sequence. Several data processing factors were also studied. Two test-retest data sets were analyzed: 1) 15 healthy older subjects scanned four times at 2-week intervals on three scanners; 2) 5 subjects scanned before and after a major scanner upgrade. Within-scanner variability of global cortical thickness measurements was {\textless}0.03 mm, and the point-wise standard deviation of measurement error was approximately 0.12 mm. Variability was 0.15 mm and 0.17 mm in average, respectively, for cross-scanner (Siemens/{GE}) and cross-field strength (1.5 T/3 T) comparisons. Scanner upgrade did not increase variability nor introduce bias. Measurements across field strength, however, were slightly biased (thicker at 3 T). The number of (single vs. multiple averaged) acquisitions had a negligible effect on reliability, but the use of a different pulse sequence had a larger impact, as did different parameters employed in data processing. Sample size estimates indicate that regional cortical thickness difference of 0.2 mm between two different groups could be identified with as few as 7 subjects per group, and a difference of 0.1 mm could be detected with 26 subjects per group. These results demonstrate that {MRI}-derived cortical thickness measures are highly reliable when {MRI} instrument and data processing factors are controlled but that it is important to consider these factors in the design of multi-site or longitudinal studies, such as clinical drug trials.},
	number = {1},
	journal = {Neuroimage},
	author = {Han, X. and Jovicich, J. and Salat, D. and van der Kouwe, A. and Quinn, B. and Czanner, S. and Busa, E. and Pacheco, J. and Albert, M. and Killiany, R. and Maguire, P. and Rosas, D. and Makris, N. and Dale, A. and Dickerson, B. and Fischl, B.},
	month = aug,
	year = {2006},
	keywords = {Aged, Aged, 80 and over, Brain Mapping, Cerebral Cortex/*anatomy \& histology, fs\_Thickness-measurement, Functional Laterality, Humans, Image Processing, Computer-Assisted, Magnetic Resonance Imaging/*methods, Reference Values, Reproducibility of Results},
	pages = {180--94},
	annote = {Han, {XiaoJovicich}, {JorgeSalat}, Davidvan der Kouwe, {AndreQuinn}, {BrianCzanner}, {SilvesterBusa}, {EvelinaPacheco}, {JenniAlbert}, {MarilynKilliany}, {RonaldMaguire}, {PaulRosas}, {DianaMakris}, {NikosDale}, {AndersDickerson}, {BradfordFischl}, {BruceengK}23 {AG} 22509/{AG}/{NIA} {NIH} {HHS}/P01 {AG} 04953/{AG}/{NIA} {NIH} {HHS}/P41 {RR} 14075/{RR}/{NCRR} {NIH} {HHS}/R01 {RR} 16594-01A1/{RR}/{NCRR} {NIH} {HHS}/U24 {RR} 021382/{RR}/{NCRR} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov't2006/05/03 09:00Neuroimage. 2006 Aug 1;32(1):180-94. Epub 2006 May 2.}
}

@article{rosas_altered_2010,
	title = {Altered white matter microstructure in the corpus callosum in Huntington's disease: implications for cortical "disconnection"},
	volume = {49},
	issn = {1095-9572 (Electronic) 1053-8119 (Linking)},
	shorttitle = {Altered white matter microstructure in the corpus callosum in Huntington's disease: implications for cortical "disconnection"},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/19850138},
	doi = {10.1016/j.neuroimage.2009.10.015},
	abstract = {The corpus callosum ({CC}) is the major conduit for information transfer between the cerebral hemispheres and plays an integral role in relaying sensory, motor and cognitive information between homologous cortical regions. The majority of fibers that make up the {CC} arise from large pyramidal neurons in layers {III} and V, which project contra-laterally. These neurons degenerate in Huntington's disease ({HD}) in a topographically and temporally selective way. Since any focus of cortical degeneration could be expected to secondarily de-afferent homologous regions of cortex, we hypothesized that regionally selective cortical degeneration would be reflected in regionally selective degeneration of the {CC}. We used conventional T1-weighted, diffusion tensor imaging ({DTI}), and a modified corpus callosum segmentation scheme to examine the {CC} in healthy controls, huntingtin gene-carriers and symptomatic {HD} subjects. We measured mid-sagittal callosal cross-sectional thickness and several {DTI} parameters, including fractional anisotropy ({FA}), which reflects the degree of white matter organization, radial diffusivity, a suggested index of myelin integrity, and axial diffusivity, a suggested index of axonal damage of the {CC}. We found a topologically selective pattern of alterations in these measures in pre-manifest subjects that were more extensive in early symptomatic {HD} subjects and that correlated with performance on distinct cognitive measures, suggesting an important role for disrupted inter-hemispheric transfer in the clinical symptoms of {HD}. Our findings provide evidence for early degeneration of commissural pyramidal neurons in the neocortex, loss of cortico-cortical connectivity, and functional compromise of associative cortical processing.},
	number = {4},
	journal = {Neuroimage},
	author = {Rosas, H. D. and Lee, S. Y. and Bender, A. C. and Zaleta, A. K. and Vangel, M. and Yu, P. and Fischl, B. and Pappu, V. and Onorato, C. and Cha, J. H. and Salat, D. H. and Hersch, S. M.},
	month = feb,
	year = {2010},
	keywords = {Adult, Corpus Callosum/*pathology, Female, Humans, Huntington Disease/*pathology, Magnetic Resonance Imaging/*methods, Male, Middle Aged, Nerve Fibers, Myelinated/*pathology},
	pages = {2995--3004},
	annote = {Rosas, H {DianaLee}, Stephanie {YBender}, Alexander {CZaleta}, Alexandra {KVangel}, {MarkYu}, {PengFischl}, {BrucePappu}, {VasanthOnorato}, {ChristinaCha}, Jang-{HoSalat}, David {HHersch}, Steven {MengAG}02238/{AG}/{NIA} {NIH} {HHS}/K01 {AG}024898-04/{AG}/{NIA} {NIH} {HHS}/K01AG024898/{AG}/{NIA} {NIH} {HHS}/M01 {RR}001066/{RR}/{NCRR} {NIH} {HHS}/M01 {RR}001066-305062/{RR}/{NCRR} {NIH} {HHS}/{NR}010827/{NR}/{NINR} {NIH} {HHS}/{NS}042861/{NS}/{NINDS} {NIH} {HHS}/{NS}058792/{NS}/{NINDS} {NIH} {HHS}/P01 {NS}058793/{NS}/{NINDS} {NIH} {HHS}/P01 {NS}058793-01A1/{NS}/{NINDS} {NIH} {HHS}/P01 {NS}058793-01A10001/{NS}/{NINDS} {NIH} {HHS}/P01 {NS}058793-01A10004/{NS}/{NINDS} {NIH} {HHS}/P01 {NS}058793-01A19001/{NS}/{NINDS} {NIH} {HHS}/P01 {NS}058793-01A19002/{NS}/{NINDS} {NIH} {HHS}/P01 {NS}058793-02/{NS}/{NINDS} {NIH} {HHS}/P41 {RR}014075-117865/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-117867/{RR}/{NCRR} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 {EB}001550/{EB}/{NIBIB} {NIH} {HHS}/R01 {NR}010827-01A1/{NR}/{NINR} {NIH} {HHS}/R01 {NS}042861/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}042861-04/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}042861-05/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}052585/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}052585-04/{NS}/{NINDS} {NIH} {HHS}/R01 {RR}016594-01A1/{RR}/{NCRR} {NIH} {HHS}/R01 {RR}16594-01A1/{RR}/{NCRR} {NIH} {HHS}/Research Support, N.I.H., Extramural2009/10/24 06:00Neuroimage. 2010 Feb 15;49(4):2995-3004. doi: 10.1016/j.neuroimage.2009.10.015. Epub 2009 Oct 19.},
	file = {Rosas-2010-Altered white matter microstructure:/autofs/cluster/freesurfer/zotero/storage/JC4MXISC/Rosas-2010-Altered white matter microstructure.pdf:application/pdf}
}

@article{koldewyn_differences_2014,
	title = {Differences in the right inferior longitudinal fasciculus but no general disruption of white matter tracts in children with autism spectrum disorder},
	issn = {0027-8424, 1091-6490},
	url = {https://surfer.nmr.mgh.harvard.edu/ftp/articles/2014/Koldewyn_Kanwisher.2014.PNAS.pdf},
	doi = {10.1073/pnas.1324037111},
	abstract = {One of the most widely cited features of the neural phenotype of autism is reduced “integrity” of long-range white matter tracts, a claim based primarily on diffusion imaging studies. However, many prior studies have small sample sizes and/or fail to address differences in data quality between those with autism spectrum disorder ({ASD}) and typical participants, and there is little consensus on which tracts are affected. To overcome these problems, we scanned a large sample of children with autism (n = 52) and typically developing children (n = 73). Data quality was variable, and worse in the {ASD} group, with some scans unusable because of head motion artifacts. When we follow standard data analysis practices (i.e., without matching head motion between groups), we replicate the finding of lower fractional anisotropy ({FA}) in multiple white matter tracts. However, when we carefully match data quality between groups, all these effects disappear except in one tract, the right inferior longitudinal fasciculus ({ILF}). Additional analyses showed the expected developmental increases in the {FA} of fiber tracts within {ASD} and typical groups individually, demonstrating that we had sufficient statistical power to detect known group differences. Our data challenge the widely claimed general disruption of white matter tracts in autism, instead implicating only one tract, the right {ILF}, in the {ASD} phenotype.},
	language = {en},
	urldate = {2014-08-25},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Koldewyn, Kami and Yendiki, Anastasia and Weigelt, Sarah and Gweon, Hyowon and Julian, Joshua and Richardson, Hilary and Malloy, Caitlin and Saxe, Rebecca and Fischl, Bruce and Kanwisher, Nancy},
	month = jan,
	year = {2014},
	pmid = {24449864},
	keywords = {Anisotropy, Brain/*pathology, Child, Child Development Disorders, Pervasive/*pathology, Child, Preschool, Cohort Studies, connectivity, Diffusion, diffusion-weighted imaging, Humans, Magnetic Resonance Imaging, Nerve Fibers, Myelinated/*pathology},
	pages = {201324037},
	annote = {Koldewyn, {KamiYendiki}, {AnastasiaWeigelt}, {SarahGweon}, {HyowonJulian}, {JoshuaRichardson}, {HilaryMalloy}, {CaitlinSaxe}, {RebeccaFischl}, {BruceKanwisher}, Nancyeng1S10RR019307/{RR}/{NCRR} {NIH} {HHS}/1S10RR023043/{RR}/{NCRR} {NIH} {HHS}/1S10RR023401/{RR}/{NCRR} {NIH} {HHS}/5P41EB015896-15/{EB}/{NIBIB} {NIH} {HHS}/5R01AG008122-22/{AG}/{NIA} {NIH} {HHS}/5U01-{MH}093765/{MH}/{NIMH} {NIH} {HHS}/{AG}022381/{AG}/{NIA} {NIH} {HHS}/R01EB006758/{EB}/{NIBIB} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov't2014/01/23 06:00Proc Natl Acad Sci U S A. 2014 Feb 4;111(5):1981-6. doi: 10.1073/pnas.1324037111. Epub 2014 Jan 21.},
	file = {Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/F7TAZTVD/Koldewyn et al. - 2014 - Differences in the right inferior longitudinal fas.pdf:application/pdf;Koldewyn-2014-Differences in the right inferi1:/autofs/cluster/freesurfer/zotero/storage/8AF5FRUJ/Koldewyn-2014-Differences in the right inferi1.pdf:application/pdf;Snapshot:/autofs/cluster/freesurfer/zotero/storage/9SBE6JN6/1324037111.html:text/html}
}

@article{fjell_high_2009,
	title = {High consistency of regional cortical thinning in aging across multiple samples},
	volume = {19},
	issn = {1460-2199 (Electronic) 1047-3211 (Linking)},
	shorttitle = {High consistency of regional cortical thinning in aging across multiple samples},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/19150922},
	doi = {10.1093/cercor/bhn232},
	abstract = {Cross-sectional magnetic resonance imaging ({MRI}) studies of cortical thickness and volume have shown age effects on large areas, but there are substantial discrepancies across studies regarding the localization and magnitude of effects. These discrepancies hinder understanding of effects of aging on brain morphometry, and limit the potential usefulness of {MR} in research on healthy and pathological age-related brain changes. The present study was undertaken to overcome this problem by assessing the consistency of age effects on cortical thickness across 6 different samples with a total of 883 participants. A surface-based segmentation procedure ({FreeSurfer}) was used to calculate cortical thickness continuously across the brain surface. The results showed consistent age effects across samples in the superior, middle, and inferior frontal gyri, superior and middle temporal gyri, precuneus, inferior and superior parietal cortices, fusiform and lingual gyri, and the temporo-parietal junction. The strongest effects were seen in the superior and inferior frontal gyri, as well as superior parts of the temporal lobe. The inferior temporal lobe and anterior cingulate cortices were relatively less affected by age. The results are discussed in relation to leading theories of cognitive aging.},
	language = {eng},
	number = {9},
	journal = {Cereb Cortex},
	author = {Fjell, A. M. and Westlye, L. T. and Amlien, I. and Espeseth, T. and Reinvang, I. and Raz, N. and Agartz, I. and Salat, D. H. and Greve, D. N. and Fischl, B. and Dale, A. M. and Walhovd, K. B.},
	month = sep,
	year = {2009},
	keywords = {Adolescent, Adult, Aged, Aged, 80 and over, Aging/*pathology, Anatomy, Cross-Sectional/*methods, Cerebral Cortex/*anatomy \& histology, Female, Humans, Magnetic Resonance Imaging/*methods, Male, Middle Aged, Organ Size, Young Adult},
	pages = {2001--12},
	annote = {Fjell, Anders {MWestlye}, Lars {TAmlien}, {IngeEspeseth}, {ThomasReinvang}, {IvarRaz}, {NaftaliAgartz}, {IngridSalat}, David {HGreve}, Doug {NFischl}, {BruceDale}, Anders {MWalhovd}, Kristine {BengP}41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 {EB}001550/{EB}/{NIBIB} {NIH} {HHS}/R01 {NS}052585-01/{NS}/{NINDS} {NIH} {HHS}/R01 {RR}16594-01A1/{RR}/{NCRR} {NIH} {HHS}/R01-{NS}39581/{NS}/{NINDS} {NIH} {HHS}/R01-{RR}13609/{RR}/{NCRR} {NIH} {HHS}/R01EB006758/{EB}/{NIBIB} {NIH} {HHS}/R37 {AG}011230/{AG}/{NIA} {NIH} {HHS}/R37 {AG}011230-14/{AG}/{NIA} {NIH} {HHS}/R37 {AG}011230-17/{AG}/{NIA} {NIH} {HHS}/R37 {AG}011230-18/{AG}/{NIA} {NIH} {HHS}/R37-{AG}11230/{AG}/{NIA} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/U54 {EB}005149/{EB}/{NIBIB} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov'{tNew} York, N.Y. : 19912009/01/20 09:00Cereb Cortex. 2009 Sep;19(9):2001-12. doi: 10.1093/cercor/bhn232. Epub 2009 Jan 15.},
	file = {Fjell-2009-High consistency of regional cortic:/autofs/cluster/freesurfer/zotero/storage/C6HQCTNZ/Fjell-2009-High consistency of regional cortic.pdf:application/pdf}
}

@article{lehmann_atrophy_2010,
	title = {Atrophy patterns in Alzheimer's disease and semantic dementia: a comparison of {FreeSurfer} and manual volumetric measurements},
	volume = {49},
	issn = {1095-9572},
	shorttitle = {Atrophy patterns in Alzheimer's disease and semantic dementia},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/19874902},
	doi = {10.1016/j.neuroimage.2009.10.056},
	abstract = {Alzheimer's disease ({AD}) and semantic dementia ({SD}) are characterized by different patterns of global and temporal lobe atrophy which can be studied using magnetic resonance imaging ({MRI}). Manual delineation of regions of interest is time-consuming. {FreeSurfer} is a freely available automated technique which has a facility to label cortical and subcortical brain regions automatically. As with all automated techniques comparison with existing methods is important. Eight temporal lobe structures in each hemisphere were delineated using {FreeSurfer} and compared with manual segmentations in 10 control, 10 {AD}, and 10 {SD} subjects. The reproducibility errors for the manual segmentations ranged from 3\% to 6\%. Differences in protocols between the two methods led to differences in absolute volumes with the greatest differences between methods found bilaterally in the hippocampus, entorhinal cortex and fusiform gyrus (p{\textless}0.005). However, good correlations between the methods were found for most regions, with the highest correlations shown for the ventricles, whole brain and left medial-inferior temporal gyrus (r{\textgreater}0.9), followed by the bilateral amygdala and hippocampus, left superior temporal gyrus, right medial-inferior temporal gyrus and left temporal lobe (r{\textgreater}0.8). Overlap ratios differed between methods bilaterally in the amygdala, superior temporal gyrus, temporal lobe, left fusiform gyrus and right parahippocampal gyrus (p{\textless}0.01). Despite differences in protocol and volumes, both methods showed similar atrophy patterns in the patient groups compared with controls, and similar right-left differences, suggesting that both methods accurately distinguish between the three groups.},
	language = {eng},
	number = {3},
	journal = {{NeuroImage}},
	author = {Lehmann, Manja and Douiri, Abdel and Kim, Lois G. and Modat, Marc and Chan, Dennis and Ourselin, Sebastien and Barnes, Josephine and Fox, Nick C.},
	month = feb,
	year = {2010},
	pmid = {19874902},
	keywords = {Alzheimer Disease, Alzheimer's disease, Atrophy, Brain, Female, {FreeSurfer}, Frontotemporal Lobar Degeneration, fs\_Validation-Evaluations, Humans, Image Interpretation, Computer-Assisted, Magnetic Resonance Imaging, Male, Middle Aged, Segmentation, Semantic dementia},
	pages = {2264--2274},
	file = {ScienceDirect Snapshot:/autofs/cluster/freesurfer/zotero/storage/TA56Z6GI/S1053811909011276.html:text/html}
}

@article{kolasinski_radial_2013,
	title = {Radial and tangential neuronal migration pathways in the human fetal brain: anatomically distinct patterns of diffusion {MRI} coherence},
	volume = {79},
	issn = {1053-8119},
	shorttitle = {Radial and tangential neuronal migration pathways in the human fetal brain},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4111232/},
	doi = {10.1016/j.neuroimage.2013.04.125},
	abstract = {Corticogenesis is underpinned by a complex process of subcortical neuroproliferation, followed by highly orchestrated cellular migration. A greater appreciation of the processes involved in human fetal corticogenesis is vital to gaining an understanding of how developmental disturbances originating in gestation could establish a variety of complex neuropathology manifesting in childhood, or even in adult life. Magnetic resonance imaging modalities offer a unique insight into anatomical structure, and increasingly infer information regarding underlying microstructure in the human brain. In this study we applied a combination of high-resolution structural and diffusion-weighted magnetic resonance imaging to a unique cohort of three post-mortem fetal brain specimens, aged between 19 and 22 post-conceptual weeks. Specifically, we sought to assess patterns of diffusion coherence associated with subcortical neuroproliferative structures: the pallial ventricular/subventricular zone and subpallial ganglionic eminence. Two distinct three-dimensional patterns of diffusion coherence were evident: a clear radial pattern originating in ventricular/subventricular zone, and a tangentio-radial patterns originating in ganglionic eminence. These patterns appeared to regress in a caudo-rostral and lateral-ventral to medial-dorsal direction across the short period of fetal development under study. Our findings demonstrate for the first time distinct patterns of diffusion coherence associated with known anatomical proliferative structures. The radial pattern associated with dorsopallial ventricular/subventricular zone and the tangentio-radial pattern associated with subpallial ganglionic eminence are consistent with reports of radial-glial mediated neuronal migration pathways identified during human corticogenesis, supported by our prior studies of comparative fetal diffusion {MRI} and histology. The ability to assess such pathways in the fetal brain using {MR} imaging offers a unique insight into three-dimensional trajectories beyond those visualized using traditional histological techniques. Our results suggest that ex-vivo fetal {MRI} is a potentially useful modality in understanding normal human development and various disease processes whose etiology may originate in aberrant fetal neuronal migration.},
	urldate = {2014-08-25},
	journal = {{NeuroImage}},
	author = {Kolasinski, James and Takahashi, Emi and Stevens, Allison A. and Benner, Thomas and Fischl, Bruce and Zollei, Lilla and Grant, P. Ellen},
	month = oct,
	year = {2013},
	pmid = {23672769},
	pmcid = {PMC4111232},
	keywords = {Brain/*anatomy \& histology/*embryology/growth \& development, Diffusion Tensor Imaging/*methods, Humans, Models, Anatomic, Models, Neurological, Nerve Fibers, Myelinated/*ultrastructure, Neural Pathways/*anatomy \& histology/*embryology/growth \& development},
	pages = {412--422},
	annote = {Kolasinski, {JamesTakahashi}, {EmiStevens}, Allison {ABenner}, {ThomasFischl}, {BruceZollei}, {LillaGrant}, P {EllenengK}99 {HD}061485/{HD}/{NICHD} {NIH} {HHS}/K99HD061485/{HD}/{NICHD} {NIH} {HHS}/{MH}081896/{MH}/{NIMH} {NIH} {HHS}/P41RR14075/{RR}/{NCRR} {NIH} {HHS}/R00 {HD}061485/{HD}/{NICHD} {NIH} {HHS}/R21HD069001/{HD}/{NICHD} {NIH} {HHS}/{RC}2MH089921/{MH}/{NIMH} {NIH} {HHS}/{RC}2MH089929/{MH}/{NIMH} {NIH} {HHS}/{RC}2MH090047/{MH}/{NIMH} {NIH} {HHS}/S10RR021110/{RR}/{NCRR} {NIH} {HHS}/Research Support, N.I.H., Extramural2013/05/16 06:00Neuroimage. 2013 Oct 1;79:412-22. doi: 10.1016/j.neuroimage.2013.04.125. Epub 2013 May 11.},
	file = {Kolasinski-2013-Radial and tangential neurona1:/autofs/cluster/freesurfer/zotero/storage/IHD8J6XB/Kolasinski-2013-Radial and tangential neurona1.pdf:application/pdf;PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/NIPXEH4R/Kolasinski et al. - 2013 - Radial and tangential neuronal migration pathways .pdf:application/pdf}
}

@article{chen_age-associated_2011,
	title = {Age-Associated Reductions in Cerebral Blood Flow Are Independent from Regional Atrophy},
	volume = {55},
	issn = {1053-8119},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3435846/},
	doi = {10.1016/j.neuroimage.2010.12.032},
	abstract = {Prior studies have demonstrated decreasing cerebral blood flow ({CBF}) in normal aging, but the full spatial pattern and potential mechanism of changes in {CBF} remain to be elucidated. Specifically, existing data have not been entirely consistent regarding the spatial distribution of such changes, potentially a result of neglecting the effect of age-related tissue atrophy in {CBF} measurements. In this work, we use pulsed arterial-spin labelling to quantify regional {CBF} in 86 cognitively and physically healthy adults, aged 23 to 88 years. Surface-based analyses were utilized to map regional decline in {CBF} and cortical thickness with advancing age, and to examine the spatial associations and dissociations between these metrics. Our results demonstrate regionally selective age-related reductions in cortical perfusion, involving the superior-frontal, orbito-frontal, superior-parietal, middle-inferior temporal, insular, precuneus, supramarginal, lateral-occipital and cingulate regions, while subcortical {CBF} was relatively preserved in aging. Regional effects of age on {CBF} differed from that of grey-matter atrophy. In addition, the pattern of {CBF} associations with age displays an interesting similarity with the default-mode network. These findings demonstrate the dissociation between regional {CBF} and structural alterations specific to normal aging, and augment our understanding of mechanisms of pathology in older adults.},
	number = {2},
	urldate = {2014-08-25},
	journal = {{NeuroImage}},
	author = {Chen, J. Jean and Rosas, H. Diana and Salat, David H.},
	month = mar,
	year = {2011},
	pmid = {21167947},
	pmcid = {PMC3435846},
	pages = {468--478},
	file = {PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/S9C6EPXP/Chen et al. - 2011 - Age-Associated Reductions in Cerebral Blood Flow A.pdf:application/pdf}
}

@article{golland_permutation_2003,
	title = {Permutation tests for classification: towards statistical significance in image-based studies},
	volume = {18},
	shorttitle = {Permutation tests for classification: towards statistical significance in image-based studies},
	url = {http://www.nmr.mgh.harvard.edu/~fischl/reprints/golland-fischl-ipmi03.pdf},
	journal = {Inf.Process Med.Imaging},
	author = {Golland, P. and Fischl, B.},
	year = {2003},
	keywords = {Algorithms, Alzheimer Disease, Brain, Brain Mapping, classification, clinical, Comparative Study, Computer Simulation, diagnosis, fs\_Misc-methodology, Humans, Image Enhancement, Image Interpretation,Computer-Assisted, Imaging,Three-Dimensional, Magnetic Resonance Imaging, methods, Models,Biological, Models,Statistical, pathology, Pattern Recognition,Automated, physiopathology, Reproducibility of Results, Research Support,U.S.Gov't,Non-P.H.S., Research Support,U.S.Gov't,P.H.S., Sensitivity and Specificity, Subtraction Technique},
	pages = {330--341},
	annote = {{DA} - 20040903NOT {IN} {FILE}}
}

@article{lee_novel_2006,
	title = {A novel quantitative cross-validation of different cortical surface reconstruction algorithms using {MRI} phantom.},
	volume = {31},
	url = {https://surfer.nmr.mgh.harvard.edu/ftp/articles/lee_j_31p572_2006.pdf},
	doi = {10.1016/j.neuroimage.2005.12.044},
	abstract = {Cortical surface reconstruction is important for functional brain mapping and morphometric analysis of the brain cortex. Several methods have been developed for the faithful reconstruction of surface models which represent the true cortical surface in both geometry and topology. However, there has been no explicit comparison study among those methods because each method has its own procedures, file formats, coordinate systems, and use of the reconstructed surface. There has also been no explicit evaluation method except visual inspection to validate the whole-cortical surface models quantitatively. In this  study, we presented a novel phantom-based validation method of the cortical surface reconstruction algorithm and quantitatively cross-validated the three most prominent cortical surface reconstruction algorithms which are used in Freesurfer, {BrainVISA}, and {CLASP}, respectively. The validation included geometrical accuracy and mesh characteristics such as Euler number, fractal dimension ({FD}), total surface area, and local density of points. {CLASP} showed the best geometric/topologic accuracy and mesh characteristics such as {FD} and total surface area compared to Freesurfer and {BrainVISA}. In the validation of local density of points, Freesurfer and {BrainVISA} showed more even distribution of points on the cortical surface compared to {CLASP}.},
	language = {eng},
	number = {2},
	journal = {{NeuroImage}},
	author = {Lee, Jun Ki and Lee, Jong-Min and Kim, June Sic and Kim, In Young and Evans, Alan C. and Kim, Sun I.},
	month = jun,
	year = {2006},
	pmid = {16503170},
	keywords = {Algorithms, Cerebral Cortex/*anatomy \& histology, fs\_Validation-Evaluations, Functional Laterality, Humans, Image Processing, Computer-Assisted, Magnetic Resonance Imaging/*methods, Phantoms, Imaging, Pia Mater/anatomy \& histology, Reproducibility of Results},
	pages = {572--584}
}

@article{rajimehr_does_2009,
	title = {Does retinotopy influence cortical folding in primate visual cortex?},
	volume = {29},
	issn = {0270-6474},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2785715/},
	doi = {10.1523/JNEUROSCI.1835-09.2009},
	abstract = {In humans and other Old World primates, much of visual cortex comprises a set of retinotopic maps, embedded in a cortical sheet with well-known, identifiable folding patterns. However, the relationship between these two prominent cortical variables has not been comprehensively studied. Here, we quantitatively tested this relationship using functional and structural {MRI} in monkeys and humans. We found that the vertical meridian of the visual field tends to be represented on gyri (convex folds), whereas the horizontal meridian is preferentially represented in sulci (concave folds), throughout visual cortex in both primate species. This relationship suggests that the retinotopic maps may constrain the pattern of cortical folding during development.},
	number = {36},
	urldate = {2014-08-25},
	journal = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
	author = {Rajimehr, Reza and Tootell, Roger B.H.},
	month = sep,
	year = {2009},
	pmid = {19741121},
	pmcid = {PMC2785715},
	pages = {11149--11152},
	file = {PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/WCDWPMTD/Rajimehr and Tootell - 2009 - Does retinotopy influence cortical folding in prim.pdf:application/pdf}
}

@article{augustinack_mri_2014,
	title = {{MRI} parcellation of ex vivo medial temporal lobe},
	volume = {93 Pt 2},
	issn = {1095-9572 (Electronic) 1053-8119 (Linking)},
	shorttitle = {{MRI} parcellation of ex vivo medial temporal lobe},
	url = {https://surfer.nmr.mgh.harvard.edu/pub/articles/2014/Augustinack.2014.NeuroimageSpecialIssue.pdf},
	doi = {10.1016/j.neuroimage.2013.05.053},
	abstract = {Recent advancements in radio frequency coils, field strength and sophisticated pulse sequences have propelled modern brain mapping and have made validation to biological standards - histology and pathology - possible. The medial temporal lobe has long been established as a pivotal brain region for connectivity, function and unique structure in the human brain, and reveals disconnection in mild Alzheimer's disease. Specific brain mapping of mesocortical areas affected with neurofibrillary tangle pathology early in disease progression provides not only an accurate description for location of these areas but also supplies spherical coordinates that allow comparison between other ex vivo cases and larger in vivo datasets. We have identified several cytoarchitectonic features in the medial temporal lobe with high resolution ex vivo {MRI}, including gray matter structures such as the entorhinal layer {II} 'islands', perirhinal layer {II}-{III} columns, presubicular 'clouds', granule cell layer of the dentate gyrus as well as lamina of the hippocampus. Localization of Brodmann areas 28 and 35 (entorhinal and perirhinal, respectively) demonstrates {MRI} based area boundaries validated with multiple methods and histological stains. Based on our findings, both myelin and Nissl staining relate to contrast in ex vivo {MRI}. Precise brain mapping serves to create modern atlases for cortical areas, allowing accurate localization with important applications to detecting early disease processes.},
	language = {en},
	urldate = {2014-08-21},
	journal = {Neuroimage},
	author = {Augustinack, J. C. and Magnain, C. and Reuter, M. and van der Kouwe, A. J. and Boas, D. and Fischl, B.},
	month = jun,
	year = {2014},
	keywords = {fs\_OCT},
	pages = {252--9},
	annote = {Augustinack, Jean {CMagnain}, {CarolineReuter}, Martinvan der Kouwe, Andre J {WBoas}, {DavidFischl}, Bruceeng1R01NS070963/{NS}/{NINDS} {NIH} {HHS}/1R21NS072652-01/{NS}/{NINDS} {NIH} {HHS}/1S10RR019307/{RR}/{NCRR} {NIH} {HHS}/1S10RR023043/{RR}/{NCRR} {NIH} {HHS}/1S10RR023401/{RR}/{NCRR} {NIH} {HHS}/5R01AG008122-22/{AG}/{NIA} {NIH} {HHS}/5U01-{MH}093765/{MH}/{NIMH} {NIH} {HHS}/{AG}022381/{AG}/{NIA} {NIH} {HHS}/K01 {AG}028521/{AG}/{NIA} {NIH} {HHS}/K01AG028521/{AG}/{NIA} {NIH} {HHS}/P41 {RR}014075/{RR}/{NCRR} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 {EB}006758/{EB}/{NIBIB} {NIH} {HHS}/R01 {NS}052585/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}052585-01/{NS}/{NINDS} {NIH} {HHS}/R01EB006758/{EB}/{NIBIB} {NIH} {HHS}/{RC}1 {AT}005728-01/{AT}/{NCCAM} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov'{tReview}2013/05/25 06:00Neuroimage. 2014 Jun;93 Pt 2:252-9. doi: 10.1016/j.neuroimage.2013.05.053. Epub 2013 May 21.}
}

@article{yeo_estimates_2014,
	title = {Estimates of segregation and overlap of functional connectivity networks in the human cerebral cortex},
	volume = {88},
	issn = {10538119},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S1053811913010690},
	doi = {10.1016/j.neuroimage.2013.10.046},
	language = {en},
	urldate = {2014-08-23},
	journal = {{NeuroImage}},
	author = {Yeo, B.T. Thomas and Krienen, Fenna M. and Chee, Michael W.L. and Buckner, Randy L.},
	month = mar,
	year = {2014},
	pages = {212--227},
	annote = {Yeo, B T {ThomasKrienen}, Fenna {MChee}, Michael W {LBuckner}, Randy {LENGP}41 {EB}015896/{EB}/{NIBIB} {NIH} {HHS}/S10 {RR}019307/{RR}/{NCRR} {NIH} {HHS}/S10 {RR}021110/{RR}/{NCRR} {NIH} {HHS}/S10 {RR}023401/{RR}/{NCRR} {NIH} {HHS}/U01 {MH}093765/{MH}/{NIMH} {NIH} {HHS}/2013/11/05 06:00Neuroimage. 2013 Nov 1;88C:212-227. doi: 10.1016/j.neuroimage.2013.10.046.}
}

@article{buckner_unified_2004,
	title = {A unified approach for morphometric and functional data analysis in young, old, and demented adults using automated atlas-based head size normalization: reliability and validation against manual measurement of total intracranial volume.},
	volume = {23},
	url = {https://surfer.nmr.mgh.harvard.edu/ftp/articles/buckner2004.pdf},
	doi = {10.1016/j.neuroimage.2004.06.018},
	abstract = {Atlas normalization, as commonly used by functional data analysis, provides an automated solution to the widely encountered problem of correcting for head size  variation in regional and whole-brain morphometric analyses, so long as an age- and population-appropriate target atlas is used. In the present article, we develop and validate an atlas normalization procedure for head size correction using manual total intracranial volume ({TIV}) measurement as a reference. The target image used for atlas transformation consisted of a merged young and old-adult template specifically created for cross age-span normalization. Automated atlas transformation generated the Atlas Scaling Factor ({ASF}) defined as the volume-scaling factor required to match each individual to the atlas target. Because atlas normalization equates head size, the {ASF} should be proportional to {TIV}. A validation analysis was performed on 147 subjects to evaluate {ASF} as a proxy for manual {TIV} measurement. In addition, 19 subjects were imaged on multiple days to assess test-retest reliability. Results indicated that the {ASF} was (1) equivalent to manual {TIV} normalization (r = 0.93), (2) reliable across multiple imaging sessions (r = 1.00; mean absolute percentage of difference = 0.51\%), (3) able to connect between-gender head size differences, and (4) minimally biased in demented older adults with marked atrophy. Hippocampal volume differences between nondemented (n = 49) and demented (n = 50) older adults (measured manually) were equivalent whether corrected using manual {TIV} or automated {ASF} (effect sizes of 1.29 and 1.46, respectively). To provide normative values, {ASF} was used to automatically derive estimated {TIV} ({eTIV}) in 335 subjects aged 15-96 including both clinically characterized nondemented (n =  77) and demented (n = 90) older adults. Differences in {eTIV} between nondemented and demented groups were negligible, thus failing to support the hypothesis that  large premorbid brain size moderates Alzheimer's disease. Gender was the only robust factor that influenced {eTIV}. Men showed an approximately approximately 12\% larger {eTIV} than women. These results demonstrate that atlas normalization using  appropriate template images provides a robust, automated method for head size correction that is equivalent to manual {TIV} correction in studies of aging and dementia. Thus, atlas normalization provides a common framework for both morphometric and functional data analysis.},
	language = {eng},
	number = {2},
	journal = {{NeuroImage}},
	author = {Buckner, Randy L. and Head, Denise and Parker, Jamie and Fotenos, Anthony F. and Marcus, Daniel and Morris, John C. and Snyder, Abraham Z.},
	month = oct,
	year = {2004},
	pmid = {15488422},
	keywords = {Adolescent, Adult, Aged, Aged, 80 and over, Aging/*physiology, Algorithms, Atrophy, Dementia/*pathology, Female, fs\_Misc-methodology, Head/*anatomy \& histology, Hippocampus/anatomy \& histology, Humans, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Male, Middle Aged, Reproducibility of Results, Sex Characteristics},
	pages = {724--738}
}

@article{fennema-notestine_feasibility_2007,
	title = {Feasibility of multi-site clinical structural neuroimaging studies of aging using legacy data},
	volume = {5},
	issn = {1539-2791},
	url = {https://surfer.nmr.mgh.harvard.edu/ftp/articles/Neuroinformatics2007.pdf},
	doi = {10.1007/s12021-007-9003-9},
	abstract = {The application of advances in biomedical computing to medical imaging research is enabling scientists to conduct quantitative clinical imaging studies using data collected across multiple sites to test new hypotheses on larger cohorts, increasing the power to detect subtle effects. Given that many research groups have valuable existing (legacy) data, one goal of the Morphometry Biomedical Informatics Research Network ({BIRN}) Testbed is to assess the feasibility of pooled analyses of legacy structural neuroimaging data in normal aging and Alzheimer's disease. The present study examined whether such data could be meaningfully reanalyzed as a larger combined data set by using rigorous data curation, image analysis, and statistical modeling methods; in this case, to test the hypothesis that hippocampal volume decreases with age and to investigate findings of hippocampal asymmetry. This report describes our work with legacy T1-weighted magnetic resonance ({MR}) and demographic data related to normal aging that have been shared through the {BIRN} by three research sites. Results suggest that, in the present application, legacy {MR} data from multiple sites can be pooled to investigate questions of scientific interest. In particular, statistical analyses suggested that a mixed-effects model employing site as a random effect best fits the data, accounting for site-specific effects while taking advantage of expected comparability of age-related effects. In the combined sample from three sites, significant age-related decline of hippocampal volume and right-dominant hippocampal asymmetry were detected in healthy elderly controls. These expected findings support the feasibility of combining legacy data to investigate novel scientific questions.},
	language = {eng},
	number = {4},
	journal = {Neuroinformatics},
	author = {Fennema-Notestine, Christine and Gamst, Anthony C. and Quinn, Brian T. and Pacheco, Jenni and Jernigan, Terry L. and Thal, Leon and Buckner, Randy and Killiany, Ron and Blacker, Deborah and Dale, Anders M. and Fischl, Bruce and Dickerson, Brad and Gollub, Randy L.},
	year = {2007},
	pmid = {17999200},
	keywords = {Aged, Aged, Aged, 80 and over, Aged, 80 and over, Brain, Brain Mapping, Brain Mapping, Brain/*physiology, *Database Management Systems, Database Management Systems, Female, Female, *Geriatric Assessment, Geriatric Assessment, Humans, Humans, Magnetic Resonance Imaging, Magnetic Resonance Imaging/*methods, Male, Male, *Medical Informatics, Medical Informatics, Middle Aged, Middle Aged},
	pages = {235--245},
	annote = {Fennema-Notestine, {ChristineGamst}, Anthony {CQuinn}, Brian {TPacheco}, {JenniJernigan}, Terry {LThal}, {LeonBuckner}, {RandyKilliany}, {RonBlacker}, {DeborahDale}, Anders {MFischl}, {BruceDickerson}, {BradGollub}, Randy {LengM}01 {RR} 00827/{RR}/{NCRR} {NIH} {HHS}/P01 {AG} 03991/{AG}/{NIA} {NIH} {HHS}/P01 {AG} 04953/{AG}/{NIA} {NIH} {HHS}/P41 {RR} 13642/{RR}/{NCRR} {NIH} {HHS}/P41 {RR} 14075/{RR}/{NCRR} {NIH} {HHS}/P50 {AG} 05131/{AG}/{NIA} {NIH} {HHS}/P50 {AG} 05681/{AG}/{NIA} {NIH} {HHS}/R01 {AG} 06849/{AG}/{NIA} {NIH} {HHS}/R01 {AG} 12674/{AG}/{NIA} {NIH} {HHS}/R01 {EB} 002010/{EB}/{NIBIB} {NIH} {HHS}/R01 {NS} 052585-01/{NS}/{NINDS} {NIH} {HHS}/R01 {RR} 16594-01A1/{RR}/{NCRR} {NIH} {HHS}/U24 {RR} 021382/{RR}/{NCRR} {NIH} {HHS}/U54 {EB} 005149/{EB}/{NIBIB} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov'{tResearch} Support, U.S. Gov't, Non-P.H.S.2007/11/14 09:00Neuroinformatics. 2007 Winter;5(4):235-45. Epub 2007 Nov 13.}
}

@article{petkov_attentional_2004,
	title = {Attentional modulation of human auditory cortex},
	volume = {7},
	issn = {1097-6256},
	url = {http://audition.ens.fr/P2web/Maria/petkov.etal2004.pdf},
	doi = {10.1038/nn1256},
	abstract = {Attention powerfully influences auditory perception, but little is understood about the mechanisms whereby attention sharpens responses to unattended sounds. We used high-resolution surface mapping techniques (using functional magnetic resonance imaging, {fMRI}) to examine activity in human auditory cortex during an intermodal selective attention task. Stimulus-dependent activations ({SDAs}), evoked by unattended sounds during demanding visual tasks, were maximal over mesial auditory cortex. They were tuned to sound frequency and location, and showed rapid adaptation to repeated sounds. Attention-related modulations ({ARMs}) were isolated as response enhancements that occurred when subjects performed pitch-discrimination tasks. In contrast to {SDAs}, {ARMs} were localized to lateral auditory cortex, showed broad frequency and location tuning, and increased in amplitude with sound repetition. The results suggest a functional dichotomy of auditory cortical fields: stimulus-determined mesial fields that faithfully transmit acoustic information, and attentionally labile lateral fields that analyze acoustic features of behaviorally relevant sounds.},
	language = {eng},
	number = {6},
	journal = {Nature Neuroscience},
	author = {Petkov, Christopher I. and Kang, Xiaojian and Alho, Kimmo and Bertrand, Olivier and Yund, E. William and Woods, David L.},
	month = jun,
	year = {2004},
	pmid = {15156150},
	keywords = {Acoustic Stimulation, Adult, Analysis of Variance, Attention, Auditory Cortex, Female, Humans, Magnetic Resonance Imaging, Male, Photic Stimulation, Psychomotor Performance},
	pages = {658--663}
}

@article{destrieux_sulcal_2009,
	title = {A sulcal depth-based anatomical parcellation of the cerebral cortex},
	url = {https://surfer.nmr.mgh.harvard.edu/pub/articles/HBM09-Destrieux-Sulcal.pdf},
	journal = {Human Brain Mapping},
	author = {Destrieux, C. and Fischl, B. and Dale, A. M. and Halgren, E.},
	year = {2009},
	keywords = {fs\_Cortical-parcellation}
}

@article{dickerson_cortical_2009,
	title = {The cortical signature of Alzheimer's disease: regionally specific cortical thinning relates to symptom severity in very mild to mild {AD} dementia and is detectable in asymptomatic amyloid-positive individuals},
	volume = {19},
	issn = {1460-2199 (Electronic) 1047-3211 (Linking)},
	shorttitle = {The cortical signature of Alzheimer's disease: regionally specific cortical thinning relates to symptom severity in very mild to mild {AD} dementia and is detectable in asymptomatic amyloid-positive individuals},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/18632739},
	doi = {10.1093/cercor/bhn113},
	abstract = {Alzheimer's disease ({AD}) is associated with neurodegeneration in vulnerable limbic and heteromodal regions of the cerebral cortex, detectable in vivo using magnetic resonance imaging. It is not clear whether abnormalities of cortical anatomy in {AD} can be reliably measured across different subject samples, how closely they track symptoms, and whether they are detectable prior to symptoms. An exploratory map of cortical thinning in mild {AD} was used to define regions of interest that were applied in a hypothesis-driven fashion to other subject samples. Results demonstrate a reliably quantifiable in vivo signature of abnormal cortical anatomy in {AD}, which parallels known regional vulnerability to {AD} neuropathology. Thinning in vulnerable cortical regions relates to symptom severity even in the earliest stages of clinical symptoms. Furthermore, subtle thinning is present in asymptomatic older controls with brain amyloid binding as detected with amyloid imaging. The reliability and clinical validity of {AD}-related cortical thinning suggests potential utility as an imaging biomarker. This "disease signature" approach to cortical morphometry, in which disease effects are mapped across the cortical mantle and then used to define {ROIs} for hypothesis-driven analyses, may provide a powerful methodological framework for studies of neuropsychiatric diseases.},
	language = {eng},
	number = {3},
	journal = {Cereb Cortex},
	author = {Dickerson, B. C. and Bakkour, A. and Salat, D. H. and Feczko, E. and Pacheco, J. and Greve, D. N. and Grodstein, F. and Wright, C. I. and Blacker, D. and Rosas, H. D. and Sperling, R. A. and Atri, A. and Growdon, J. H. and Hyman, B. T. and Morris, J. C. and Fischl, B. and Buckner, R. L.},
	month = mar,
	year = {2009},
	keywords = {Aged, Aged, 80 and over, Alzheimer Disease/*diagnosis/metabolism/*pathology, Amyloid/*biosynthesis, Brain Mapping/methods, Cerebral Cortex/*pathology, Dementia/diagnosis/metabolism/pathology, Female, Humans, Male, Middle Aged, Plaque, Amyloid/pathology, Severity of Illness Index},
	pages = {497--510},
	annote = {Dickerson, Bradford {CBakkour}, {AkramSalat}, David {HFeczko}, {EricPacheco}, {JenniGreve}, Douglas {NGrodstein}, {FranWright}, Christopher {IBlacker}, {DeborahRosas}, H {DianaSperling}, Reisa {AAtri}, {AlirezaGrowdon}, John {HHyman}, Bradley {TMorris}, John {CFischl}, {BruceBuckner}, Randy {LengK}23-{AG}22509/{AG}/{NIA} {NIH} {HHS}/P01-{AG}03991/{AG}/{NIA} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/P50-{AG}05134/{AG}/{NIA} {NIH} {HHS}/P50-{AG}05681/{AG}/{NIA} {NIH} {HHS}/R01 {AG}021910-05/{AG}/{NIA} {NIH} {HHS}/R01 {AG}034556-01/{AG}/{NIA} {NIH} {HHS}/R01-{AG}29411/{AG}/{NIA} {NIH} {HHS}/R01-{NS}042861/{NS}/{NINDS} {NIH} {HHS}/R21-{AG}29840/{AG}/{NIA} {NIH} {HHS}/U24-{RR}021382/{RR}/{NCRR} {NIH} {HHS}/Howard Hughes Medical Institute/Comparative {StudyResearch} Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov'{tNew} York, N.Y. : 19912008/07/18 09:00Cereb Cortex. 2009 Mar;19(3):497-510. doi: 10.1093/cercor/bhn113. Epub 2008 Jul 16.},
	file = {Dickerson-2009-The cortical signature of Alzhe:/autofs/cluster/freesurfer/zotero/storage/4ZB3U4U7/Dickerson-2009-The cortical signature of Alzhe.pdf:application/pdf;PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/AHUF5WQA/Dickerson et al. - 2009 - The Cortical Signature of Alzheimer's Disease Reg.pdf:application/pdf}
}

@article{hadjikhani_mechanisms_2001,
	title = {Mechanisms of migraine aura revealed by functional {MRI} in human visual cortex},
	volume = {98},
	issn = {0027-8424 (Print) 0027-8424 (Linking)},
	shorttitle = {Mechanisms of migraine aura revealed by functional {MRI} in human visual cortex},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/11287655},
	doi = {10.1073/pnas.071582498},
	abstract = {Cortical spreading depression ({CSD}) has been suggested to underlie migraine visual aura. However, it has been challenging to test this hypothesis in human cerebral cortex. Using high-field functional {MRI} with near-continuous recording during visual aura in three subjects, we observed blood oxygenation level-dependent ({BOLD}) signal changes that demonstrated at least eight characteristics of {CSD}, time-locked to percept/onset of the aura. Initially, a focal increase in {BOLD} signal (possibly reflecting vasodilation), developed within extrastriate cortex (area V3A). This {BOLD} change progressed contiguously and slowly (3.5 +/- 1.1 mm/min) over occipital cortex, congruent with the retinotopy of the visual percept. Following the same retinotopic progression, the {BOLD} signal then diminished (possibly reflecting vasoconstriction after the initial vasodilation), as did the {BOLD} response to visual activation. During periods with no visual stimulation, but while the subject was experiencing scintillations, {BOLD} signal followed the retinotopic progression of the visual percept. These data strongly suggest that an electrophysiological event such as {CSD} generates the aura in human visual cortex.},
	number = {8},
	journal = {Proc Natl Acad Sci U S A},
	author = {Hadjikhani, N. and Sanchez Del Rio, M. and Wu, O. and Schwartz, D. and Bakker, D. and Fischl, B. and Kwong, K. K. and Cutrer, F. M. and Rosen, B. R. and Tootell, R. B. and Sorensen, A. G. and Moskowitz, M. A.},
	month = apr,
	year = {2001},
	keywords = {Adult, Humans, Magnetic Resonance Imaging, Male, Middle Aged, Migraine with Aura/*physiopathology, Vision Disorders/*physiopathology, Visual Cortex/*physiopathology},
	pages = {4687--92},
	annote = {Hadjikhani, {NSanchez} Del Rio, {MWu}, {OSchwartz}, {DBakker}, {DFischl}, {BKwong}, K {KCutrer}, F {MRosen}, B {RTootell}, R {BSorensen}, A {GMoskowitz}, M Aeng5 {PO}1 {NS} 35611/{NS}/{NINDS} {NIH} {HHS}/{EY} 07980/{EY}/{NEI} {NIH} {HHS}/K08-{NS}01803A/{NS}/{NINDS} {NIH} {HHS}/P41 {RR} 14075/{RR}/{NCRR} {NIH} {HHS}/Research Support, Non-U.S. Gov'{tResearch} Support, U.S. Gov't, P.H.S.2001/04/05 10:00Proc Natl Acad Sci U S A. 2001 Apr 10;98(8):4687-92. Epub 2001 Apr 3.},
	file = {Hadjikhani-2001-Mechanisms of migraine aura re:/autofs/cluster/freesurfer/zotero/storage/SGH9HXPB/Hadjikhani-2001-Mechanisms of migraine aura re.pdf:application/pdf}
}

@inproceedings{van_der_kouwe_automatic_2007,
	title = {Automatic prospective spectroscopy {VOI} placement based on brain segmentation},
	shorttitle = {Automatic prospective spectroscopy {VOI} placement based on brain segmentation},
	author = {Van der Kouwe, Balasubramanian, M., Busa, E.A., Fischl, B., A.J.},
	year = {2007},
	pages = {3885}
}

@article{walhovd_consistent_2011,
	title = {Consistent neuroanatomical age-related volume differences across multiple samples},
	volume = {32},
	issn = {1558-1497 (Electronic) 0197-4580 (Linking)},
	shorttitle = {Consistent neuroanatomical age-related volume differences across multiple samples},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/19570593},
	doi = {10.1016/j.neurobiolaging.2009.05.013},
	abstract = {Magnetic resonance imaging ({MRI}) is the principal method for studying structural age-related brain changes in vivo. However, previous research has yielded inconsistent results, precluding understanding of structural changes of the aging brain. This inconsistency is due to methodological differences and/or different aging patterns across samples. To overcome these problems, we tested age effects on 17 different neuroanatomical structures and total brain volume across five samples, of which one was split to further investigate consistency (883 participants). Widespread age-related volume differences were seen consistently across samples. In four of the five samples, all structures, except the brainstem, showed age-related volume differences. The strongest and most consistent effects were found for cerebral cortex, pallidum, putamen and accumbens volume. Total brain volume, cerebral white matter, caudate, hippocampus and the ventricles consistently showed non-linear age functions. Healthy aging appears associated with more widespread and consistent age-related neuroanatomical volume differences than previously believed.},
	language = {Eng},
	number = {5},
	journal = {Neurobiol Aging},
	author = {Walhovd, K. B. and Westlye, L. T. and Amlien, I. and Espeseth, T. and Reinvang, I. and Raz, N. and Agartz, I. and Salat, D. H. and Greve, D. N. and Fischl, B. and Dale, A. M. and Fjell, A. M.},
	month = may,
	year = {2011},
	keywords = {Adult, Aged, Aged, 80 and over, Age Factors, Aging/*pathology, Brain/*pathology, Female, Humans, Magnetic Resonance Imaging, Male, Middle Aged, Organ Size, Young Adult},
	pages = {916--32},
	annote = {Walhovd, Kristine {BWestlye}, Lars {TAmlien}, {IngeEspeseth}, {ThomasReinvang}, {IvarRaz}, {NaftaliAgartz}, {IngridSalat}, David {HGreve}, Doug {NFischl}, {BruceDale}, Anders {MFjell}, Anders {MengP}41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 {AG}011230-10/{AG}/{NIA} {NIH} {HHS}/R01-{AG}11230/{AG}/{NIA} {NIH} {HHS}/R01-{NS}39581/{NS}/{NINDS} {NIH} {HHS}/R01-{RR}13609/{RR}/{NCRR} {NIH} {HHS}/R01-{RR}16594/{RR}/{NCRR} {NIH} {HHS}/R37 {AG}011230/{AG}/{NIA} {NIH} {HHS}/R37 {AG}011230-17/{AG}/{NIA} {NIH} {HHS}/R37 {AG}011230-18/{AG}/{NIA} {NIH} {HHS}/Comparative {StudyResearch} Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov't2009/07/03 09:00Neurobiol Aging. 2011 May;32(5):916-32. doi: 10.1016/j.neurobiolaging.2009.05.013. Epub 2009 Jun 30.},
	file = {Walhovd-2011-Consistent neuroanatomical age-re:/autofs/cluster/freesurfer/zotero/storage/PGNCG36F/Walhovd-2011-Consistent neuroanatomical age-re.pdf:application/pdf}
}

@article{augustinack_predicting_2013,
	title = {Predicting the location of human perirhinal cortex, Brodmann's area 35, from {MRI}},
	volume = {64},
	issn = {1095-9572 (Electronic) 1053-8119 (Linking)},
	shorttitle = {Predicting the location of human perirhinal cortex, Brodmann's area 35, from {MRI}},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/22960087},
	doi = {10.1016/j.neuroimage.2012.08.071},
	abstract = {The perirhinal cortex (Brodmann's area 35) is a multimodal area that is important for normal memory function. Specifically, perirhinal cortex is involved in the detection of novel objects and manifests neurofibrillary tangles in Alzheimer's disease very early in disease progression. We scanned ex vivo brain hemispheres at standard resolution (1 mm x 1 mm x 1 mm) to construct pial/white matter surfaces in {FreeSurfer} and scanned again at high resolution (120 mum x 120 mum x 120 mum) to determine cortical architectural boundaries. After labeling perirhinal area 35 in the high resolution images, we mapped the high resolution labels to the surface models to localize area 35 in fourteen cases. We validated the area boundaries determined using histological Nissl staining. To test the accuracy of the probabilistic mapping, we measured the Hausdorff distance between the predicted and true labels and found that the median Hausdorff distance was 4.0mm for the left hemispheres (n=7) and 3.2mm for the right hemispheres (n=7) across subjects. To show the utility of perirhinal localization, we mapped our labels to a subset of the Alzheimer's Disease Neuroimaging Initiative dataset and found decreased cortical thickness measures in mild cognitive impairment and Alzheimer's disease compared to controls in the predicted perirhinal area 35. Our ex vivo probabilistic mapping of the perirhinal cortex provides histologically validated, automated and accurate labeling of architectonic regions in the medial temporal lobe, and facilitates the analysis of atrophic changes in a large dataset for earlier detection and diagnosis.},
	journal = {Neuroimage},
	author = {Augustinack, J. C. and Huber, K. E. and Stevens, A. A. and Roy, M. and Frosch, M. P. and van der Kouwe, A. J. and Wald, L. L. and Van Leemput, K. and McKee, A. C. and Fischl, B. and Alzheimer's Disease Neuroimaging, Initiative},
	month = jan,
	year = {2013},
	keywords = {Aged, *Algorithms, Artificial Intelligence, Cadaver, Female, Humans, Image Enhancement/methods, Image Interpretation, Computer-Assisted/*methods, Magnetic Resonance Imaging/*methods, Male, Nerve Net/*anatomy \& histology, Pattern Recognition, Automated/*methods, Reproducibility of Results, Sensitivity and Specificity, Temporal Lobe/*anatomy \& histology},
	pages = {32--42},
	annote = {Augustinack, Jean {CHuber}, Kristen {EStevens}, Allison {ARoy}, {MichelleFrosch}, Matthew Pvan der Kouwe, Andre J {WWald}, Lawrence {LVan} Leemput, {KoenMcKee}, Ann {CFischl}, Bruceeng1R01NS070963/{NS}/{NINDS} {NIH} {HHS}/1R21NS072652-01/{NS}/{NINDS} {NIH} {HHS}/1S10RR019307/{RR}/{NCRR} {NIH} {HHS}/1S10RR023043/{RR}/{NCRR} {NIH} {HHS}/1S10RR023401/{RR}/{NCRR} {NIH} {HHS}/5P50AG005134-28/{AG}/{NIA} {NIH} {HHS}/{AG}022381/{AG}/{NIA} {NIH} {HHS}/{AG}028521/{AG}/{NIA} {NIH} {HHS}/K01 {AG}028521/{AG}/{NIA} {NIH} {HHS}/K01 {AG}030514/{AG}/{NIA} {NIH} {HHS}/P30 {AG}010129/{AG}/{NIA} {NIH} {HHS}/P30-{AG}13846/{AG}/{NIA} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 {AG}1649/{AG}/{NIA} {NIH} {HHS}/R01 {EB}006758/{EB}/{NIBIB} {NIH} {HHS}/R01 {EB}013565/{EB}/{NIBIB} {NIH} {HHS}/R01 {NS}052585-01/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}070963/{NS}/{NINDS} {NIH} {HHS}/R01EB006758/{EB}/{NIBIB} {NIH} {HHS}/{RC}1AT005728-01/{AT}/{NCCAM} {NIH} {HHS}/U01 {AG}024904/{AG}/{NIA} {NIH} {HHS}/U01-{MH}093765/{MH}/{NIMH} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov't2012/09/11 06:00Neuroimage. 2013 Jan 1;64:32-42. doi: 10.1016/j.neuroimage.2012.08.071. Epub 2012 Aug 30.},
	file = {Augustinack-2013-Predicting the location of hu:/autofs/cluster/freesurfer/zotero/storage/8BUFSBQ4/Augustinack-2013-Predicting the location of hu.pdf:application/pdf;PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/CCZXJN5N/Augustinack et al. - 2013 - Predicting the Location of Human Perirhinal Cortex.pdf:application/pdf}
}

@inproceedings{becker_amyloid_2008,
	title = {Amyloid deposition related to cortical thinning},
	shorttitle = {Amyloid deposition related to cortical thinning},
	author = {Becker, Fischl, Greve, DeLuca, LaViolette, O'Keefe, Fischman, Rentz, Sperling, Johnson, Carmasin},
	year = {2008}
}

@article{makris_human_2003,
	title = {Human cerebellum: surface-assisted cortical parcellation and volumetry with magnetic resonance imaging},
	volume = {15},
	issn = {0898-929X (Print) 0898-929X (Linking)},
	shorttitle = {Human cerebellum: surface-assisted cortical parcellation and volumetry with magnetic resonance imaging},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/12803969},
	doi = {10.1162/089892903321662967},
	abstract = {We describe a system of surface-assisted parcellation ({SAP}) of the human cerebellar cortex derived from neural systems functional and behavioral anatomy. This system is based on {MRI} and preserves the unique morphologic and topographic features of the individual cerebellum. All major fissures of the cerebellum were identified and traced in the flattened representation of the cerebellar cortex using the program "{FreeSurfer}." Parcellation of the cerebellar cortex followed using the fissure information in conjunction with landmarks using the program "Cardviews" to create 64 gyral-based cerebellar parcellation units. Computer-assisted algorithms enable the execution of the cerebellar parcellation procedure as well as volumetric measurements and topographic localization. The {SAP} technique makes it possible to represent multimodal structural and functional imaging data on the flattened surface of the cerebellar cortex as illustrated in one functional {MRI} experiment.},
	number = {4},
	journal = {J Cogn Neurosci},
	author = {Makris, N. and Hodge, S. M. and Haselgrove, C. and Kennedy, D. N. and Dale, A. and Fischl, B. and Rosen, B. R. and Harris, G. and Caviness, Jr., V. S. and Schmahmann, J. D.},
	month = may,
	year = {2003},
	keywords = {Adult, Brain Mapping/*methods, Cerebellar Cortex/*anatomy \& histology/physiology, Cerebellum/anatomy \& histology/physiology, Humans, Magnetic Resonance Imaging/*methods, Male},
	pages = {584--99},
	annote = {Makris, {NikosHodge}, Steven {MHaselgrove}, {ChristianKennedy}, David {NDale}, {AndersFischl}, {BruceRosen}, Bruce {RHarris}, {GordonCaviness}, Verne S {JrSchmahmann}, Jeremy {DengNS}34189/{NS}/{NINDS} {NIH} {HHS}/{NS}39581/{NS}/{NINDS} {NIH} {HHS}/P01 03610/{PHS} {HHS}/{RR}16594-01A1/{RR}/{NCRR} {NIH} {HHS}/Research Support, Non-U.S. Gov'{tResearch} Support, U.S. Gov't, P.H.S.2003/06/14 05:00J Cogn Neurosci. 2003 May 15;15(4):584-99.}
}

@article{yu_cortical_2007-1,
	title = {Cortical surface shape analysis based on spherical wavelets},
	volume = {26},
	issn = {0278-0062},
	url = {https://surfer.nmr.mgh.harvard.edu/ftp/articles/yu_tmi_0704.pdf},
	doi = {10.1109/TMI.2007.892499},
	abstract = {In vivo quantification of neuroanatomical shape variations is possible due to recent advances in medical imaging and has proven useful in the study of neuropathology and neurodevelopment. In this paper, we apply a spherical wavelet transformation to extract shape features of cortical surfaces reconstructed from magnetic resonance images ({MRIs}) of a set of subjects. The spherical wavelet transformation can characterize the underlying functions in a local fashion in both space and frequency, in contrast to spherical harmonics that have a global basis set. We perform principal component analysis ({PCA}) on these wavelet shape features to study patterns of shape variation within normal population from coarse to fine resolution. In addition, we study the development of cortical folding in newborns using the Gompertz model in the wavelet domain, which allows us to characterize the order of development of large-scale and finer folding patterns independently. Given a limited amount of training data, we use a regularization framework to estimate the parameters of the Gompertz model to improve the prediction performance on new data. We develop an efficient method to estimate this regularized Gompertz model based on the Broyden-Fletcher-Goldfarb-Shannon ({BFGS}) approximation. Promising results are presented using both {PCA} and the folding development model in the wavelet domain. The cortical folding development model provides quantitative anatomic information regarding macroscopic cortical folding development and may be of potential use as a biomarker for early diagnosis of neurologic deficits in newborns.},
	language = {eng},
	number = {4},
	journal = {{IEEE} transactions on medical imaging},
	author = {Yu, Peng and Grant, P. Ellen and Qi, Yuan and Han, Xiao and Ségonne, Florent and Pienaar, Rudolph and Busa, Evelina and Pacheco, Jenni and Makris, Nikos and Buckner, Randy L. and Golland, Polina and Fischl, Bruce},
	month = apr,
	year = {2007},
	pmid = {17427744},
	keywords = {Algorithms, Algorithms, *Artificial Intelligence, Artificial Intelligence, Cerebral Cortex, Cerebral Cortex/*anatomy \& histology, Humans, Humans, Image Enhancement, Image Enhancement/*methods, Image Interpretation, Computer-Assisted, Image Interpretation, Computer-Assisted/*methods, Imaging, Three-Dimensional, Imaging, Three-Dimensional/*methods, Magnetic Resonance Imaging, Magnetic Resonance Imaging/*methods, Numerical Analysis, Computer-Assisted, Numerical Analysis, Computer-Assisted, Pattern Recognition, Automated, Pattern Recognition, Automated/*methods, Reproducibility of Results, Reproducibility of Results, Sensitivity and Specificity, Sensitivity and Specificity},
	pages = {582--597},
	annote = {Yu, {PengGrant}, P {EllenQi}, {YuanHan}, {XiaoSegonne}, {FlorentPienaar}, {RudolphBusa}, {EvelinaPacheco}, {JenniMakris}, {NikosBuckner}, Randy {LGolland}, {PolinaFischl}, {BruceengBIRN}002/{PHS} {HHS}/K23 {NS}42758/{NS}/{NINDS} {NIH} {HHS}/P01 {AG}03991/{AG}/{NIA} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/P50 {AG}05681/{AG}/{NIA} {NIH} {HHS}/R01 {EB}001550/{EB}/{NIBIB} {NIH} {HHS}/R01 {RR}16594-01A1/{RR}/{NCRR} {NIH} {HHS}/R01-{NS}051826/{NS}/{NINDS} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/U54 {EB}005149/{EB}/{NIBIB} {NIH} {HHS}/Evaluation {StudiesResearch} Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov't2007/04/13 09:00IEEE Trans Med Imaging. 2007 Apr;26(4):582-97.}
}

@article{hagler_smoothing_2006,
	title = {Smoothing and cluster thresholding for cortical surface-based group analysis of {fMRI} data},
	volume = {33},
	issn = {1053-8119 (Print) 1053-8119 (Linking)},
	shorttitle = {Smoothing and cluster thresholding for cortical surface-based group analysis of {fMRI} data},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/17011792},
	doi = {10.1016/j.neuroimage.2006.07.036},
	abstract = {Cortical surface-based analysis of {fMRI} data has proven to be a useful method with several advantages over 3-dimensional volumetric analyses. Many of the statistical methods used in 3D analyses can be adapted for use with surface-based analyses. Operating within the framework of the {FreeSurfer} software package, we have implemented a surface-based version of the cluster size exclusion method used for multiple comparisons correction. Furthermore, we have a developed a new method for generating regions of interest on the cortical surface using a sliding threshold of cluster exclusion followed by cluster growth. Cluster size limits for multiple probability thresholds were estimated using random field theory and validated with Monte Carlo simulation. A prerequisite of {RFT} or cluster size simulation is an estimate of the smoothness of the data. In order to estimate the intrinsic smoothness of group analysis statistics, independent of true activations, we conducted a group analysis of simulated noise data sets. Because smoothing on a cortical surface mesh is typically implemented using an iterative method, rather than directly applying a Gaussian blurring kernel, it is also necessary to determine the width of the equivalent Gaussian blurring kernel as a function of smoothing steps. Iterative smoothing has previously been modeled as continuous heat diffusion, providing a theoretical basis for predicting the equivalent kernel width, but the predictions of the model were not empirically tested. We generated an empirical heat diffusion kernel width function by performing surface-based smoothing simulations and found a large disparity between the expected and actual kernel widths.},
	language = {en},
	number = {4},
	urldate = {2014-08-21},
	journal = {Neuroimage},
	author = {Hagler, Jr., D. J. and Saygin, A. P. and Sereno, M. I.},
	month = dec,
	year = {2006},
	keywords = {Cerebral Cortex/*physiology, Humans, *Imaging, Three-Dimensional, Magnetic Resonance Imaging/*methods/statistics \& numerical data},
	pages = {1093--103},
	annote = {Hagler, Donald J {JrSaygin}, Ayse {PinarSereno}, Martin Ieng5F32MH066578-02/{MH}/{NIMH} {NIH} {HHS}/F32 {MH}066578/{MH}/{NIMH} {NIH} {HHS}/F32 {MH}066578-01A1/{MH}/{NIMH} {NIH} {HHS}/F32 {MH}066578-02/{MH}/{NIMH} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, U.S. Gov't, Non-P.H.S.2006/10/03 09:00Neuroimage. 2006 Dec;33(4):1093-103. Epub 2006 Oct 2.},
	file = {Hagler-2006-Smoothing and cluster thresholdin1:/autofs/cluster/freesurfer/zotero/storage/S4W3R494/Hagler-2006-Smoothing and cluster thresholdin1.pdf:application/pdf;PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/XUPQ9X2A/Hagler et al. - 2006 - Smoothing and cluster thresholding for cortical su.pdf:application/pdf}
}

@article{oliveira_jr_cortical_2010,
	title = {Cortical Thickness Reduction of Normal Appearing Cortex in Patients with Polymicrogyria},
	volume = {20},
	issn = {10512284, 15526569},
	url = {http://onlinelibrary.wiley.com/enhanced/doi/10.1111/j.1552-6569.2009.00372.x/},
	doi = {10.1111/j.1552-6569.2009.00372.x},
	language = {en},
	number = {1},
	urldate = {2014-08-23},
	journal = {Journal of Neuroimaging},
	author = {Oliveira Jr, Pedro Paulo de Magalhães and Valente, Kette Dualibi and Shergill, Sukhwinder S. and Leite, Claudia da Costa and Amaro Jr, Edson},
	month = jan,
	year = {2010},
	pages = {46--52},
	file = {Cortical Thickness Reduction of Normal Appearing Cortex in Patients with Polymicrogyria - Oliveira Jr - 2009 - Journal of Neuroimaging - Wiley Online Library:/autofs/cluster/freesurfer/zotero/storage/2Z8WDQUQ/j.1552-6569.2009.00372.html:text/html}
}

@article{mcdonald_regional_2008,
	title = {Regional neocortical thinning in mesial temporal lobe epilepsy},
	volume = {49},
	issn = {0013-9580},
	doi = {10.1111/j.1528-1167.2008.01539.x},
	abstract = {{PURPOSE}: To determine the nature and extent of regional cortical thinning in patients with mesial temporal lobe epilepsy ({MTLE}).
{METHODS}: High-resolution volumetric {MRIs} were obtained on 21 patients with {MTLE} and 21 controls. Mean cortical thickness was measured within regions of interest and point-by-point across the neocortex using cortical reconstruction and parcellation software.
{RESULTS}: Bilateral thinning was observed within frontal and lateral temporal regions in {MTLE} patients relative to controls. The most striking finding was bilateral cortical thinning in the precentral gyrus and immediately adjacent paracentral region and pars opercularis of the inferior frontal gyrus, extending to the orbital region. Within the temporal lobe, bilateral thinning was observed in Heschl's gyrus only. Ipsilateral only thinning was observed in the superior and middle temporal gyri, as well as in the medial orbital cortex. Greater asymmetries in cortical thickness were observed in medial temporal cortex in patients relative to controls. Individual subject analyses revealed that this asymmetry reflected significant ipsilateral thinning of medial temporal cortex in 33\% of patients, whereas it reflected ipsilateral thickening in 20\% of {MTLEs}.
{DISCUSSION}: Patients with {MTLE} show widespread, bilateral pathology in neocortical regions that is not appreciated on standard imaging. Future studies are needed that elucidate the clinical implications of neocortical thinning in {MTLE}.},
	language = {eng},
	number = {5},
	journal = {Epilepsia},
	author = {McDonald, Carrie R. and Hagler, Donald J. and Ahmadi, Mazyar E. and Tecoma, Evelyn and Iragui, Vicente and Gharapetian, Lusineh and Dale, Anders M. and Halgren, Eric},
	month = may,
	year = {2008},
	pmid = {18266751},
	keywords = {Adult, Atrophy, Brain Mapping, Epilepsy, Temporal Lobe, Female, Frontal Lobe, Functional Laterality, Hippocampus, Humans, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Male, Middle Aged, Neocortex, Preoperative Care, Sclerosis, Temporal Lobe},
	pages = {794--803},
	file = {Regional neocortical thinning in mesial temporal lobe epilepsy - McDonald - 2008 - Epilepsia - Wiley Online Library:/autofs/cluster/freesurfer/zotero/storage/8ZXDI4K7/j.1528-1167.2008.01539.html:text/html}
}

@article{bernal-rusiel_statistical_2012,
	title = {Statistical analysis of longitudinal neuroimage data with Linear Mixed Effects models},
	volume = {66C},
	issn = {1095-9572 (Electronic) 1053-8119 (Linking)},
	shorttitle = {Statistical analysis of longitudinal neuroimage data with Linear Mixed Effects models},
	url = {https://surfer.nmr.mgh.harvard.edu/ftp/articles/Long-LME_2012.pdf},
	doi = {10.1016/j.neuroimage.2012.10.065},
	abstract = {Longitudinal neuroimaging ({LNI}) studies are rapidly becoming more prevalent and growing in size. Today, no standardized computational tools exist for the analysis of {LNI} data and widely used methods are sub-optimal for the types of data encountered in real-life studies. Linear Mixed Effects ({LME}) modeling, a mature approach well known in the statistics community, offers a powerful and versatile framework for analyzing real-life {LNI} data. This article presents the theory behind {LME} models, contrasts it with other popular approaches in the context of {LNI}, and is accompanied with an array of computational tools that will be made freely available through {FreeSurfer} - a popular Magnetic Resonance Image ({MRI}) analysis software package. Our core contribution is to provide a quantitative empirical evaluation of the performance of {LME} and competing alternatives popularly used in prior longitudinal structural {MRI} studies, namely repeated measures {ANOVA} and the analysis of annualized longitudinal change measures (e.g. atrophy rate). In our experiments, we analyzed {MRI}-derived longitudinal hippocampal volume and entorhinal cortex thickness measurements from a public dataset consisting of Alzheimer's patients, subjects with mild cognitive impairment and healthy controls. Our results suggest that the {LME} approach offers superior statistical power in detecting longitudinal group differences.},
	language = {en},
	urldate = {2014-08-21},
	journal = {Neuroimage},
	author = {Bernal-Rusiel, J. L. and Greve, D. N. and Reuter, M. and Fischl, B. and Sabuncu, M. R. and for the Alzheimer's Disease Neuroimaging, Initiative},
	month = oct,
	year = {2012},
	keywords = {fs\_Longitudinal-processing, longitudinal processing},
	pages = {249--260},
	annote = {Bernal-Rusiel, Jorge {LGreve}, Douglas {NReuter}, {MartinFischl}, {BruceSabuncu}, Mert {RENGK}25 {EB}013649/{EB}/{NIBIB} {NIH} {HHS}/P41 {EB}015896/{EB}/{NIBIB} {NIH} {HHS}/2012/11/06 06:00Neuroimage. 2012 Oct 30;66C:249-260. doi: 10.1016/j.neuroimage.2012.10.065.},
	file = {Bernal-Rusiel-2012-Statistical analysis of lon:/autofs/cluster/freesurfer/zotero/storage/JGEKFJGW/Bernal-Rusiel-2012-Statistical analysis of lon.pdf:application/pdf}
}

@article{hadjikhani_anatomical_2006,
	title = {Anatomical differences in the mirror neuron system and social cognition network in autism},
	volume = {16},
	issn = {1047-3211},
	doi = {10.1093/cercor/bhj069},
	abstract = {Autism spectrum disorder ({ASD}) is a neurodevelopmental disorder associated with impaired social and emotional skills, the anatomical substrate of which is still unknown. In this study, we compared a group of 14 high-functioning {ASD} adults with a group of controls matched for sex, age, intelligence quotient, and handedness. We used an automated technique of analysis that accurately measures the thickness of the cerebral cortex and generates cross-subject statistics in a coordinate system based on cortical anatomy. We found local decreases of gray matter in the {ASD} group in areas belonging to the mirror neuron system ({MNS}), argued to be the basis of empathic behavior. Cortical thinning of the {MNS} was correlated with {ASD} symptom severity. Cortical thinning was also observed in areas involved in emotion recognition and social cognition. These findings suggest that the social and emotional deficits characteristic of autism may reflect abnormal thinning of the {MNS} and the broader network of cortical areas subserving social cognition.},
	language = {eng},
	number = {9},
	journal = {Cerebral Cortex (New York, N.Y.: 1991)},
	author = {Hadjikhani, Nouchine and Joseph, Robert M. and Snyder, Josh and Tager-Flusberg, Helen},
	month = sep,
	year = {2006},
	pmid = {16306324},
	keywords = {Adult, Autistic Disorder, Cerebral Cortex, Cognition, Empathy, Humans, Interpersonal Relations, Male, Nerve Net, Neural Pathways, Neurons, Social Perception},
	pages = {1276--1282}
}

@article{hinds_intrinsic_2008,
	title = {The intrinsic shape of human and macaque primary visual cortex},
	volume = {18},
	issn = {1460-2199 (Electronic) 1047-3211 (Linking)},
	shorttitle = {The intrinsic shape of human and macaque primary visual cortex},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/18308709},
	doi = {10.1093/cercor/bhn016},
	abstract = {Previous studies have reported considerable variability in primary visual cortex (V1) shape in both humans and macaques. Here, we demonstrate that much of this variability is due to the pattern of cortical folds particular to an individual and that V1 shape is similar among individual humans and macaques as well as between these 2 species. Human V1 was imaged ex vivo using high-resolution (200 microm) magnetic resonance imaging at 7 T. Macaque V1 was identified in published histological serial section data. Manual tracings of the stria of Gennari were used to construct a V1 surface, which was computationally flattened with minimal metric distortion of the cortical surface. Accurate flattening allowed investigation of intrinsic geometric features of cortex, which are largely independent of the highly variable cortical folds. The intrinsic shape of V1 was found to be similar across human subjects using both nonparametric boundary matching and a simple elliptical shape model fit to the data and is very close to that of the macaque monkey. This result agrees with predictions derived from current models of V1 topography. In addition, V1 shape similarity suggests that similar developmental mechanisms are responsible for establishing V1 shape in these 2 species.},
	number = {11},
	journal = {Cereb Cortex},
	author = {Hinds, O. and Polimeni, J. R. and Rajendran, N. and Balasubramanian, M. and Wald, L. L. and Augustinack, J. C. and Wiggins, G. and Rosas, H. D. and Fischl, B. and Schwartz, E. L.},
	month = nov,
	year = {2008},
	keywords = {Animals, Brain Diseases/pathology, Humans, *Imaging, Three-Dimensional, Macaca, *Magnetic Resonance Imaging, Models, Neurological, Probability, Species Specificity, Visual Cortex/*anatomy \& histology},
	pages = {2586--95},
	annote = {Hinds, {OliverPolimeni}, Jonathan {RRajendran}, {NiranjiniBalasubramanian}, {MukundWald}, Lawrence {LAugustinack}, Jean {CWiggins}, {GrahamRosas}, H {DianaFischl}, {BruceSchwartz}, Eric {LengP}41 {RR}14075/{RR}/{NCRR} {NIH} {HHS}/P50 {AG}05134/{AG}/{NIA} {NIH} {HHS}/R01 {EB}001550/{EB}/{NIBIB} {NIH} {HHS}/R01 {NS}052585/{NS}/{NINDS} {NIH} {HHS}/R01 {RR}16594/{RR}/{NCRR} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/U54 {EB}005149/{EB}/{NIBIB} {NIH} {HHS}/Comparative {StudyResearch} Support, N.I.H., {ExtramuralNew} York, N.Y. : 19912008/03/01 09:00Cereb Cortex. 2008 Nov;18(11):2586-95. doi: 10.1093/cercor/bhn016. Epub 2008 Feb 27.},
	file = {Hinds-2008-The intrinsic shape of human and ma:/autofs/cluster/freesurfer/zotero/storage/HRDAF3TM/Hinds-2008-The intrinsic shape of human and ma.pdf:application/pdf}
}

@article{golland_discriminative_2002,
	title = {Discriminative Analysis for Image-Based Studies},
	volume = {1},
	shorttitle = {Discriminative Analysis for Image-Based Studies},
	url = {http://www.nmr.mgh.harvard.edu/~fischl/reprints/Golland_MICCAI2002.pdf},
	journal = {{MICCAI}},
	author = {Golland, P and Fischl, B. and Spiridon, M. and Kanwisher, N and Buckner, R. L. and Shenton, M. E. and Kikinis, R. and Dale, A. M. and Grimson, W. E. L.},
	year = {2002},
	keywords = {fs\_Misc-methodology},
	pages = {508--515}
}

@article{rosas_tale_2011,
	title = {A tale of two factors: what determines the rate of progression in Huntington's disease? A longitudinal {MRI} study},
	volume = {26},
	issn = {1531-8257 (Electronic) 0885-3185 (Linking)},
	shorttitle = {A tale of two factors: what determines the rate of progression in Huntington's disease? A longitudinal {MRI} study},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/21611979},
	doi = {10.1002/mds.23762},
	abstract = {Over the past several years, increased attention has been devoted to understanding regionally selective brain changes that occur in Huntington's disease and their relationships to phenotypic variability. Clinical progression is also heterogeneous, and although {CAG} repeat length influences age of onset, its role, if any, in progression has been less clear. We evaluated progression in Huntington's disease using a novel longitudinal magnetic resonance imaging analysis. Our hypothesis was that the rate of brain atrophy is influenced by the age of onset of Huntington's disease. We scanned 22 patients with Huntington's disease at approximately 1-year intervals; individuals were divided into 1 of 3 groups, determined by the relative age of onset. We found significant differences in the rates of atrophy of cortex, white matter, and subcortical structures; patients who developed symptoms earlier demonstrated the most rapid rates of atrophy compared with those who developed symptoms during middle age or more advanced age. Rates of cortical atrophy were topologically variable, with the most rapid changes occurring in sensorimotor, posterior frontal, and portions of the parietal cortex. There were no significant differences in the rates of atrophy in basal ganglia structures. Although both {CAG} repeat length and age influenced the rate of change in some regions, there was no significant correlation in many regions. Rates of regional brain atrophy seem to be influenced by the age of onset of Huntington's disease symptoms and are only partially explained by {CAG} repeat length. These findings suggest that other genetic, epigenetic, and environmental factors play important roles in neurodegeneration in Huntington's disease.},
	number = {9},
	journal = {Mov Disord},
	author = {Rosas, H. D. and Reuter, M. and Doros, G. and Lee, S. Y. and Triggs, T. and Malarick, K. and Fischl, B. and Salat, D. H. and Hersch, S. M.},
	month = aug,
	year = {2011},
	keywords = {Age of Onset, Atrophy/pathology, Cerebral Cortex/*pathology, Disease Progression, Female, Humans, Huntington Disease/genetics/*pathology/*physiopathology, Longitudinal Studies, *Magnetic Resonance Imaging, Male, Trinucleotide Repeats/genetics},
	pages = {1691--7},
	annote = {Rosas, H {DianaReuter}, {MartinDoros}, {GheorgheLee}, Stephanie {YTriggs}, {TylerMalarick}, {KeithFischl}, {BruceSalat}, David {HHersch}, Steven {MengAG}022381/{AG}/{NIA} {NIH} {HHS}/{NR}010827/{NR}/{NINR} {NIH} {HHS}/{NS}052585/{NS}/{NINDS} {NIH} {HHS}/{NS}05792/{NS}/{NINDS} {NIH} {HHS}/{NS}058793/{NS}/{NINDS} {NIH} {HHS}/P01 {NS}058793-01A1/{NS}/{NINDS} {NIH} {HHS}/P41 {RR}014075/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-01A1/{RR}/{NCRR} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 {EB}006758-01A1/{EB}/{NIBIB} {NIH} {HHS}/R01 {NR}010827-01A1/{NR}/{NINR} {NIH} {HHS}/R01 {NS}042861/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}042861-01A2/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}052585-01A1/{NS}/{NINDS} {NIH} {HHS}/R01EB006758/{EB}/{NIBIB} {NIH} {HHS}/R21 {NS}072652-01/{NS}/{NINDS} {NIH} {HHS}/R21NS072652/{NS}/{NINDS} {NIH} {HHS}/{RR}021382/{RR}/{NCRR} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/U24 {RR}021382-01/{RR}/{NCRR} {NIH} {HHS}/U24-01/{PHS} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov't2011/05/26 06:00Mov Disord. 2011 Aug 1;26(9):1691-7. doi: 10.1002/mds.23762. Epub 2011 May 24.},
	file = {Rosas-2011-A tale of two factors_ what determi:/autofs/cluster/freesurfer/zotero/storage/EAJSFX5N/Rosas-2011-A tale of two factors_ what determi.pdf:application/pdf}
}

@article{fennema-notestine_presence_2011,
	title = {Presence of {ApoE} epsilon4 allele associated with thinner frontal cortex in middle age},
	volume = {26 Suppl 3},
	issn = {1875-8908 (Electronic) 1387-2877 (Linking)},
	shorttitle = {Presence of {ApoE} epsilon4 allele associated with thinner frontal cortex in middle age},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/21971450},
	doi = {10.3233/JAD-2011-0002},
	abstract = {The presence of an {ApoE} epsilon4 allele (epsilon4+) increases the risk of developing Alzheimer's disease ({AD}). Previous studies support an adverse relationship between epsilon4+ status and brain structure and function in mild cognitive impairment and {AD}; in contrast, the presence of an epsilon2 allele may be protective. Whether these findings reflect disease-related effects or pre-existing endophenotypes, however, remains unclear. The present study examined the influence of {ApoE} allele status on brain structure solely during middle-age in a large, national sample. Participants were 482 men, ages 51-59, from the Vietnam Era Twin Study of Aging ({VETSA}). T1-weighted images were used in volumetric segmentation and cortical surface reconstruction methods to measure regional volume and thickness. Primary linear mixed effects models predicted structural measures with {ApoE} status (epsilon3/3, epsilon2/3, epsilon3/4) and control variables for effects of site, non-independence of twin data, age, and average cranial vault or cortical thickness. Relative to the epsilon3/3 group, the epsilon3/4 group demonstrated significantly thinner cortex in superior frontal and left rostral and right caudal midfrontal regions; there were no significant effects of epsilon4 status on any temporal lobe measures. The epsilon2/3 group demonstrated significantly thicker right parahippocampal cortex relative to the epsilon3/3 group. The {ApoE} epsilon4 allele may influence cortical thickness in frontal areas, which are later developing regions thought to be more susceptible to the natural aging process. Previous conflicting findings for mesial temporal regions may be driven by the inclusion of older individuals, who may evidence preclinical manifestations of disease, and by unexamined moderators of epsilon4-related effects. The presence of the epsilon2 allele was related to thicker cortex, supporting a protective role. Ongoing follow-up of the {VETSA} sample may shed light on the potential for age- and disease-related mediation of the influence of {ApoE} allele status.},
	journal = {J Alzheimers Dis},
	author = {Fennema-Notestine, C. and Panizzon, M. S. and Thompson, W. R. and Chen, C. H. and Eyler, L. T. and Fischl, B. and Franz, C. E. and Grant, M. D. and Jak, A. J. and Jernigan, T. L. and Lyons, M. J. and Neale, M. C. and Seidman, L. J. and Tsuang, M. T. and Xian, H. and Dale, A. M. and Kremen, W. S.},
	year = {2011},
	keywords = {Alleles, Apolipoprotein E4/classification/*genetics, Brain Diseases/*genetics, Brain Mapping, Frontal Lobe/*pathology, Functional Laterality, Genotype, Humans, Image Processing, Computer-Assisted, Longitudinal Studies, Magnetic Resonance Imaging, Male, Middle Aged, Twin Studies as Topic, Vietnam},
	pages = {49--60},
	annote = {Fennema-Notestine, {ChristinePanizzon}, Matthew {SThompson}, Wesley {RChen}, Chi-{HuaEyler}, Lisa {TFischl}, {BruceFranz}, Carol {EGrant}, Michael {DJak}, Amy {JJernigan}, Terry {LLyons}, Michael {JNeale}, Michael {CSeidman}, Larry {JTsuang}, Ming {TXian}, {HongDale}, Anders {MKremen}, William {SengP}41 {RR}014075/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-06/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 {AG}018384/{AG}/{NIA} {NIH} {HHS}/R01 {AG}018384-10/{AG}/{NIA} {NIH} {HHS}/R01 {AG}018386/{AG}/{NIA} {NIH} {HHS}/R01 {AG}018386-10/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022381/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022381-10/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022982/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022982-04/{AG}/{NIA} {NIH} {HHS}/R01 {EB}006758/{EB}/{NIBIB} {NIH} {HHS}/R01 {EB}006758-04/{EB}/{NIBIB} {NIH} {HHS}/R01 {NS}052585-01/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}052585-01A1/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}070963/{NS}/{NINDS} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/U24 {RR}021382-05/{RR}/{NCRR} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov'{tResearch} Support, U.S. Gov't, Non-P.H.S.Netherlands2011/10/06 06:00J Alzheimers Dis. 2011;26 Suppl 3:49-60. doi: 10.3233/{JAD}-2011-0002.},
	file = {Fennema-Notesti-2011-Presence of ApoE epsilon4:/autofs/cluster/freesurfer/zotero/storage/GHEI6F7N/Fennema-Notesti-2011-Presence of ApoE epsilon4.pdf:application/pdf}
}

@inproceedings{segonne_topological_2003,
	title = {Topological Correction of Subcortical Segmentation},
	shorttitle = {Topological Correction of Subcortical Segmentation},
	url = {http://www.nmr.mgh.harvard.edu/~fischl/reprints/segonne_subcortical_topology_miccai2003.pdf},
	author = {Ségonne, F. and Grimson, E. and Fischl, B.},
	year = {2003},
	keywords = {fs\_Subcortical-segmentation, fs\_Topology-correction}
}

@article{manoach_reduced_2007,
	title = {Reduced microstructural integrity of the white matter underlying anterior cingulate cortex is associated with increased saccadic latency in schizophrenia},
	volume = {37},
	issn = {1053-8119 (Print) 1053-8119 (Linking)},
	shorttitle = {Reduced microstructural integrity of the white matter underlying anterior cingulate cortex is associated with increased saccadic latency in schizophrenia},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/17590354},
	doi = {10.1016/j.neuroimage.2007.04.062},
	abstract = {The anterior cingulate cortex ({ACC}) is a key component of a network that directs both spatial attention and saccadic eye movements, which are tightly linked. Diffusion tensor imaging ({DTI}) has demonstrated reduced microstructural integrity of the anterior cingulum bundle as indexed by fractional anisotropy ({FA}) in schizophrenia, but the functional significance of these abnormalities is unclear. Using {DTI}, we examined the white matter underlying anterior cingulate cortex in schizophrenia to determine whether reduced {FA} is associated with prolonged latencies of volitional saccades. Seventeen chronic, medicated schizophrenia outpatients and nineteen healthy controls had high-resolution {DTI} scans. {FA} maps were registered to structural scans and mapped across participants using a surface-based coordinate system. Cingulate white matter was divided into rostral and dorsal anterior regions and a posterior region. Patients showed reduced {FA} in cingulate white matter of the right hemisphere. Reduced {FA} in the white matter underlying anterior cingulate cortex, frontal eye field, and posterior parietal cortex of the right hemisphere was associated with longer saccadic latencies in schizophrenia, though given the relatively small sample size, these relations warrant replication. These findings demonstrate that in schizophrenia, increased latency of volitional saccades is associated with reduced microstructural integrity of the white matter underlying key cortical components of a right-hemisphere dominant network for visuospatial attention and ocular motor control. Moreover, they suggest that anterior cingulate white matter abnormalities contribute to slower performance of volitional saccades and to inter-individual variability of saccadic latency in chronic, medicated schizophrenia.},
	number = {2},
	journal = {Neuroimage},
	author = {Manoach, D. S. and Ketwaroo, G. A. and Polli, F. E. and Thakkar, K. N. and Barton, J. J. and Goff, D. C. and Fischl, B. and Vangel, M. and Tuch, D. S.},
	month = aug,
	year = {2007},
	keywords = {Adult, Anisotropy, *Brain Mapping, Diffusion Magnetic Resonance Imaging, Female, Gyrus Cinguli/*pathology, Humans, Male, Saccades/*physiology, Schizophrenia/*pathology/*physiopathology},
	pages = {599--610},
	annote = {Manoach, Dara {SKetwaroo}, G {AvinashPolli}, Frida {EThakkar}, Katharine {NBarton}, Jason J {SGoff}, Donald {CFischl}, {BruceVangel}, {MarkTuch}, David {SengBIRN}002/{PHS} {HHS}/P01 31154/{PHS} {HHS}/P41 {RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 31340/{PHS} {HHS}/R01 67720/{PHS} {HHS}/R01 {EB}001550/{EB}/{NIBIB} {NIH} {HHS}/R01 {RR}16594-01A1/{RR}/{NCRR} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/U54 {EB}005149/{EB}/{NIBIB} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov't2007/06/26 09:00Neuroimage. 2007 Aug 15;37(2):599-610. Epub 2007 May 21.}
}

@article{almeida_reduced_2010,
	title = {Reduced right frontal cortical thickness in children, adolescents and adults with {ADHD} and its correlation to clinical variables: a cross-sectional study},
	volume = {44},
	issn = {1879-1379},
	shorttitle = {Reduced right frontal cortical thickness in children, adolescents and adults with {ADHD} and its correlation to clinical variables},
	doi = {10.1016/j.jpsychires.2010.04.026},
	abstract = {{OBJECTIVE}: Some longitudinal magnetic resonance imaging ({MRI}) studies have shown reduced volume or cortical thickness ({CT}) in the frontal cortices of individuals with attention-deficit/hyperactivity disorder ({ADHD}). These studies indicated that the aforementioned anatomical abnormalities disappear during adolescence. In contrast, cross-sectional studies on adults with {ADHD} have shown anatomical abnormalities in the frontal lobe region. It is not known whether the anatomical abnormalities in {ADHD} are a delay or a deviation in the encephalic maturation. The aim of this study was to compare {CT} in the frontal lobe of children, adolescents and adults of both genders presenting {ADHD} with that in corresponding healthy controls and to explore its relationship with the severity of the illness.
{METHOD}: An {MRI} scan study was performed on never-medicated {ADHD} patients. Twenty-one children (6-10 year-olds), twenty adolescents (14-17 year-olds) and twenty adults (25-35 year-olds) were matched with healthy controls according to age and sex. {CT} measurements were performed using the Freesurfer image analysis suite.
{RESULTS}: The data showed regions in the right superior frontal gyrus where {CT} was reduced in children, adolescents and adults with {ADHD} in contrast to their respective healthy controls. The {CT} of these regions correlated with the severity of the illness.
{CONCLUSIONS}: In subjects with {ADHD}, there is a thinning of the cortical surface in the right frontal lobe, which is present in the children, adolescents and in adults.},
	language = {eng},
	number = {16},
	journal = {Journal of Psychiatric Research},
	author = {Almeida, Luis G. and Ricardo-Garcell, Josefina and Prado, Hugo and Barajas, Lázaro and Fernández-Bouzas, Antonio and Avila, David and Martínez, Reyna B.},
	month = dec,
	year = {2010},
	pmid = {20510424},
	keywords = {Adolescent, Adult, Age Factors, Attention Deficit Disorder with Hyperactivity, Child, Comorbidity, Cross-Sectional Studies, Female, Frontal Lobe, Functional Laterality, Humans, Image Processing, Computer-Assisted, Longitudinal Studies, Magnetic Resonance Imaging, Male, Psychiatric Status Rating Scales, Psychometrics, Statistics as Topic, Statistics, Nonparametric, Tomography, X-Ray Computed, Young Adult},
	pages = {1214--1223}
}

@article{rosas_regional_2005,
	title = {Regional cortical thinning in preclinical Huntington disease and its relationship to cognition},
	volume = {65},
	issn = {1526-632X (Electronic) 0028-3878 (Linking)},
	shorttitle = {Regional cortical thinning in preclinical Huntington disease and its relationship to cognition},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/16157910},
	doi = {10.1212/01.wnl.0000174432.87383.87},
	abstract = {The authors studied presymptomatic individuals with the Huntington disease ({HD}) mutation to determine whether cortical thinning was present. They found thinning that was regionally selective, semi-independent of striatal volume loss, and correlated with cognitive performance. Early, extensive cortical involvement occurs during the preclinical stages of {HD}.},
	number = {5},
	journal = {Neurology},
	author = {Rosas, H. D. and Hevelone, N. D. and Zaleta, A. K. and Greve, D. N. and Salat, D. H. and Fischl, B.},
	month = sep,
	year = {2005},
	keywords = {Adult, Atrophy/genetics/pathology/physiopathology, Brain Mapping, Cerebral Cortex/*pathology/physiopathology, Cognition Disorders/*pathology/physiopathology/psychology, Corpus Striatum/pathology/physiopathology, {DNA} Mutational Analysis, Female, Genetic Testing, Genotype, Humans, Huntington Disease/genetics/*pathology/physiopathology, Magnetic Resonance Imaging, Male, Middle Aged, Nerve Tissue Proteins/genetics, Neuropsychological Tests, Nuclear Proteins/genetics, Trinucleotide Repeats/genetics},
	pages = {745--7},
	annote = {Rosas, H {DHevelone}, N {DZaleta}, A {KGreve}, D {NSalat}, D {HFischl}, {BengNS}042861/{NS}/{NINDS} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 {RR}16594-01A1/{RR}/{NCRR} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov'{tResearch} Support, U.S. Gov't, P.H.S.2005/09/15 09:00Neurology. 2005 Sep 13;65(5):745-7.},
	file = {Rosas-2005-Regional cortical thinning in precl:/autofs/cluster/freesurfer/zotero/storage/8ZDSPXN9/Rosas-2005-Regional cortical thinning in precl.pdf:application/pdf}
}

@article{polimeni_laminar_2010,
	title = {Laminar analysis of 7T {BOLD} using an imposed spatial activation pattern in human V1},
	volume = {52},
	issn = {1095-9572 (Electronic) 1053-8119 (Linking)},
	shorttitle = {Laminar analysis of 7T {BOLD} using an imposed spatial activation pattern in human V1},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/20460157},
	doi = {10.1016/j.neuroimage.2010.05.005},
	abstract = {With sufficient image encoding, high-resolution {fMRI} studies are limited by the biological point-spread of the hemodynamic signal. The extent of this spread is determined by the local vascular distribution and by the spatial specificity of blood flow regulation, as well as by measurement parameters that (i) alter the relative sensitivity of the acquisition to activation-induced hemodynamic changes and (ii) determine the image contrast as a function of vessel size. In particular, large draining vessels on the cortical surface are a major contributor to both the {BOLD} signal change and to the spatial bias of the {BOLD} activation away from the site of neuronal activity. In this work, we introduce a laminar surface-based analysis method and study the relationship between spatial localization and activation strength as a function of laminar depth by acquiring 1mm isotropic, single-shot {EPI} at 7 T and sampling the {BOLD} signal exclusively from the superficial, middle, or deep cortical laminae. We show that highly-accelerated {EPI} can limit image distortions to the point where a boundary-based registration algorithm accurately aligns the {EPI} data to the surface reconstruction. The spatial spread of the {BOLD} response tangential to the cortical surface was analyzed as a function of cortical depth using our surface-based analysis. Although sampling near the pial surface provided the highest signal strength, it also introduced the most spatial error. Thus, avoiding surface laminae improved spatial localization by about 40\% at a cost of 36\% in z-statistic, implying that optimal spatial resolution in functional imaging of the cortex can be achieved using anatomically-informed spatial sampling to avoid large pial vessels.},
	number = {4},
	journal = {Neuroimage},
	author = {Polimeni, J. R. and Fischl, B. and Greve, D. N. and Wald, L. L.},
	month = oct,
	year = {2010},
	keywords = {*Algorithms, Brain Mapping/*methods, Evoked Potentials, Visual/*physiology, Humans, Magnetic Resonance Imaging/*methods, Visual Cortex/*physiology, Visual Perception/*physiology},
	pages = {1334--46},
	annote = {Polimeni, Jonathan {RFischl}, {BruceGreve}, Douglas {NWald}, Lawrence {LengAG}02238/{AG}/{NIA} {NIH} {HHS}/P41 {RR}014075/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 {AG}018386-09/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022381-01/{AG}/{NIA} {NIH} {HHS}/R01 {EB}006758/{EB}/{NIBIB} {NIH} {HHS}/R01 {EB}006758-01A1/{EB}/{NIBIB} {NIH} {HHS}/R01 {EB}006847/{EB}/{NIBIB} {NIH} {HHS}/R01 {EB}006847-01A2/{EB}/{NIBIB} {NIH} {HHS}/R01 {NS}052585-01/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}052585-02/{NS}/{NINDS} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov't2010/05/13 06:00Neuroimage. 2010 Oct 1;52(4):1334-46. doi: 10.1016/j.neuroimage.2010.05.005. Epub 2010 May 9.},
	file = {Polimeni-2010-Laminar analysis of 7T BOLD usin:/autofs/cluster/freesurfer/zotero/storage/2Q45VCJI/Polimeni-2010-Laminar analysis of 7T BOLD usin.pdf:application/pdf;PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/TQMX4RNB/Polimeni et al. - 2010 - Laminar analysis of 7 T BOLD using an imposed spat.pdf:application/pdf}
}

@book{yeo_what_2007,
	title = {What Data to Co-register for Computing Atlases},
	url = {http://people.csail.mit.edu/~polina/papers/Yeo_MMBIA-2007.pdf},
	author = {Yeo, B. T. Thomas and Sabuncu, Mert and Zilles, Karl and Golland, Polina and Mohlberg, Hartmut and Amunts, Katrin and Fischl, Bruce},
	year = {2007},
	keywords = {fs\_Misc-methodology}
}

@article{hinds_accurate_2008,
	title = {Accurate prediction of V1 location from cortical folds in a surface coordinate system},
	volume = {39},
	issn = {1053-8119 (Print) 1053-8119 (Linking)},
	shorttitle = {Accurate prediction of V1 location from cortical folds in a surface coordinate system},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/18055222},
	doi = {10.1016/j.neuroimage.2007.10.033},
	abstract = {Previous studies demonstrated substantial variability of the location of primary visual cortex (V1) in stereotaxic coordinates when linear volume-based registration is used to match volumetric image intensities [Amunts, K., Malikovic, A., Mohlberg, H., Schormann, T., and Zilles, K. (2000). Brodmann's areas 17 and 18 brought into stereotaxic space-where and how variable? Neuroimage, 11(1):66-84]. However, other qualitative reports of V1 location [Smith, G. (1904). The morphology of the occipital region of the cerebral hemisphere in man and the apes. Anatomischer Anzeiger, 24:436-451; Stensaas, S.S., Eddington, D.K., and Dobelle, W.H. (1974). The topography and variability of the primary visual cortex in man. J Neurosurg, 40(6):747-755; Rademacher, J., Caviness, V.S., Steinmetz, H., and Galaburda, A.M. (1993). Topographical variation of the human primary cortices: implications for neuroimaging, brain mapping, and neurobiology. Cereb Cortex, 3(4):313-329] suggested a consistent relationship between V1 and the surrounding cortical folds. Here, the relationship between folds and the location of V1 is quantified using surface-based analysis to generate a probabilistic atlas of human V1. High-resolution (about 200 microm) magnetic resonance imaging ({MRI}) at 7 T of ex vivo human cerebral hemispheres allowed identification of the full area via the stria of Gennari: a myeloarchitectonic feature specific to V1. Separate, whole-brain scans were acquired using {MRI} at 1.5 T to allow segmentation and mesh reconstruction of the cortical gray matter. For each individual, V1 was manually identified in the high-resolution volume and projected onto the cortical surface. Surface-based intersubject registration [Fischl, B., Sereno, M.I., Tootell, R.B., and Dale, A.M. (1999b). High-resolution intersubject averaging and a coordinate system for the cortical surface. Hum Brain Mapp, 8(4):272-84] was performed to align the primary cortical folds of individual hemispheres to those of a reference template representing the average folding pattern. An atlas of V1 location was constructed by computing the probability of V1 inclusion for each cortical location in the template space. This probabilistic atlas of V1 exhibits low prediction error compared to previous V1 probabilistic atlases built in volumetric coordinates. The increased predictability observed under surface-based registration suggests that the location of V1 is more accurately predicted by the cortical folds than by the shape of the brain embedded in the volume of the skull. In addition, the high quality of this atlas provides direct evidence that surface-based intersubject registration methods are superior to volume-based methods at superimposing functional areas of cortex and therefore are better suited to support multisubject averaging for functional imaging experiments targeting the cerebral cortex.},
	number = {4},
	journal = {Neuroimage},
	author = {Hinds, O. P. and Rajendran, N. and Polimeni, J. R. and Augustinack, J. C. and Wiggins, G. and Wald, L. L. and Diana Rosas, H. and Potthast, A. and Schwartz, E. L. and Fischl, B.},
	month = feb,
	year = {2008},
	keywords = {Aged, Algorithms, Autopsy, Cerebral Cortex/*anatomy \& histology, Female, fs\_Cortical-parcellation, fs\_Misc-methodology, Functional Laterality/physiology, Humans, Image Processing, Computer-Assisted/*methods/statistics \& numerical data, Magnetic Resonance Imaging, Male, Middle Aged, Models, Statistical, Predictive Value of Tests, Stereotaxic Techniques, Visual Cortex/*anatomy \& histology},
	pages = {1585--99},
	annote = {Hinds, Oliver {PRajendran}, {NiranjiniPolimeni}, Jonathan {RAugustinack}, Jean {CWiggins}, {GrahamWald}, Lawrence {LDiana} Rosas, {HPotthast}, {AndreasSchwartz}, Eric {LFischl}, Bruceeng5 P50 {AG} 05134/{AG}/{NIA} {NIH} {HHS}/P41 {RR} 14075/{RR}/{NCRR} {NIH} {HHS}/P50 {AG} 005134/{AG}/{NIA} {NIH} {HHS}/R01 {EB} 001550/{EB}/{NIBIB} {NIH} {HHS}/R01 {EB}001550-01/{EB}/{NIBIB} {NIH} {HHS}/R01 {NS} 052585/{NS}/{NINDS} {NIH} {HHS}/R01 {RR} 16594/{RR}/{NCRR} {NIH} {HHS}/U24 {RR} 021382/{RR}/{NCRR} {NIH} {HHS}/U54 {EB} 005149/{EB}/{NIBIB} {NIH} {HHS}/Research Support, N.I.H., Extramural2007/12/07 09:00Neuroimage. 2008 Feb 15;39(4):1585-99. Epub 2007 Nov 6.},
	file = {Hinds-2008-Accurate prediction of V1 location:/autofs/cluster/freesurfer/zotero/storage/JCDNBBRF/Hinds-2008-Accurate prediction of V1 location.pdf:application/pdf}
}

@article{magnain_blockface_2014,
	title = {Blockface histology with optical coherence tomography: a comparison with Nissl staining},
	volume = {84},
	issn = {1095-9572 (Electronic) 1053-8119 (Linking)},
	shorttitle = {Blockface histology with optical coherence tomography},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/24041872},
	doi = {10.1016/j.neuroimage.2013.08.072},
	abstract = {Spectral domain optical coherence tomography ({SD}-{OCT}) is a high resolution imaging technique that generates excellent contrast based on intrinsic optical properties of the tissue, such as neurons and fibers. The {SD}-{OCT} data acquisition is performed directly on the tissue block, diminishing the need for cutting, mounting and staining. We utilized {SD}-{OCT} to visualize the laminar structure of the isocortex and compared cortical cytoarchitecture with the gold standard Nissl staining, both qualitatively and quantitatively. In histological processing, distortions routinely affect registration to the blockface image and prevent accurate 3D reconstruction of regions of tissue. We compared blockface registration to {SD}-{OCT} and Nissl, respectively, and found that {SD}-{OCT}-blockface registration was significantly more accurate than Nissl-blockface registration. Two independent observers manually labeled cortical laminae (e.g. {III}, {IV} and V) in {SD}-{OCT} images and Nissl stained sections. Our results show that {OCT} images exhibit sufficient contrast in the cortex to reliably differentiate the cortical layers. Furthermore, the modalities were compared with regard to cortical laminar organization and showed good agreement. Taken together, these {SD}-{OCT} results suggest that {SD}-{OCT} contains information comparable to standard histological stains such as Nissl in terms of distinguishing cortical layers and architectonic areas. Given these data, we propose that {SD}-{OCT} can be used to reliably generate 3D reconstructions of multiple cubic centimeters of cortex that can be used to accurately and semi-automatically perform standard histological analyses.},
	language = {en},
	urldate = {2014-08-21},
	journal = {Neuroimage},
	author = {Magnain, C. and Augustinack, J. C. and Reuter, M. and Wachinger, C. and Frosch, M. P. and Ragan, T. and Akkin, T. and Wedeen, V. J. and Boas, D. A. and Fischl, B.},
	month = jan,
	year = {2014},
	keywords = {fs\_OCT},
	pages = {524--33},
	annote = {Magnain, {CarolineAugustinack}, Jean {CReuter}, {MartinWachinger}, {ChristianFrosch}, Matthew {PRagan}, {TimothyAkkin}, {TanerWedeen}, Van {JBoas}, David {AFischl}, Bruceeng1R01NS070963/{NS}/{NINDS} {NIH} {HHS}/1R21NS072652-01/{NS}/{NINDS} {NIH} {HHS}/1S10RR019307/{RR}/{NCRR} {NIH} {HHS}/1S10RR023043/{RR}/{NCRR} {NIH} {HHS}/1S10RR023401/{RR}/{NCRR} {NIH} {HHS}/5R01AG008122-22/{AG}/{NIA} {NIH} {HHS}/5U01-{MH}093765/{MH}/{NIMH} {NIH} {HHS}/{AG}022381/{AG}/{NIA} {NIH} {HHS}/K01AG028521/{AG}/{NIA} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 {NS}052585-01/{NS}/{NINDS} {NIH} {HHS}/R01EB006758/{EB}/{NIBIB} {NIH} {HHS}/{RC}1 {AT}005728-01/{AT}/{NCCAM} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov't2013/09/18 06:00Neuroimage. 2014 Jan 1;84:524-33. doi: 10.1016/j.neuroimage.2013.08.072. Epub 2013 Sep 13.}
}

@article{rimol_cortical_2010-1,
	title = {Cortical thickness and subcortical volumes in schizophrenia and bipolar disorder},
	volume = {68},
	issn = {1873-2402},
	doi = {10.1016/j.biopsych.2010.03.036},
	abstract = {{BACKGROUND}: Schizophrenia and bipolar disorder are severe psychiatric diseases with overlapping symptomatology. Widespread brain morphologic abnormalities, including cortical thinning and subcortical volume reductions, have been demonstrated in schizophrenia but it is unclear whether similar abnormalities are present in bipolar disorder. The purpose of this study was to compare cortical thickness and subcortical volumes in schizophrenia and bipolar disorder, to assess differences and similarities in cortical and subcortical brain structure.
{METHODS}: We analyzed magnetic resonance images from a sample of 173 patients with schizophrenia spectrum disorder, 139 patients with bipolar disorder, and 207 healthy control subjects. Cortical thickness was compared between the groups in multiple locations across the continuous cortical surface. Subcortical volumes were compared on a structure-by-structure basis.
{RESULTS}: There was widespread cortical thinning in schizophrenia compared with control subjects, in frontal, temporal, occipital, and smaller parietal regions. There was no cortical thinning in bipolar disorder compared with control subjects or in schizophrenia compared with bipolar disorder. However, the subgroup of patients with bipolar disorder Type 1 showed cortical thinning, primarily in the frontal lobes and superior temporal and temporoparietal regions. Both patient groups showed substantial subcortical volume reductions bilaterally in the hippocampus, the left thalamus, the right nucleus accumbens, the left cerebellar cortex, and the brainstem, along with substantial ventricular enlargements.
{CONCLUSIONS}: We found substantial overlap in the underlying brain morphologic abnormalities in schizophrenia and bipolar disorder in subcortical structures, and between schizophrenia and bipolar disorder Type 1 in the cerebral cortex.},
	language = {eng},
	number = {1},
	journal = {Biological Psychiatry},
	author = {Rimol, Lars M. and Hartberg, Cecilie B. and Nesvåg, Ragnar and Fennema-Notestine, Christine and Hagler, Donald J. and Pung, Chris J. and Jennings, Robin G. and Haukvik, Unn K. and Lange, Elisabeth and Nakstad, Per H. and Melle, Ingrid and Andreassen, Ole A. and Dale, Anders M. and Agartz, Ingrid},
	month = jul,
	year = {2010},
	pmid = {20609836},
	keywords = {Adult, Antidepressive Agents, Antipsychotic Agents, Bipolar Disorder, Brain, Brain Mapping, Female, Follow-Up Studies, Functional Laterality, Humans, Image Processing, Computer-Assisted, Linear Models, Magnetic Resonance Imaging, Male, Middle Aged, Psychiatric Status Rating Scales, Schizophrenia},
	pages = {41--50}
}

@article{jovicich_reliability_2006,
	title = {Reliability in multi-site structural {MRI} studies: effects of gradient non-linearity correction on phantom and human data},
	volume = {30},
	issn = {1053-8119 (Print) 1053-8119 (Linking)},
	shorttitle = {Reliability in multi-site structural {MRI} studies: effects of gradient non-linearity correction on phantom and human data},
	url = {https://surfer.nmr.mgh.harvard.edu/ftp/articles/jovicich_neuroimage_2006.pdf},
	doi = {10.1016/j.neuroimage.2005.09.046},
	abstract = {Longitudinal and multi-site clinical studies create the imperative to characterize and correct technological sources of variance that limit image reproducibility in high-resolution structural {MRI} studies, thus facilitating precise, quantitative, platform-independent, multi-site evaluation. In this work, we investigated the effects that imaging gradient non-linearity have on reproducibility of multi-site human {MRI}. We applied an image distortion correction method based on spherical harmonics description of the gradients and verified the accuracy of the method using phantom data. The correction method was then applied to the brain image data from a group of subjects scanned twice at multiple sites having different 1.5 T platforms. Within-site and across-site variability of the image data was assessed by evaluating voxel-based image intensity reproducibility. The image intensity reproducibility of the human brain data was significantly improved with distortion correction, suggesting that this method may offer improved reproducibility in morphometry studies. We provide the source code for the gradient distortion algorithm together with the phantom data.},
	number = {2},
	journal = {Neuroimage},
	author = {Jovicich, J. and Czanner, S. and Greve, D. and Haley, E. and van der Kouwe, A. and Gollub, R. and Kennedy, D. and Schmitt, F. and Brown, G. and Macfall, J. and Fischl, B. and Dale, A.},
	month = apr,
	year = {2006},
	keywords = {Calibration, Computer Simulation, fs\_Misc-methodology, Humans, Image Processing, Computer-Assisted/*methods, Magnetic Resonance Imaging/*statistics \& numerical data, Multicenter Studies as Topic/methods, Nonlinear Dynamics, Reproducibility of Results},
	pages = {436--43},
	annote = {Jovicich, {JorgeCzanner}, {SilvesterGreve}, {DouglasHaley}, Elizabethvan der Kouwe, {AndreGollub}, {RandyKennedy}, {DavidSchmitt}, {FranzBrown}, {GregoryMacfall}, {JamesFischl}, {BruceDale}, {AndersengU}24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/Research Support, N.I.H., Extramural2005/11/23 09:00Neuroimage. 2006 Apr 1;30(2):436-43. Epub 2005 Nov 21.}
}

@article{milad_role_2007,
	title = {A role for the human dorsal anterior cingulate cortex in fear expression},
	volume = {62},
	issn = {0006-3223 (Print) 0006-3223 (Linking)},
	shorttitle = {A role for the human dorsal anterior cingulate cortex in fear expression},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/17707349},
	doi = {10.1016/j.biopsych.2007.04.032},
	abstract = {{BACKGROUND}: Rodent studies implicate the prelimbic ({PL}) region of the medial prefrontal cortex in the expression of conditioned fear. Human studies suggest that the dorsal anterior cingulate cortex ({dACC}) plays a role similar to {PL} in mediating or modulating fear responses. This study examined the role of {dACC} during fear conditioning in healthy humans with magnetic resonance imaging ({MRI}). {METHODS}: Novel analyses were conducted on data from two cohorts that had previously undergone scanning to study fear extinction. Structural and functional brain data were acquired with {MRI}; the functional {MRI} ({fMRI}) component employed an event-related design. Skin conductance response ({SCR}) was the index of conditioned responses. {RESULTS}: We found that: 1) cortical thickness within {dACC} is positively correlated with {SCR} during conditioning; 2) {dACC} is activated by a conditioned fear stimulus; and 3) this activation is positively correlated with differential {SCR}. Moreover, the {dACC} region implicated in this research corresponds to the target of anterior cingulotomy, an ablative surgical treatment for patients with mood and anxiety disorders. {CONCLUSIONS}: Convergent structural, functional, and lesion findings from separate groups of subjects suggest that {dACC} mediates or modulates fear expression in humans. Collectively, these data implicate this territory as a potential target for future anti-anxiety therapies.},
	number = {10},
	journal = {Biol Psychiatry},
	author = {Milad, M. R. and Quirk, G. J. and Pitman, R. K. and Orr, S. P. and Fischl, B. and Rauch, S. L.},
	month = nov,
	year = {2007},
	keywords = {Adult, Brain Mapping, Expressed Emotion/*physiology, *Fear, Female, Galvanic Skin Response/physiology, Gyrus Cinguli/blood supply/*physiology, Humans, Image Processing, Computer-Assisted/methods, Magnetic Resonance Imaging/methods, Male, Oxygen/blood, Regression Analysis},
	pages = {1191--4},
	annote = {Milad, Mohammed {RQuirk}, Gregory {JPitman}, Roger {KOrr}, Scott {PFischl}, {BruceRauch}, Scott Leng1R21MH072156-1/{MH}/{NIMH} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov't2007/08/21 09:00Biol Psychiatry. 2007 Nov 15;62(10):1191-4. Epub 2007 Aug 20.}
}

@article{hatton_white_2014,
	title = {White matter tractography in early psychosis: clinical and neurocognitive associations},
	volume = {39},
	issn = {1488-2434},
	shorttitle = {White matter tractography in early psychosis},
	url = {http://jpn.ca/wp-content/uploads/2014/08/39-4-130280.pdf},
	abstract = {{BACKGROUND}: While many diffusion tensor imaging ({DTI}) investigations have noted disruptions to white matter integrity in individuals with chronic psychotic disorders, fewer studies have been conducted in young people at the early stages of disease onset. Using whole tract reconstruction techniques, the aim of this study was to identify the white matter pathology associated with the common clinical symptoms and executive function impairments observed in young people with psychosis.
{METHODS}: We obtained {MRI} scans from young people with psychosis and healthy controls. Eighteen major white matter tracts were reconstructed to determine group differences in fractional anisotropy ({FA}), axial diffusivity ({AD}) and radial diffusivity ({RD}) and then were subsequently correlated with symptomatology and neurocognitive performance.
{RESULTS}: Our study included 42 young people with psychosis (mean age 23 yr) and 45 healthy controls (mean age 25 yr). Compared with the control group, the psychosis group had reduced {FA} and {AD} in the left inferior longitudinal fasciculus ({ILF}) and forceps major indicative of axonal disorganization, reduction and/or loss. These changes were associated with worse overall psychiatric symptom severity, increases in positive and negative symptoms, and worse current levels of depression. The psychosis group also showed {FA} reductions in the left superior longitudinal fasciculus that were associated with impaired neurocognitive performance in attention and semantic fluency.
{LIMITATIONS}: Our analysis grouped 4 subcategories of psychosis together, and a larger follow-up study comparing affective and nonaffective psychoses is warranted.
{CONCLUSION}: Our findings suggest that impaired axonal coherence in the left {ILF} and forceps major underpin psychiatric symptoms in young people in the early stages of psychosis.},
	language = {{ENG}},
	number = {4},
	journal = {Journal of psychiatry \& neuroscience: {JPN}},
	author = {Hatton, Sean N. and Lagopoulos, Jim and Hermens, Daniel F. and Hickie, Ian B. and Scott, Elizabeth and Bennett, Maxwell R.},
	month = aug,
	year = {2014},
	pmid = {25111788},
	pages = {130280}
}

@article{kuperberg_regionally_2003,
	title = {Regionally localized thinning of the cerebral cortex in schizophrenia},
	volume = {60},
	issn = {0003-990X (Print) 0003-990X (Linking)},
	shorttitle = {Regionally localized thinning of the cerebral cortex in schizophrenia},
	url = {http://www.nmr.mgh.harvard.edu/~fischl/reprints/Kuperberg_and_Fischl_ArchGenPsy_03.pdf},
	doi = {10.1001/archpsyc.60.9.878},
	abstract = {{BACKGROUND}: Schizophrenia is characterized by small reductions in cortical gray matter volume, particularly in the temporal and prefrontal cortices. The question of whether cortical thickness is reduced in schizophrenia has not been addressed using magnetic resonance imaging ({MRI}) techniques. Our objectives were to test the hypothesis that cortical thinning in patients with schizophrenia (relative to control subjects) is greater in temporal and prefrontal regions of interest ({ROIs}) than in control {ROIs} (superior parietal, calcarine, postcentral, central, and precentral cortices), and to obtain an unbiased estimate of the distribution of cortical thinning in patients (relative to controls) by constructing mean and statistical cortical thickness difference maps. {METHODS}: Participants included 33 right-handed outpatients receiving medication and meeting {DSM}-{IV} criteria for schizophrenia and 32 healthy volunteers, matched on age and parental socioeconomic status. After high-resolution {MRI} scans, models of the gray-white and pial surfaces were generated for each individual's cortex, and the distance between these 2 surfaces was used to compute cortical thickness. A surface-based averaging technique that aligned the main cortical folds across individuals allowed between-group comparisons of thickness within {ROIs}, and at multiple, uniformly sampled loci across the cortical ribbon. {RESULTS}: Relative to controls, patients showed greater cortical thinning in temporal-prefrontal {ROIs} than in control {ROIs}, as revealed by a significant (P{\textless}.009) interaction between group and region type. Cortical thickness difference maps revealed significant (at P{\textless}.05, corrected) thinning within the orbitofrontal cortices bilaterally; the inferior frontal, inferior temporal, and occipitotemporal cortices on the left; and within the medial temporal and medial frontal cortices on the right. Superior parietal and primary somatosensory and motor cortices were relatively spared, even at subthreshold significance levels. {CONCLUSIONS}: Patients with chronic schizophrenia showed widespread cortical thinning that particularly affected the prefrontal and temporal cortices. This thinning might reflect underlying neuropathological abnormalities in cortical structure.},
	language = {eng},
	number = {9},
	journal = {Arch Gen Psychiatry},
	author = {Kuperberg, G. R. and Broome, M. R. and McGuire, P. K. and David, A. S. and Eddy, M. and Ozawa, F. and Goff, D. and West, W. C. and Williams, S. C. and van der Kouwe, A. J. and Salat, D. H. and Dale, A. M. and Fischl, B.},
	month = sep,
	year = {2003},
	keywords = {Adult, Adult, Ambulatory Care, Ambulatory Care, Atrophy, Atrophy, Cerebral Cortex, Cerebral Cortex/*anatomy \& histology/pathology, Chronic Disease, Chronic Disease, Female, Female, Functional Laterality, Functional Laterality, Humans, Humans, Magnetic Resonance Imaging, Magnetic Resonance Imaging, Male, Male, Parietal Lobe, Parietal Lobe/anatomy \& histology/pathology, Prefrontal Cortex, Prefrontal Cortex/anatomy \& histology/pathology, Schizophrenia, Schizophrenia/*diagnosis/pathology, Temporal Lobe, Temporal Lobe/anatomy \& histology/pathology},
	pages = {878--88},
	annote = {Kuperberg, Gina {RBroome}, Matthew {RMcGuire}, Philip {KDavid}, Anthony {SEddy}, {MariannaOzawa}, {FujiroGoff}, {DonaldWest}, W {CarolineWilliams}, Steven C Rvan der Kouwe, Andre J {WSalat}, David {HDale}, Anders {MFischl}, {BruceengK}23 {PA}-00-004/{PHS} {HHS}/Comparative {StudyResearch} Support, Non-U.S. Gov'{tResearch} Support, U.S. Gov't, P.H.S.2003/09/10 05:00Arch Gen Psychiatry. 2003 Sep;60(9):878-88.},
	file = {Kuperberg-2003-Regionally localized thinning o:/autofs/cluster/freesurfer/zotero/storage/RR759KI5/Kuperberg-2003-Regionally localized thinning o.pdf:application/pdf}
}

@article{bigler_diffuse_2010,
	title = {Diffuse damage in pediatric traumatic brain injury: a comparison of automated versus operator-controlled quantification methods},
	volume = {50},
	issn = {1095-9572},
	shorttitle = {Diffuse damage in pediatric traumatic brain injury},
	doi = {10.1016/j.neuroimage.2010.01.003},
	abstract = {This investigation had two main objectives: 1) to assess the comparability of volumes determined by operator-controlled image quantification with automated image analysis in evaluating atrophic brain changes related to traumatic brain injury ({TBI}) in children, and 2) to assess the extent of diffuse structural changes throughout the brain as determined by reduced volume of a brain structure or region of interest ({ROI}). Operator-controlled methods used {ANALYZE} software for segmentation and tracing routines of pre-defined brain structures and {ROIs}. For automated image analyses, the open-access {FreeSurfer} program was used. Sixteen children with moderate-to-severe {TBI} were compared to individually matched, typically developing control children and the volumes of 18 brain structures and/or {ROIs} were compared between the two methods. Both methods detected atrophic changes but differed in the magnitude of the atrophic effect with the best agreement in subcortical structures. The volumes of all brain structures/{ROIs} were smaller in the {TBI} group regardless of method used; overall effect size differences were minimal for caudate and putamen but moderate to large for all other measures. This is reflective of the diffuse nature of {TBI} and its widespread impact on structural brain integrity, indicating that both {FreeSurfer} and operator-controlled methods can reliably assess cross-sectional volumetric changes in pediatric {TBI}.},
	language = {eng},
	number = {3},
	journal = {{NeuroImage}},
	author = {Bigler, Erin D. and Abildskov, Tracy J. and Wilde, Elisabeth A. and McCauley, Stephen R. and Li, Xiaoqi and Merkley, Tricia L. and Fearing, Michael A. and Newsome, Mary R. and Scheibel, Randall S. and Hunter, Jill V. and Chu, Zili and Levin, Harvey S.},
	month = apr,
	year = {2010},
	pmid = {20060915},
	keywords = {Adolescent, Age Factors, Automation, Brain, Brain Injuries, Caudate Nucleus, Child, Child, Preschool, Female, fs\_Validation-Evaluations, Humans, Image Processing, Computer-Assisted, Infant, Magnetic Resonance Imaging, Male, Observer Variation, Organ Size, Putamen, Severity of Illness Index, Software},
	pages = {1017--1026}
}

@article{salat_neuroimaging_2006,
	title = {Neuroimaging H.M.: a 10-year follow-up examination},
	volume = {16},
	issn = {1050-9631 (Print) 1050-9631 (Linking)},
	shorttitle = {Neuroimaging H.M.: a 10-year follow-up examination},
	url = {https://surfer.nmr.mgh.harvard.edu/pub/articles/salat_2006.pdf},
	doi = {10.1002/hipo.20222},
	abstract = {In 1997, Corkin et al. described the anatomical boundaries of the amnesic patient H.M.'s surgical resection, based on a comprehensive analysis of magnetic resonance imaging ({MRI}) scans collected in 1992 and 1993 (Corkin et al. (1997) J Neurosci 17:3964-3979). We subsequently scanned H.M. on several occasions, employing more advanced data acquisition and analysis methods, and now describe additional details about his brain anatomy and pathology. This account combines results from high-resolution T1-weighted scans, which provide measures of cortical and subcortical morphometry, diffusion tensor images, which provide quantitative information about white matter microstructure and the anatomy of major fasciculi, and T2-weighted images, which highlight damage to deep white matter. We applied new {MRI} analysis techniques to these scans to assess the integrity of areas throughout H.M.'s brain. We documented a number of new changes, including cortical thinning, atrophy of deep gray matter structures, and a large volume of abnormal white matter and deep gray matter signal. Most of these alterations were not apparent in his prior scans, suggesting that they are of recent origin. Advanced age and hypertension likely contributed to these new findings.},
	number = {11},
	journal = {Hippocampus},
	author = {Salat, D. H. and van der Kouwe, A. J. and Tuch, D. S. and Quinn, B. T. and Fischl, B. and Dale, A. M. and Corkin, S.},
	year = {2006},
	keywords = {Aged, Aged, Amnesia, Amnesia/*pathology/physiopathology, Brain Mapping, Brain Mapping, *Diagnostic Imaging, Diagnostic Imaging, Functional Laterality, Functional Laterality, Humans, Humans, Longitudinal Studies, Longitudinal Studies, Male, Male},
	pages = {936--45},
	annote = {Salat, D Hvan der Kouwe, A J {WTuch}, D {SQuinn}, B {TFischl}, {BDale}, A {MCorkin}, {SengAG}24898/{AG}/{NIA} {NIH} {HHS}/P41RR14075/{RR}/{NCRR} {NIH} {HHS}/Case {ReportsComparative} {StudyResearch} Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov't2006/10/04 09:00Hippocampus. 2006;16(11):936-45.}
}

@article{westlye_increased_2009,
	title = {Increased sensitivity to effects of normal aging and Alzheimer's disease on cortical thickness by adjustment for local variability in gray/white contrast: a multi-sample {MRI} study},
	volume = {47},
	issn = {1095-9572 (Electronic) 1053-8119 (Linking)},
	shorttitle = {Increased sensitivity to effects of normal aging and Alzheimer's disease on cortical thickness by adjustment for local variability in gray/white contrast: a multi-sample {MRI} study},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/19501655},
	doi = {10.1016/j.neuroimage.2009.05.084},
	abstract = {{MRI}-based estimates of cerebral morphometric properties, e.g. cortical thickness, are pivotal to studies of normal and pathological brain changes. These measures are based on automated or manual segmentation procedures, which utilize the tissue contrast between gray and white matter on T(1)-weighted {MR} images. Tissue contrast is unlikely to remain a constant property across groups of different age and health. An important question is therefore how the sensitivity of cortical thickness estimates is influenced by variability in {WM}/{GM} contrast. The effect of adjusting for variability in {WM}/{GM} contrast on age sensitivity of cortical thickness was tested in 1189 healthy subjects from six different samples, enabling evaluation of consistency of effects within and between sites and scanners. Further, the influence of Alzheimer's disease ({AD}) diagnosis on cortical thickness with and without correction for contrast was tested in an additional sample of 96 patients. In healthy controls, regional increases in the sensitivity of the cortical thickness measure to age were found after correcting for contrast. Across samples, the strongest effects were observed in frontal, lateral temporal and parietal areas. Controlling for contrast variability also increased the cortical thickness estimates' sensitivity to {AD}, thus replicating the finding in an independent clinical sample. The results showed increased sensitivity of cortical estimates to {AD} in areas earlier reported to be compromised in {AD}, including medial temporal, inferior and superior parietal regions. In sum, the findings indicate that adjusting for contrast can increase the sensitivity of {MR} morphometry to variables of interest.},
	language = {eng},
	number = {4},
	journal = {Neuroimage},
	author = {Westlye, L. T. and Walhovd, K. B. and Dale, A. M. and Espeseth, T. and Reinvang, I. and Raz, N. and Agartz, I. and Greve, D. N. and Fischl, B. and Fjell, A. M.},
	month = oct,
	year = {2009},
	keywords = {Adult, Aging/*pathology, Algorithms, Alzheimer Disease/*pathology, Cerebral Cortex/*pathology, Female, Humans, Image Enhancement/*methods, Image Interpretation, Computer-Assisted/*methods, Imaging, Three-Dimensional/*methods, Magnetic Resonance Imaging/*methods, Male, Middle Aged, Reproducibility of Results, Sensitivity and Specificity, Young Adult},
	pages = {1545--57},
	annote = {Westlye, Lars {TWalhovd}, Kristine {BDale}, Anders {MEspeseth}, {ThomasReinvang}, {IvarRaz}, {NaftaliAgartz}, {IngridGreve}, Douglas {NFischl}, {BruceFjell}, Anders {MengP}41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 {EB}001550/{EB}/{NIBIB} {NIH} {HHS}/R01 {NS}039581/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}039581-04/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}052585-01/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}052585-01A1/{NS}/{NINDS} {NIH} {HHS}/R01 {RR}013609/{RR}/{NCRR} {NIH} {HHS}/R01 {RR}013609-04/{RR}/{NCRR} {NIH} {HHS}/R01 {RR}16594-01A1/{RR}/{NCRR} {NIH} {HHS}/R01-{NS}39581/{NS}/{NINDS} {NIH} {HHS}/R01-{RR}13609/{RR}/{NCRR} {NIH} {HHS}/R01EB006758/{EB}/{NIBIB} {NIH} {HHS}/R37 {AG}011230/{AG}/{NIA} {NIH} {HHS}/R37 {AG}011230-14/{AG}/{NIA} {NIH} {HHS}/R37 {AG}011230-17/{AG}/{NIA} {NIH} {HHS}/R37 {AG}011230-18/{AG}/{NIA} {NIH} {HHS}/R37-{AG}11230/{AG}/{NIA} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/U54 {EB}005149/{EB}/{NIBIB} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov't2009/06/09 09:00Neuroimage. 2009 Oct 1;47(4):1545-57. doi: 10.1016/j.neuroimage.2009.05.084. Epub 2009 Jun 6.},
	file = {Westlye-2009-Increased sensitivity to effects:/autofs/cluster/freesurfer/zotero/storage/HPG3MS6Z/Westlye-2009-Increased sensitivity to effects.pdf:application/pdf}
}

@article{liu_changes_2007,
	title = {Changes in cerebral cortex of children treated for medulloblastoma},
	volume = {68},
	issn = {0360-3016 (Print) 0360-3016 (Linking)},
	shorttitle = {Changes in cerebral cortex of children treated for medulloblastoma},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/17379433},
	doi = {10.1016/j.ijrobp.2007.01.034},
	abstract = {{PURPOSE}: Children with medulloblastoma undergo surgery, radiotherapy, and chemotherapy. After treatment, these children have numerous structural abnormalities. Using high-resolution magnetic resonance imaging, we measured the thickness of the cerebral cortex in a group of medulloblastoma patients and a group of normally developing children. {METHODS} {AND} {MATERIALS}: We obtained magnetic resonance imaging scans and measured the cortical thickness in 9 children after treatment of medulloblastoma. The measurements from these children were compared with the measurements from age- and gender-matched normally developing children previously scanned. For additional comparison, the pattern of thickness change was compared with the cortical thickness maps from a larger group of 65 normally developing children. {RESULTS}: In the left hemisphere, relatively thinner cortex was found in the perirolandic region and the parieto-occipital lobe. In the right hemisphere, relatively thinner cortex was found in the parietal lobe, posterior superior temporal gyrus, and lateral temporal lobe. These regions of cortical thinning overlapped with the regions of cortex that undergo normal age-related thinning. {CONCLUSION}: The spatial distribution of cortical thinning suggested that the areas of cortex that are undergoing development are more sensitive to the effects of treatment of medulloblastoma. Such quantitative methods may improve our understanding of the biologic effects that treatment has on the cerebral development and their neuropsychological implications.},
	number = {4},
	journal = {Int J Radiat Oncol Biol Phys},
	author = {Liu, A. K. and Marcus, K. J. and Fischl, B. and Grant, P. E. and Poussaint, T. Y. and Rivkin, M. J. and Davis, P. and Tarbell, N. J. and Yock, T. I.},
	month = jul,
	year = {2007},
	keywords = {Adolescent, Adolescent, Cerebellar Neoplasms, Cerebellar Neoplasms/*therapy, Cerebral Cortex, Cerebral Cortex/*pathology, Child, Child, Child, Preschool, Child, Preschool, Female, Female, Humans, Humans, Magnetic Resonance Imaging, Magnetic Resonance Imaging/*methods, Male, Male, Medulloblastoma, Medulloblastoma/*therapy},
	pages = {992--8},
	annote = {Liu, Arthur {KMarcus}, Karen {JFischl}, {BruceGrant}, P {EllenPoussaint}, Tina {YoungRivkin}, Michael {JDavis}, {PeterTarbell}, Nancy {JYock}, Torunn Ieng5 P01 {CA} 21239-26/{CA}/{NCI} {NIH} {HHS}/N01 {HD} 023343/{HD}/{NICHD} {NIH} {HHS}/N01 {MH} 90002/{MH}/{NIMH} {NIH} {HHS}/N01 {NS} 92314/{NS}/{NINDS} {NIH} {HHS}/N01 {NS} 92315/{NS}/{NINDS} {NIH} {HHS}/N01 {NS} 92316/{NS}/{NINDS} {NIH} {HHS}/N01 {NS} 92317/{NS}/{NINDS} {NIH} {HHS}/N01 {NS} 92319/{NS}/{NINDS} {NIH} {HHS}/N01 {NS} 92320/{NS}/{NINDS} {NIH} {HHS}/P41 {RR} 14075/{RR}/{NCRR} {NIH} {HHS}/R01 {EB} 001550/{EB}/{NIBIB} {NIH} {HHS}/R01 {RR} 16594-01A1/{RR}/{NCRR} {NIH} {HHS}/U24 {RR} 021382/{RR}/{NCRR} {NIH} {HHS}/Multicenter {StudyResearch} Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov't2007/03/24 09:00Int J Radiat Oncol Biol Phys. 2007 Jul 15;68(4):992-8. Epub 2007 Mar 26.}
}

@article{lazar_meditation_2005,
	title = {Meditation experience is associated with increased cortical thickness},
	volume = {16},
	issn = {0959-4965 (Print) 0959-4965 (Linking)},
	shorttitle = {Meditation experience is associated with increased cortical thickness},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1361002/},
	abstract = {Previous research indicates that long-term meditation practice is associated with altered resting electroencephalogram patterns, suggestive of long lasting changes in brain activity. We hypothesized that meditation practice might also be associated with changes in the brain's physical structure. Magnetic resonance imaging was used to assess cortical thickness in 20 participants with extensive Insight meditation experience, which involves focused attention to internal experiences. Brain regions associated with attention, interoception and sensory processing were thicker in meditation participants than matched controls, including the prefrontal cortex and right anterior insula. Between-group differences in prefrontal cortical thickness were most pronounced in older participants, suggesting that meditation might offset age-related cortical thinning. Finally, the thickness of two regions correlated with meditation experience. These data provide the first structural evidence for experience-dependent cortical plasticity associated with meditation practice.},
	number = {17},
	journal = {Neuroreport},
	author = {Lazar, S. W. and Kerr, C. E. and Wasserman, R. H. and Gray, J. R. and Greve, D. N. and Treadway, M. T. and McGarvey, M. and Quinn, B. T. and Dusek, J. A. and Benson, H. and Rauch, S. L. and Moore, C. I. and Fischl, B.},
	month = nov,
	year = {2005},
	keywords = {Adult, Adult, Attention, Attention, Cognition, Cognition, Female, Female, Humans, Humans, Magnetic Resonance Imaging, Magnetic Resonance Imaging, Male, Male, Meditation, *Meditation, *Neuronal Plasticity, Neuronal Plasticity, Prefrontal Cortex, Prefrontal Cortex/*anatomy \& histology},
	pages = {1893--7},
	annote = {Lazar, Sara {WKerr}, Catherine {EWasserman}, Rachel {HGray}, Jeremy {RGreve}, Douglas {NTreadway}, Michael {TMcGarvey}, {MettaQuinn}, Brian {TDusek}, Jeffery {ABenson}, {HerbertRauch}, Scott {LMoore}, Christopher {IFischl}, {BruceengH}75/{CCH} 123424/{CC}/{ODCDC} {CDC} {HHS}/H75/{CCH}119124/{CC}/{ODCDC} {CDC} {HHS}/K01 {AT}000694-01/{AT}/{NCCAM} {NIH} {HHS}/K01 {AT}000694-02/{AT}/{NCCAM} {NIH} {HHS}/K01 {AT}000694-03/{AT}/{NCCAM} {NIH} {HHS}/K01 {AT}000694-04/{AT}/{NCCAM} {NIH} {HHS}/K01 {AT}000694-05/{AT}/{NCCAM} {NIH} {HHS}/K01AT00694-01/{AT}/{NCCAM} {NIH} {HHS}/P41RR14075/{RR}/{NCRR} {NIH} {HHS}/R21AT002860-02/{AT}/{NCCAM} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, U.S. Gov't, P.H.S.England2005/11/08 09:00Neuroreport. 2005 Nov 28;16(17):1893-7.},
	file = {Lazar-2005-Meditation experience is associated:/autofs/cluster/freesurfer/zotero/storage/BXCS8473/Lazar-2005-Meditation experience is associated.pdf:application/pdf}
}

@article{duering_incident_2012,
	title = {Incident subcortical infarcts induce focal thinning in connected cortical regions},
	volume = {79},
	issn = {1526-632X},
	doi = {10.1212/WNL.0b013e3182749f39},
	abstract = {{OBJECTIVE}: Brain atrophy is common in subcortical ischemic vascular disease, but the underlying mechanisms are poorly understood. We set out to examine the effects of incident subcortical infarcts on cortical morphology.
{METHODS}: A total of 276 subjects with cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy, an inherited small vessel disease, were enrolled in a prospective study. Incident subcortical infarcts were identified on follow-up magnetic resonance scans after 18, 36, and 54 months using difference images. Probabilistic fiber tracking and cortical thickness measurements were applied to study the longitudinal relationship between incident infarcts and connected cortical areas. Cortical thickness was assessed before and after infarction using {FreeSurfer} software. Focal cortical thinning was defined as change of cortical thickness in the connected region of interest exceeding the global change of cortical thickness.
{RESULTS}: Nine subjects had a single incident infarct during the follow-up and were suitable for analysis. There was a strong correlation between the probability of connectivity and mean focal cortical thinning (p = 0.0039). In all subjects, there was focal cortical thinning in cortical regions with high probability of connectivity with the incident infarct. This pattern was not observed when using control tractography seeds.
{CONCLUSIONS}: Our findings provide in vivo evidence for secondary cortical neurodegeneration after subcortical ischemia as a mechanism for brain atrophy in cerebrovascular disease.},
	language = {eng},
	number = {20},
	journal = {Neurology},
	author = {Duering, Marco and Righart, Ruthger and Csanadi, Endy and Jouvent, Eric and Hervé, Dominique and Chabriat, Hugues and Dichgans, Martin},
	month = nov,
	year = {2012},
	pmid = {23054230},
	keywords = {Adult, {CADASIL}, Cerebral Cortex, Cerebral Infarction, Female, Follow-Up Studies, Humans, Image Processing, Computer-Assisted, Incidence, Leukoencephalopathies, Magnetic Resonance Imaging, Male, Middle Aged, Nerve Fibers, Myelinated, Oxygen, Prospective Studies, Statistics, Nonparametric, Time Factors},
	pages = {2025--2028}
}

@article{sanchez-benavides_manual_2010,
	title = {Manual validation of {FreeSurfer}'s automated hippocampal segmentation in normal aging, mild cognitive impairment, and Alzheimer Disease subjects},
	volume = {181},
	issn = {0165-1781},
	doi = {10.1016/j.pscychresns.2009.10.011},
	abstract = {Hippocampal volume is reduced in Alzheimer Disease ({AD}) and has been proposed as a possible surrogate biomarker to aid early diagnosis. Whilst automated methods to segment the hippocampus from magnetic resonance images are available, manual segmentation, in spite of being time-consuming and unsuitable for large samples, is still the standard. In order to study the validity of {FreeSurfer}'s automated method, we compared hippocampal automated measures with manual tracing in a sample composed of healthy elderly (N=41), Mild Cognitive Impairment ({MCI}) (N=23), and {AD} (N=25) subjects. Percent volume overlap, percent volume difference, correlations, and Bland-Altman plots were studied. Automated measures were slightly larger than hand tracing ones (mean difference 10\%). Percent volume overlap showed good results, but was far from perfect (78\%). Manual and automated volume correlations were approximately 0.84 and the Bland-Altman analysis showed acceptable interchangeability of methods. Within-group analysis demonstrated that patient samples obtained smaller values in validity indexes than controls. Globally, {FreeSurfer}'s automated hippocampal volumetry showed adequate validity when compared to manual tracing, with a tendency to overestimation. Nevertheless, the greater difference between automated and manual segmentation in atrophic brains suggests that studies in {AD} based on this software could be more likely to produce false negatives.},
	language = {eng},
	number = {3},
	journal = {Psychiatry Research},
	author = {Sánchez-Benavides, Gonzalo and Gómez-Ansón, Beatriz and Sainz, Aitor and Vives, Yolanda and Delfino, Manuel and Peña-Casanova, Jordi},
	month = mar,
	year = {2010},
	pmid = {20153146},
	keywords = {Aged, Aged, 80 and over, Aging, Alzheimer Disease, Analysis of Variance, Brain Mapping, Cognition Disorders, Female, fs\_Validation-Evaluations, Functional Laterality, Hippocampus, Humans, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Male, Middle Aged, Reproducibility of Results},
	pages = {219--225}
}

@article{goldman_heritability_2008,
	title = {Heritability of brain morphology related to schizophrenia: a large-scale automated magnetic resonance imaging segmentation study},
	volume = {63},
	issn = {1873-2402},
	shorttitle = {Heritability of brain morphology related to schizophrenia},
	url = {https://surfer.nmr.mgh.harvard.edu/pub/articles/Goldman-BiolPsychiatry2008.pdf},
	doi = {10.1016/j.biopsych.2007.06.006},
	abstract = {{BACKGROUND}: Schizophrenia is a devastating psychiatric disorder with a strong genetic component that has been related to a number of structural brain alterations. Currently available data on the heritability of these structural changes are inconsistent.
{METHODS}: To examine heritability of morphological alterations in a large sample, we used a novel and validated fully-automated whole brain segmentation technique to study disease-related variability and heritability in anatomically defined regions of interest in 221 healthy control subjects, 169 patients with schizophrenia, and 183 unaffected siblings.
{RESULTS}: Compared with healthy control subjects, patients showed a bilateral decrease in hippocampal and cortical gray matter volume and increases in bilateral dorsal striatum and right lateral ventricle. No significant volumetric differences were found in unaffected siblings compared with normal control subjects in any structure. Post hoc analysis of the dorsal striatum showed the volumetric increase to be widespread, including caudate, putamen, and globus pallidus. With Risch's lambda (lambda(s)), we found strong evidence for heritability of reduced cortical volume and moderate evidence for hippocampal volume, whereas abnormal striatal and ventricle volumes showed no sign of heritability. Additional exploratory analyses were performed on amygdala, thalamus, nucleus accumbens, ventral diencephalon, and cerebral and cerebellar cortex and white matter. Of these regions, patients showed increased volume in ventral diencephalon and cerebellum.
{CONCLUSIONS}: These findings support evidence of genetic control of brain volume even in adults, particularly of hippocampal and neocortical volume and of cortical volumetric reductions being familial, but do not support measures of subcortical volumes per se as representing intermediate biologic phenotypes.},
	language = {eng},
	number = {5},
	journal = {Biological Psychiatry},
	author = {Goldman, Aaron L. and Pezawas, Lukas and Mattay, Venkata S. and Fischl, Bruce and Verchinski, Beth A. and Zoltick, Brad and Weinberger, Daniel R. and Meyer-Lindenberg, Andreas},
	month = mar,
	year = {2008},
	pmid = {17727823},
	keywords = {Adolescent, Adult, Bipolar Disorder, Brain, Cerebral Cortex, Comorbidity, Depressive Disorder, Major, Dominance, Cerebral, Female, Hippocampus, Humans, Image Processing, Computer-Assisted, Imaging, Three-Dimensional, Male, Mental Disorders, Middle Aged, Psychiatric Status Rating Scales, Psychotic Disorders, Reference Values, Schizophrenia, Schizotypal Personality Disorder, Siblings, Software},
	pages = {475--483}
}

@article{desikan_selective_2010,
	title = {Selective Disruption of the Cerebral Neocortex in Alzheimer's Disease},
	volume = {5},
	issn = {1932-6203},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2944799/},
	doi = {10.1371/journal.pone.0012853},
	abstract = {Background
Alzheimer's disease ({AD}) and its transitional state mild cognitive impairment ({MCI}) are characterized by amyloid plaque and tau neurofibrillary tangle ({NFT}) deposition within the cerebral neocortex and neuronal loss within the hippocampal formation. However, the precise relationship between pathologic changes in neocortical regions and hippocampal atrophy is largely unknown.

Methodology/Principal Findings
In this study, combining structural {MRI} scans and automated image analysis tools with reduced cerebrospinal fluid ({CSF}) Aß levels, a surrogate for intra-cranial amyloid plaques and elevated {CSF} phosphorylated tau (p-tau) levels, a surrogate for neocortical {NFTs}, we examined the relationship between the presence of Alzheimer's pathology, gray matter thickness of select neocortical regions, and hippocampal volume in cognitively normal older participants and individuals with {MCI} and {AD} (n = 724). Amongst all 3 groups, only select heteromodal cortical regions significantly correlated with hippocampal volume. Amongst {MCI} and {AD} individuals, gray matter thickness of the entorhinal cortex and inferior temporal gyrus significantly predicted longitudinal hippocampal volume loss in both amyloid positive and p-tau positive individuals. Amongst cognitively normal older adults, thinning only within the medial portion of the orbital frontal cortex significantly differentiated amyloid positive from amyloid negative individuals whereas thinning only within the entorhinal cortex significantly discriminated p-tau positive from p-tau negative individuals.

Conclusions/Significance
Cortical Aβ and tau pathology affects gray matter thinning within select neocortical regions and potentially contributes to downstream hippocampal degeneration. Neocortical Alzheimer's pathology is evident even amongst older asymptomatic individuals suggesting the existence of a preclinical phase of dementia.},
	number = {9},
	urldate = {2014-08-25},
	journal = {{PLoS} {ONE}},
	author = {Desikan, Rahul S. and Sabuncu, Mert R. and Schmansky, Nicholas J. and Reuter, Martin and Cabral, Howard J. and Hess, Christopher P. and Weiner, Michael W. and Biffi, Alessandro and Anderson, Christopher D. and Rosand, Jonathan and Salat, David H. and Kemper, Thomas L. and Dale, Anders M. and Sperling, Reisa A. and Fischl, Bruce},
	month = sep,
	year = {2010},
	pmid = {20886094},
	pmcid = {PMC2944799},
	keywords = {Aged, Aged, 80 and over, Alzheimer Disease/cerebrospinal fluid/*metabolism/*pathology/radiography, Amyloid beta-Peptides/cerebrospinal fluid/metabolism, Female, Hippocampus/metabolism/pathology/radiography, Humans, Magnetic Resonance Imaging, Male, Neocortex/*metabolism/*pathology/radiography, tau Proteins/cerebrospinal fluid/metabolism},
	annote = {Desikan, Rahul {SSabuncu}, Mert {RSchmansky}, Nicholas {JReuter}, {MartinCabral}, Howard {JHess}, Christopher {PWeiner}, Michael {WBiffi}, {AlessandroAnderson}, Christopher {DRosand}, {JonathanSalat}, David {HKemper}, Thomas {LDale}, Anders {MSperling}, Reisa {AFischl}, {BruceengAG}021910/{AG}/{NIA} {NIH} {HHS}/{AG}02238/{AG}/{NIA} {NIH} {HHS}/K01 {AG}030514/{AG}/{NIA} {NIH} {HHS}/P01 {AG}03991/{AG}/{NIA} {NIH} {HHS}/P30 {AG}010129/{AG}/{NIA} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/P50 {AG}05681/{AG}/{NIA} {NIH} {HHS}/R01 {EB}001550/{EB}/{NIBIB} {NIH} {HHS}/R01 {NS}052585-01/{NS}/{NINDS} {NIH} {HHS}/R01 {RR} 16594-01A1/{RR}/{NCRR} {NIH} {HHS}/R01EB006758/{EB}/{NIBIB} {NIH} {HHS}/U01 {AG}024904/{AG}/{NIA} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov'{tResearch} Support, U.S. Gov't, P.H.S.2010/10/05 06:00PLoS One. 2010 Sep 23;5(9):e12853. doi: 10.1371/journal.pone.0012853.},
	file = {Desikan-2010-Selective disruption of the cereb:/autofs/cluster/freesurfer/zotero/storage/8H5TKIVP/Desikan-2010-Selective disruption of the cereb.pdf:application/pdf;PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/HDZVVEKT/Desikan et al. - 2010 - Selective Disruption of the Cerebral Neocortex in .pdf:application/pdf}
}

@article{cohen-adad_vivo_2011,
	title = {In vivo evidence of disseminated subpial T2* signal changes in multiple sclerosis at 7 T: a surface-based analysis},
	volume = {57},
	issn = {1095-9572 (Electronic) 1053-8119 (Linking)},
	shorttitle = {In vivo evidence of disseminated subpial T2* signal changes in multiple sclerosis at 7 T: a surface-based analysis},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/21511042},
	doi = {10.1016/j.neuroimage.2011.04.009},
	abstract = {Cortical subpial demyelination is frequent in multiple sclerosis ({MS}) and is closely associated with disease progression and poor neurological outcome. Although cortical lesions have been difficult to detect using conventional {MRI}, preliminary data using T2*-weighted imaging at ultra-high field 7T {MRI} showed improved sensitivity for detecting and categorizing different histological types of cortical {MS} lesions. In this study we combined high-resolution 7T {MRI} with a surface-based analysis technique to quantify and map subpial T2*-weighted signal changes in seventeen patients with {MS}. We applied a robust method to register 7T data with the reconstructed cortical surface of each individual and used a general linear model to assess in vivo an increase in subpial T2*-weighted signal in patients versus age-matched controls, and to investigate the spatial distribution of cortical subpial changes across the cortical ribbon. We also assessed the relationship between subpial T2* signal changes at 7T, Expanded Disability Status Scale ({EDSS}) score and white matter lesion load ({WMLL}). Patients with {MS} showed significant T2*-weighted signal increase in the frontal lobes (parsopercularis, precentral gyrus, middle and superior frontal gyrus, orbitofrontal cortex), anterior cingulate, temporal (superior, middle and inferior temporal gyri), and parietal cortices (superior and inferior parietal cortex, precuneus), but also in occipital regions of the left hemisphere. We found significant correlations between subpial T2*-weighted signal and {EDSS} score in the precentral gyrus (rho=0.56, P=0.02) and between T2*-weighted signal and {WMLL} in the lateral orbitofrontal, superior parietal, cuneus, precentral and superior frontal regions. Our data support the presence of disseminated subpial increases in T2* signal in subjects with {MS}, which may reflect the diffuse subpial pathology described in neuropathology.},
	number = {1},
	journal = {Neuroimage},
	author = {Cohen-Adad, J. and Benner, T. and Greve, D. and Kinkel, R. P. and Radding, A. and Fischl, B. and Rosen, B. R. and Mainero, C.},
	month = jul,
	year = {2011},
	keywords = {Adult, Brain Mapping/*methods, Brain/*pathology, Female, Humans, Image Interpretation, Computer-Assisted/*methods, Magnetic Resonance Imaging/*methods, Male, Multiple Sclerosis/*pathology},
	pages = {55--62},
	annote = {Cohen-Adad, {JBenner}, {TGreve}, {DKinkel}, R {PRadding}, {AFischl}, {BRosen}, B {RMainero}, {CengAG}022381/{AG}/{NIA} {NIH} {HHS}/P41 {RR}014075/{RR}/{NCRR} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 {AG}022381/{AG}/{NIA} {NIH} {HHS}/R01 {EB}006758/{EB}/{NIBIB} {NIH} {HHS}/R01 {NS}052585/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}052585-01/{NS}/{NINDS} {NIH} {HHS}/R01EB006758/{EB}/{NIBIB} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/U54 {EB}005149/{EB}/{NIBIB} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov't2011/04/23 06:00Neuroimage. 2011 Jul 1;57(1):55-62. doi: 10.1016/j.neuroimage.2011.04.009. Epub 2011 Apr 13.},
	file = {Cohen-Adad-2011-In vivo evidence of disseminat:/autofs/cluster/freesurfer/zotero/storage/P7MG84S4/Cohen-Adad-2011-In vivo evidence of disseminat.pdf:application/pdf}
}

@inproceedings{reuter_registration_2012,
	title = {Registration of Histology and {MRI} using Blockface as Intermediate Space},
	shorttitle = {Registration of Histology and {MRI} using Blockface as Intermediate Space},
	author = {Reuter, Martin and Sand, Peter and Huber, Kristen and Nguyen, Khoa and Saygin, Zeynep and Rosas, H. Diana and Augustinack, Jean and Fischl, Bruce},
	year = {2012}
}

@article{hartley_brain_2011,
	title = {Brain structure correlates of individual differences in the acquisition and inhibition of conditioned fear},
	volume = {21},
	issn = {1460-2199 (Electronic) 1047-3211 (Linking)},
	shorttitle = {Brain structure correlates of individual differences in the acquisition and inhibition of conditioned fear},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/21263037},
	doi = {10.1093/cercor/bhq253},
	abstract = {Research employing aversive conditioning paradigms has elucidated the neurocircuitry involved in acquiring and diminishing fear responses. However, the factors underlying individual differences in fear acquisition and inhibition are not presently well understood. In this study, we explored whether the magnitude of individuals' acquired fear responses and the modulation of these responses via 2 fear reduction methods were correlated with structural differences in brain regions involved in affective processing. Physiological and structural magnetic resonance imaging data were obtained from experiments exploring extinction retention and intentional cognitive regulation. Our results identified 2 regions in which individual variation in brain structure correlated with subjects' fear-related arousal. Confirming previous results, increased thickness in ventromedial prefrontal cortex was correlated with the degree of extinction retention. Additionally, subjects with greater thickness in the posterior insula exhibited larger conditioned responses during acquisition. The data suggest a trend toward a negative correlation between amygdala volume and fear acquisition magnitude. There was no significant correlation between fear reduction via cognitive regulation and thickness in our prefrontal regions of interest. Acquisition and regulation measures were uncorrelated, suggesting that while certain individuals may have a propensity toward increased expression of conditioned fear, these responses can be diminished via both extinction and cognitive regulation.},
	number = {9},
	journal = {Cereb Cortex},
	author = {Hartley, C. A. and Fischl, B. and Phelps, E. A.},
	month = sep,
	year = {2011},
	keywords = {Adolescent, Adult, Brain Mapping, Brain/*physiology, Cerebral Cortex/anatomy \& histology/physiology, Cluster Analysis, Cognition/physiology, Conditioning (Psychology)/*physiology, Electroshock, Extinction, Psychological, Fear/*psychology, Female, Humans, Image Processing, Computer-Assisted, *Individuality, Magnetic Resonance Imaging, Male, Photic Stimulation, Young Adult},
	pages = {1954--62},
	annote = {Hartley, Catherine {AFischl}, {BrucePhelps}, Elizabeth {AengAG}02238/{AG}/{NIA} {NIH} {HHS}/{MH}072279/{MH}/{NIMH} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/R01 {RR}16594-01A1/{RR}/{NCRR} {NIH} {HHS}/R01EB001550/{EB}/{NIBIB} {NIH} {HHS}/R01EB006758/{EB}/{NIBIB} {NIH} {HHS}/R01NS052585-01/{NS}/{NINDS} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/U54 {EB}005149/{EB}/{NIBIB} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov'{tResearch} Support, U.S. Gov't, Non-P.H.S.New York, N.Y. : 19912011/01/26 06:00Cereb Cortex. 2011 Sep;21(9):1954-62. doi: 10.1093/cercor/bhq253. Epub 2011 Jan 24.},
	file = {Hartley-2011-Brain structure correlates of ind:/autofs/cluster/freesurfer/zotero/storage/P2C55RBQ/Hartley-2011-Brain structure correlates of ind.pdf:application/pdf}
}

@article{salat_thinning_2004,
	title = {Thinning of the cerebral cortex in aging},
	volume = {14},
	issn = {1047-3211 (Print) 1047-3211 (Linking)},
	shorttitle = {Thinning of the cerebral cortex in aging},
	url = {http://cercor.oxfordjournals.org/content/14/7/721.full.pdf},
	doi = {10.1093/cercor/bhh032},
	abstract = {The thickness of the cerebral cortex was measured in 106 non-demented participants ranging in age from 18 to 93 years. For each participant, multiple acquisitions of structural T1-weighted magnetic resonance imaging ({MRI}) scans were averaged to yield high-resolution, high-contrast data sets. Cortical thickness was estimated as the distance between the gray/white boundary and the outer cortical surface, resulting in a continuous estimate across the cortical mantle. Global thinning was apparent by middle age. Men and women showed a similar degree of global thinning, and did not differ in mean thickness in the younger or older groups. Age-associated differences were widespread but demonstrated a patchwork of regional atrophy and sparing. Examination of subsets of the data from independent samples produced highly similar age-associated patterns of atrophy, suggesting that the specific anatomic patterns within the maps were reliable. Certain results, including prominent atrophy of prefrontal cortex and relative sparing of temporal and parahippocampal cortex, converged with previous findings. Other results were unexpected, such as the finding of prominent atrophy in frontal cortex near primary motor cortex and calcarine cortex near primary visual cortex. These findings demonstrate that cortical thinning occurs by middle age and spans widespread cortical regions that include primary as well as association cortex.},
	language = {eng},
	number = {7},
	journal = {Cereb Cortex},
	author = {Salat, D. H. and Buckner, R. L. and Snyder, A. Z. and Greve, D. N. and Desikan, R. S. and Busa, E. and Morris, J. C. and Dale, A. M. and Fischl, B.},
	month = jul,
	year = {2004},
	keywords = {Adolescent, Adolescent, Adult, Adult, Aged, Aged, Aged, 80 and over, Aged, 80 and over, Aging, Aging/*physiology, Atrophy, Atrophy/pathology, Brain Mapping, Brain Mapping, Cerebral Cortex, Cerebral Cortex/anatomy \& histology/*growth \& development, Female, Female, Humans, Humans, Image Processing, Computer-Assisted, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Magnetic Resonance Imaging, Male, Male, Middle Aged, Middle Aged, Sex Characteristics, Sex Characteristics},
	pages = {721--30},
	annote = {Salat, David {HBuckner}, Randy {LSnyder}, Abraham {ZGreve}, Douglas {NDesikan}, Rahul S {RBusa}, {EvelinaMorris}, John {CDale}, Anders {MFischl}, {BruceengAG}03991/{AG}/{NIA} {NIH} {HHS}/{AG}05681/{AG}/{NIA} {NIH} {HHS}/{AG}05886/{AG}/{NIA} {NIH} {HHS}/{NS}39581/{NS}/{NINDS} {NIH} {HHS}/P41RR14075/{RR}/{NCRR} {NIH} {HHS}/{RR}14075/{RR}/{NCRR} {NIH} {HHS}/Clinical {TrialComparative} {StudyResearch} Support, Non-U.S. Gov'{tResearch} Support, U.S. Gov't, P.H.S.New York, N.Y. : 19912004/04/01 05:00Cereb Cortex. 2004 Jul;14(7):721-30. Epub 2004 Mar 28.},
	file = {Salat-2004-Thinning of the cerebral cortex in:/autofs/cluster/freesurfer/zotero/storage/6R7JFB9R/Salat-2004-Thinning of the cerebral cortex in.pdf:application/pdf}
}

@article{bischoff-grethe_technique_2007,
	title = {A technique for the deidentification of structural brain {MR} images},
	volume = {28},
	issn = {1065-9471 (Print) 1065-9471 (Linking)},
	shorttitle = {A technique for the deidentification of structural brain {MR} images},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/17295313},
	doi = {10.1002/hbm.20312},
	abstract = {Due to the increasing need for subject privacy, the ability to deidentify structural {MR} images so that they do not provide full facial detail is desirable. A program was developed that uses models of nonbrain structures for removing potentially identifying facial features. When a novel image is presented, the optimal linear transform is computed for the input volume (Fischl et al. [2002]: Neuron 33:341-355; Fischl et al. [2004]: Neuroimage 23 (Suppl 1):S69-S84). A brain mask is constructed by forming the union of all voxels with nonzero probability of being brain and then morphologically dilated. All voxels outside the mask with a nonzero probability of being a facial feature are set to 0. The algorithm was applied to 342 datasets that included two different T1-weighted pulse sequences and four different diagnoses (depressed, Alzheimer's, and elderly and young control groups). Visual inspection showed none had brain tissue removed. In a detailed analysis of the impact of defacing on skull-stripping, 16 datasets were bias corrected with N3 (Sled et al. [1998]: {IEEE} Trans Med Imaging 17:87-97), defaced, and then skull-stripped using either a hybrid watershed algorithm (Segonne et al. [2004]: Neuroimage 22:1060-1075, in {FreeSurfer}) or Brain Surface Extractor (Sandor and Leahy [1997]: {IEEE} Trans Med Imaging 16:41-54; Shattuck et al. [2001]: Neuroimage 13:856-876); defacing did not appreciably influence the outcome of skull-stripping. Results suggested that the automatic defacing algorithm is robust, efficiently removes nonbrain tissue, and does not unduly influence the outcome of the processing methods utilized; in some cases, skull-stripping was improved. Analyses support this algorithm as a viable method to allow data sharing with minimal data alteration within large-scale multisite projects.},
	language = {eng},
	number = {9},
	journal = {Hum Brain Mapp},
	author = {Bischoff-Grethe, A. and Ozyurt, I. B. and Busa, E. and Quinn, B. T. and Fennema-Notestine, C. and Clark, C. P. and Morris, S. and Bondi, M. W. and Jernigan, T. L. and Dale, A. M. and Brown, G. G. and Fischl, B.},
	month = sep,
	year = {2007},
	keywords = {Adult, Aged, Aging/physiology, Algorithms, Alzheimer Disease/pathology, Brain/*anatomy \& histology, Data Interpretation, Statistical, Depression/pathology, Female, fs\_Misc-methodology, Humans, Image Processing, Computer-Assisted/*methods, Magnetic Resonance Imaging/*methods, Male, Middle Aged, Skull/anatomy \& histology},
	pages = {892--903},
	annote = {Bischoff-Grethe, {AmandaOzyurt}, I {BurakBusa}, {EvelinaQuinn}, Brian {TFennema}-Notestine, {ChristineClark}, Camellia {PMorris}, {ShaunnaBondi}, Mark {WJernigan}, Terry {LDale}, Anders {MBrown}, Gregory {GFischl}, Bruceeng5K01DA015499/{DA}/{NIDA} {NIH} {HHS}/5K08MH01642/{MH}/{NIMH} {NIH} {HHS}/{AG}04085/{AG}/{NIA} {NIH} {HHS}/{AG}12674/{AG}/{NIA} {NIH} {HHS}/K08 {MH}001642-05/{MH}/{NIMH} {NIH} {HHS}/M01 {RR}000827-328412/{RR}/{NCRR} {NIH} {HHS}/M01RR00827/{RR}/{NCRR} {NIH} {HHS}/{MH}45294/{MH}/{NIMH} {NIH} {HHS}/P41-{RR}14075/{RR}/{NCRR} {NIH} {HHS}/P50 {AG}05131/{AG}/{NIA} {NIH} {HHS}/R01 {AG}006849/{AG}/{NIA} {NIH} {HHS}/R01 {RR}16594-01A1/{RR}/{NCRR} {NIH} {HHS}/R01MH42575/{MH}/{NIMH} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, Non-U.S. Gov'{tResearch} Support, U.S. Gov't, Non-P.H.S.2007/02/14 09:00Hum Brain Mapp. 2007 Sep;28(9):892-903.},
	file = {Bischoff-Grethe-2007-A technique for the deide:/autofs/cluster/freesurfer/zotero/storage/P9MR9KGS/Bischoff-Grethe-2007-A technique for the deide.pdf:application/pdf}
}

@article{woodward_smaller_2009,
	title = {Smaller global and regional cortical volume in combat-related posttraumatic stress disorder},
	volume = {66},
	issn = {1538-3636},
	doi = {10.1001/archgenpsychiatry.2009.160},
	abstract = {{CONTEXT}: Two sets of findings predict smaller cerebral cortical gray matter volume in adult posttraumatic stress disorder ({PTSD}). Measures of intracranial tissue volume and cerebral tissue volume have been observed to be smaller in adolescents with maltreatment-related {PTSD}. Second, lower intelligence, a risk factor for {PTSD}, is associated with smaller cerebral tissue volumes. Nevertheless, to our knowledge, only 1 study has observed globally smaller cerebral tissue volume in adults with {PTSD}.
{OBJECTIVES}: To apply a recently developed method providing improved estimates of cortical volume and to estimate associations between adult {PTSD} and selected regional cortical volumes not yet investigated.
{DESIGN}: Between-group comparison of global and regional cerebral cortical volumes in adult patients with combat-related {PTSD} and controls.
{SETTING}: Two Department of Veterans Affairs medical centers with large inpatient and outpatient {PTSD} catchments.
{PARTICIPANTS}: Ninety-seven combat-exposed veterans of the Vietnam and Persian Gulf wars.
{MAIN} {OUTCOME} {MEASURE}: Global and regional cortical volumes determined using the {FreeSurfer} software program and the Desikan et al parcellation (modified).
{RESULTS}: Cerebral cortical volume, thickness, and area were observed to be smaller in association with adult combat-related {PTSD}. Robust associations were observed between {PTSD} and smaller cortical volumes in the parahippocampal gyrus, superior temporal cortex, lateral orbital frontal cortex, and pars orbitalis of the inferior frontal gyrus.
{CONCLUSIONS}: Cerebral cortical volume, thickness, and area may be smaller in adult chronic severe {PTSD}; however, the extracted structural variables did not mediate relations between intelligence and {PTSD}. The 4 regions exhibiting especially smaller cortical volumes in this sample share involvement in mechanisms subserving "top-down" facilitation of the identification of objects and words. Compromise of these regions may result in difficulty in relearning pretrauma schemata for interpreting the civilian physical and social environments.},
	language = {eng},
	number = {12},
	journal = {Archives of General Psychiatry},
	author = {Woodward, Steven H. and Schaer, Marie and Kaloupek, Danny G. and Cediel, Lucia and Eliez, Stephan},
	month = dec,
	year = {2009},
	pmid = {19996042},
	keywords = {Adult, Age Factors, Atrophy, Brain, Cerebral Cortex, Cohort Studies, Combat Disorders, Frontal Lobe, Humans, Iraq War, 2003-2011, Magnetic Resonance Imaging, Middle Aged, Parahippocampal Gyrus, Personality Inventory, Stress Disorders, Post-Traumatic, Temporal Lobe, Veterans, Vietnam Conflict, Wechsler Scales},
	pages = {1373--1382}
}

@article{kahler_candidate_2011,
	title = {Candidate gene analysis of the human natural killer-1 carbohydrate pathway and perineuronal nets in schizophrenia: B3GAT2 is associated with disease risk and cortical surface area},
	volume = {69},
	issn = {1873-2402},
	shorttitle = {Candidate gene analysis of the human natural killer-1 carbohydrate pathway and perineuronal nets in schizophrenia},
	doi = {10.1016/j.biopsych.2010.07.035},
	abstract = {{BACKGROUND}: The Human Natural Killer-1 carbohydrate ({HNK}-1) is involved in neurodevelopment and synaptic plasticity. Extracellular matrix structures called perineuronal nets, condensed around subsets of neurons and proximal dendrites during brain maturation, regulate synaptic transmission and plasticity.
{METHODS}: Ten genes of importance for {HNK}-1 biosynthesis (B3GAT1, B3GAT2, and {CHST}10) or for the formation of perineuronal nets ({TNR}, {BCAN}, {NCAN}, {HAPLN}1, {HAPLN}2, {HAPLN}3, and {HAPLN}4) were investigated for potential involvement in schizophrenia ({SCZ}) susceptibility, by genotyping 104 {tagSNPs} in the Scandinavian Collaboration on Psychiatric Etiology sample (849 cases; 1602 control subjects). Genome-wide association study imputation data from the European {SGENE}-plus sample (2663 cases; 13,498 control subjects) were used for comparison. The effect of {SCZ} risk alleles on brain structure was investigated in a Norwegian subset (98 cases; 177 control subjects) with structural magnetic resonance imaging data.
{RESULTS}: Five single nucleotide polymorphisms ({SNPs}), located in two adjacent estimated linkage disequilibrium blocks in the first intron of β-1,3-glucuronyltransferase 2 (B3GAT2), were nominally associated with {SCZ} (.004 ≤ P(empirical) ≤ .05). The rs2460691 was significantly associated in the comparison sample and in the meta-analysis after correction for all 121 {SNP}/haplotype tests (P(raw) = 1 × 10(-4); P(corrected) = .018). Increased dosage of the rs2460691 {SCZ} risk allele was associated with decreased cortical area (p = .002) but not thickness or hippocampal volume. A second {SNP} (r(2) = .24 with rs10945275), which conferred the highest {SCZ} risk effect in the Norwegian subset, was also associated with cortical area.
{CONCLUSIONS}: The present results suggest that effects on biosynthesis of the neuronal epitope {HNK}-1, through common B3GAT2 variation, could increase the risk of {SCZ}, possibly by decreasing cortical area.},
	language = {eng},
	number = {1},
	journal = {Biological Psychiatry},
	author = {Kähler, Anna K. and Djurovic, Srdjan and Rimol, Lars M. and Brown, Andrew Anand and Athanasiu, Lavinia and Jönsson, Erik G. and Hansen, Thomas and Gústafsson, Omar and Hall, Håkan and Giegling, Ina and Muglia, Pierandrea and Cichon, Sven and Rietschel, Marcella and Pietiläinen, Olli P. H. and Peltonen, Leena and Bramon, Elvira and Collier, David and St Clair, David and Sigurdsson, Engilbert and Petursson, Hannes and Rujescu, Dan and Melle, Ingrid and Werge, Thomas and Steen, Vidar M. and Dale, Anders M. and Matthews, Russell T. and Agartz, Ingrid and Andreassen, Ole A.},
	month = jan,
	year = {2011},
	pmid = {20950796},
	keywords = {Alleles, Antigens, {CD}57, Atrophy, Case-Control Studies, Cerebral Cortex, Extracellular Matrix Proteins, Genetic Predisposition to Disease, Genome-Wide Association Study, Genotype, Glucuronosyltransferase, Hippocampus, Humans, Linkage Disequilibrium, Nerve Tissue Proteins, Neurons, Polymorphism, Single Nucleotide, Signal Transduction},
	pages = {90--96}
}

@article{messina_patterns_2011,
	title = {Patterns of brain atrophy in Parkinson's disease, progressive supranuclear palsy and multiple system atrophy},
	volume = {17},
	issn = {1873-5126},
	url = {https://surfer.nmr.mgh.harvard.edu/pub/articles/Parkinsonisms_and_Related_Disorders_2011.pdf},
	doi = {10.1016/j.parkreldis.2010.12.010},
	abstract = {{BACKGROUND} {AND} {PURPOSE}: Quantitative analysis of brain atrophy may be useful in differentiating Parkinson's Disease ({PD}) from Progressive Supranuclear Palsy ({PSP}) and parkinsonian variant of Multiple System Atrophy ({MSA}-P); the aim of this study was to identify the volumetric differences of subcortical structures in patients with {PD}, {PSP} and {MSA}-P using a novel and validated fully-automated whole brain segmentation method.
{METHODS}: Volumetric {MRIs} were obtained in 72 patients with {PD}, 32 patients with {PSP}, 15 patients with {MSA}-P, and in 46 control subjects. Subcortical volume was measured automatically by {FreeSurfer}. Multivariate analysis of covariance, adjusted for intracranial volume ({ICV}), sex and age, was used to explore group differences.
{RESULTS}: No volumetric differences were found between {PD} and controls group; otherwise the volumes of the cerebellum, the thalamus, the putamen, the pallidum, the hippocampus, and the brainstem were significantly reduced in {PSP} and {MSA}-P compared to patients with {PD} and control subjects. {PSP} and {MSA}-P patients only differed in thalamus volume which was smaller in {PSP} group (p {\textless} 0.001). Moreover, patients with {PSP} and {MSA}-P showed a ventricular system (including lateral, third and fourth ventricles) larger than that detected in {PD} and controls (p {\textless} 0.001).
{CONCLUSIONS}: Volumetric data obtained with automated segmentation of cerebral regions show a significant atrophy of different brain structures in parkinsonisms rather than in {PD}. Our study also demonstrates that the atrophy of the thalamus only occurs in {PSP} while the enlargement of the whole ventricular system characterizes both {PSP} and {MSA}-P.},
	language = {eng},
	number = {3},
	journal = {Parkinsonism \& Related Disorders},
	author = {Messina, Demetrio and Cerasa, Antonio and Condino, Francesca and Arabia, Gennarina and Novellino, Fabiana and Nicoletti, Giuseppe and Salsone, Maria and Morelli, Maurizio and Lanza, Pier Luigi and Quattrone, Aldo},
	month = mar,
	year = {2011},
	pmid = {21236720},
	keywords = {Aged, Aged, Atrophy, Atrophy/etiology, Brain, Brain Mapping, Brain Mapping, Brain/*pathology, Case-Control Studies, Case-Control Studies, Female, Female, Humans, Humans, Image Processing, Computer-Assisted, Image Processing, Computer-Assisted/methods, Magnetic Resonance Imaging, Magnetic Resonance Imaging/methods, Male, Male, Middle Aged, Middle Aged, Multiple System Atrophy, Multiple System Atrophy/complications/*pathology, Parkinson Disease, Parkinson Disease/complications/*pathology, Statistics, Nonparametric, Statistics, Nonparametric, Supranuclear Palsy, Progressive, Supranuclear Palsy, Progressive/complications/*pathology},
	pages = {172--176},
	annote = {Messina, {DemetrioCerasa}, {AntonioCondino}, {FrancescaArabia}, {GennarinaNovellino}, {FabianaNicoletti}, {GiuseppeSalsone}, {MariaMorelli}, {MaurizioLanza}, Pier {LuigiQuattrone}, {AldoengEngland}2011/01/18 06:00Parkinsonism Relat Disord. 2011 Mar;17(3):172-6. doi: 10.1016/j.parkreldis.2010.12.010. Epub 2011 Jan 13.}
}

@article{reuter_avoiding_2011,
	title = {Avoiding asymmetry-induced bias in longitudinal image processing},
	volume = {57},
	issn = {1095-9572 (Electronic) 1053-8119 (Linking)},
	shorttitle = {Avoiding asymmetry-induced bias in longitudinal image processing},
	url = {http://reuter.mit.edu/papers/reuter-bias11.pdf},
	doi = {10.1016/j.neuroimage.2011.02.076},
	abstract = {Longitudinal image processing procedures frequently transfer or pool information across time within subject, with the dual goals of reducing the variability and increasing the accuracy of the derived measures. In this note, we discuss common difficulties in longitudinal image processing, focusing on the introduction of bias, and describe the approaches we have taken to avoid them in the {FreeSurfer} longitudinal processing stream.},
	number = {1},
	journal = {Neuroimage},
	author = {Reuter, M. and Fischl, B.},
	month = jul,
	year = {2011},
	keywords = {*Bias (Epidemiology), fs\_Longitudinal-processing, Humans, Image Interpretation, Computer-Assisted/*methods, longitudinal processing, Longitudinal Studies/*methods},
	pages = {19--21},
	annote = {Reuter, {MartinFischl}, {BruceengP}01 {NS}058793-05/{NS}/{NINDS} {NIH} {HHS}/P41 {RR}014075/{RR}/{NCRR} {NIH} {HHS}/P41 {RR}014075-09/{RR}/{NCRR} {NIH} {HHS}/R01 {AG}022381/{AG}/{NIA} {NIH} {HHS}/R01 {AG}022381-10/{AG}/{NIA} {NIH} {HHS}/R01 {EB}006758-04/{EB}/{NIBIB} {NIH} {HHS}/R01 {NS}042861/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}042861-09/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}052585-05/{NS}/{NINDS} {NIH} {HHS}/R01 {NS}070963-02/{NS}/{NINDS} {NIH} {HHS}/R21 {NS}072652-02/{NS}/{NINDS} {NIH} {HHS}/{RC}1 {AT}005728-02/{AT}/{NCCAM} {NIH} {HHS}/S10 {RR}019307-01/{RR}/{NCRR} {NIH} {HHS}/S10 {RR}023043-01/{RR}/{NCRR} {NIH} {HHS}/S10 {RR}023401-01A2/{RR}/{NCRR} {NIH} {HHS}/U01 {MH}093765/{MH}/{NIMH} {NIH} {HHS}/U01 {MH}093765-03/{MH}/{NIMH} {NIH} {HHS}/U24 {RR}021382/{RR}/{NCRR} {NIH} {HHS}/U24 {RR}021382-05/{RR}/{NCRR} {NIH} {HHS}/2011/03/08 06:00Neuroimage. 2011 Jul 1;57(1):19-21. doi: 10.1016/j.neuroimage.2011.02.076. Epub 2011 Mar 3.},
	file = {Reuter-2011-Avoiding asymmetry-induced bias in:/autofs/cluster/freesurfer/zotero/storage/IRVBTE6P/Reuter-2011-Avoiding asymmetry-induced bias in.pdf:application/pdf}
}

@article{righart_impact_2013,
	title = {Impact of regional cortical and subcortical changes on processing speed in cerebral small vessel disease},
	volume = {2},
	issn = {2213-1582},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3777834/},
	doi = {10.1016/j.nicl.2013.06.006},
	abstract = {Slowed processing speed is common in elderly subjects and frequently related to cerebral small vessel disease. Previous studies have demonstrated associations between processing speed and subcortical ischemic lesions as well as cortical alterations but the precise functional–anatomical relationships remain poorly understood. Here we assessed the impact of both cortical and subcortical changes on processing speed by measuring regional cortical thickness and regional lesion volumes within distinct white-matter tracts. To limit confounding effects from age-related pathologies we studied patients with {CADASIL}, a genetic small vessel disease. General linear model analysis revealed significant associations between cortical thickness in the medial frontal and occipito-temporal cortex and processing speed. Bayesian network analysis showed a robust conditional dependency between the volume of lacunar lesions in the left anterior thalamic radiation and cortical thickness of the left medial frontal cortex, and between thickness of the left medial frontal cortex and processing speed, whereas there was no direct dependency between lesion volumes in the left anterior thalamic radiation and processing speed. Our results suggest that the medial frontal cortex has an intermediate position between lacunar lesions in the anterior thalamic radiation and deficits in processing speed. In contrast, we did not observe such a relationship for the occipito-temporal region. These findings reinforce the key role of frontal–subcortical circuits in cognitive impairment resulting from cerebral small vessel disease., 
          
            
              •
              Slowed processing speed is a key feature of cerebral small vessel disease.
            
            
              •
              Processing speed correlates with cortical thickness in frontal and occipital areas.
            
            
              •
              Effects of ischemic lesions on processing speed are mediated by cortical changes.},
	urldate = {2014-08-23},
	journal = {{NeuroImage} : Clinical},
	author = {Righart, Ruthger and Duering, Marco and Gonik, Mariya and Jouvent, Eric and Reyes, Sonia and Herve, Dominique and Chabriat, Hugues and Dichgans, Martin},
	month = jun,
	year = {2013},
	pmid = {24179837},
	pmcid = {PMC3777834},
	pages = {854--861},
	annote = {Righart, {RuthgerDuering}, {MarcoGonik}, {MariyaJouvent}, {EricReyes}, {SoniaHerve}, {DominiqueChabriat}, {HuguesDichgans}, {MartinengNetherlands}2013/11/02 06:00Neuroimage Clin. 2013 Jun 19;2:854-61. doi: 10.1016/j.nicl.2013.06.006. {eCollection} 2013.},
	file = {PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/I4UID44H/Righart et al. - 2013 - Impact of regional cortical and subcortical change.pdf:application/pdf;Righart-2013-Impact of regional cortical and 1:/autofs/cluster/freesurfer/zotero/storage/SZ2RTR96/Righart-2013-Impact of regional cortical and 1.pdf:application/pdf}
}

@article{wolosin_abnormal_2009,
	title = {Abnormal Cerebral Cortex Structure in Children with {ADHD}},
	volume = {30},
	issn = {1065-9471},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2883170/},
	doi = {10.1002/hbm.20496},
	abstract = {Objective
Examination of cerebral cortical structure in children with Attention-Deficit/Hyperactivity Disorder ({ADHD}) has thus far been principally limited to volume measures. In the current study, an automated surface-based analysis technique was used to examine the {ADHD}-associated differences in additional morphologic features of cerebral cortical gray matter structure, including surface area, thickness, and cortical folding.

Methods
{MPRAGE} images were acquired from 21 children with {ADHD} (9 girls) and 35 typically developing controls (15 girls), aged 8–12 years. Statistical difference maps were used to compare mean cortical thickness between groups along the cortical surface. Cortical volume, surface area, mean thickness, and cortical folding were measured within regions of interest, including the right/left hemispheres, frontal, temporal, parietal, and occipital lobes within each hemisphere, and sub-lobar regions.

Results
Children with {ADHD} showed a decrease in total cerebral volume and total cortical volume of over 7 and 8\%, respectively; volume reduction was observed throughout the cortex, with significant reduction in all four lobes bilaterally. The {ADHD} group also showed a decrease in surface area of over 7\% bilaterally, and a significant decrease in cortical folding bilaterally. No significant differences in cortical thickness were detected.

Conclusions
Results from the present study reveal that {ADHD} is associated with decreased cortical volume, surface area, and folding throughout the cerebral cortex. The findings suggest that decreased cortical folding is a key morphologic feature associated with {ADHD}. This would be consistent with onset early in neural development and could help to identify neurodevelopmental mechanisms that contribute to {ADHD}.},
	number = {1},
	urldate = {2014-08-23},
	journal = {Human brain mapping},
	author = {Wolosin, Sasha M. and Richardson, Marin E. and Hennessey, Joseph G. and Denckla, Martha B. and Mostofsky, Stewart H.},
	month = jan,
	year = {2009},
	pmid = {17985349},
	pmcid = {PMC2883170},
	pages = {175--184},
	file = {PubMed Central Full Text PDF:/autofs/cluster/freesurfer/zotero/storage/M6R68AZJ/Wolosin et al. - 2009 - Abnormal Cerebral Cortex Structure in Children wit.pdf:application/pdf}
}

@article{knake_aids_2004,
	title = {Aids to telemetry in the presurgical evaluation of epilepsy patients: {MRI}, {MEG} and other non-invasive imaging techniques},
	volume = {57},
	issn = {1567-424X (Print) 1567-424X (Linking)},
	shorttitle = {Aids to telemetry in the presurgical evaluation of epilepsy patients: {MRI}, {MEG} and other non-invasive imaging techniques},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/16106650},
	language = {eng},
	journal = {Suppl Clin Neurophysiol},
	author = {Knake, S. and Grant, P. E. and Stufflebeam, S. M. and Wald, L. L. and Shiraishi, H. and Rosenow, F. and Schomer, D. L. and Fischl, B. and Dale, A. M. and Halgren, E.},
	year = {2004},
	keywords = {Brain Mapping, Epilepsy/*pathology/ultrasonography, *Evaluation Studies as Topic, Functional Laterality, Humans, Magnetic Resonance Imaging/*methods, Magnetoencephalography/*methods, Nonlinear Dynamics, Telemetry/*methods, Ultrasonography, Doppler, Transcranial/methods},
	pages = {494--502},
	annote = {Knake, {SusanneGrant}, P {EllenStufflebeam}, Steven {MWald}, Lawrence {LShiraishi}, {HideakiRosenow}, {FelixSchomer}, Donald {LFischl}, {BruceDale}, Anders {MHalgren}, {EricengP}41RR14075/{RR}/{NCRR} {NIH} {HHS}/R01 {NS}18741/{NS}/{NINDS} {NIH} {HHS}/Research Support, N.I.H., {ExtramuralResearch} Support, U.S. Gov't, P.H.S.{ReviewNetherlands}2005/08/19 09:00Suppl Clin Neurophysiol. 2004;57:494-502.}
}