cd /autofs/cluster/freesurfer/tutorials/tutorial_data/fsfast-functional/group/workmem.sm05.mni305/encode-v-base /autofs/space/topaz_001/users/ah221/test/freesurfer/bin/mri_glmfit-sim --glmdir my-glm --perm 1000 3 pos --cwp 0.5 --3spaces $Id: mri_glmfit-sim,v 1.66 2016/11/16 20:52:22 greve Exp $ Sun Sep 30 20:41:32 EDT 2018 Linux topaz.nmr.mgh.harvard.edu 3.10.0-693.11.1.el7.x86_64 #1 SMP Mon Dec 4 23:52:40 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux ah221 setenv SUBJECTS_DIR /autofs/cluster/freesurfer/tutorials/tutorial_data/fsfast-tutorial.subjects FREESURFER_HOME /autofs/space/topaz_001/users/ah221/test/freesurfer Original mri_glmfit command line: cmdline mri_glmfit.bin --y ces.nii.gz --osgm --glmdir my-glm --nii.gz --save-eres DoSim = 1 UseCache = 0 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 0 nSimPerJob = 1000 1/1 Sun Sep 30 20:41:32 EDT 2018 mri_glmfit --C my-glm/tmp.mri_glmfit-sim-23587/osgm.mtx --sim perm 1000 3 my-glm/csd/perm.th30.pos.j001 --sim-sign pos --fwhm 0 --X my-glm/Xg.dat --mask my-glm/mask.nii.gz --y my-glm/eres.nii.gz --perm-force simbase my-glm/csd/perm.th30.pos.j001 FWHM = 0.000000 $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $ cwd /autofs/cluster/freesurfer/tutorials/tutorial_data/fsfast-functional/group/workmem.sm05.mni305/encode-v-base cmdline mri_glmfit.bin --C my-glm/tmp.mri_glmfit-sim-23587/osgm.mtx --sim perm 1000 3 my-glm/csd/perm.th30.pos.j001 --sim-sign pos --fwhm 0 --X my-glm/Xg.dat --mask my-glm/mask.nii.gz --y my-glm/eres.nii.gz --perm-force sysname Linux hostname topaz.nmr.mgh.harvard.edu machine x86_64 user ah221 FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /autofs/cluster/freesurfer/tutorials/tutorial_data/fsfast-functional/group/workmem.sm05.mni305/encode-v-base/my-glm/eres.nii.gz logyflag 0 X my-glm/Xg.dat usedti 0 mask my-glm/mask.nii.gz maskinv 0 glmdir (null) IllCondOK 0 ReScaleX 1 DoFFx 0 Loading y from /autofs/cluster/freesurfer/tutorials/tutorial_data/fsfast-functional/group/workmem.sm05.mni305/encode-v-base/my-glm/eres.nii.gz ... done reading. Computing normalized matrix Normalized matrix condition is 1 Matrix condition is 1 Found 51000 voxels in mask search space = 408000.000000 Design detected as one-sample group mean, adjusting permutation simulation DOF = 17 thresh = 3, threshadj = 2.69897 Starting simulation sim over 1000 trials mri_glmfit simulation done 4.934 Sun Sep 30 20:46:28 EDT 2018 mri_volcluster --in my-glm/osgm/sig.nii.gz --mask my-glm/mask.nii.gz --reg /autofs/space/topaz_001/users/ah221/test/freesurfer/subjects/fsaverage/mri.2mm/reg.2mm.dat --no-fixmni --cwsig my-glm/osgm/perm.th30.pos.sig.cluster.nii.gz --sum my-glm/osgm/perm.th30.pos.sig.cluster.summary --ocn my-glm/osgm/perm.th30.pos.sig.ocn.nii.gz --cwpvalthresh 0.5 --seg fsaverage aparc+aseg.mgz --out my-glm/osgm/perm.th30.pos.sig.masked.nii.gz --allowdiag --bonferroni 3 --csdpdf my-glm/osgm/perm.th30.pos.pdf.dat --csd my-glm/csd/perm.th30.pos.j001-osgm.csd --vwsig my-glm/osgm/perm.th30.pos.sig.voxel.nii.gz --vwsigmax my-glm/osgm/perm.th30.pos.sig.voxel.max.dat Adjusting threshold for 1-tailed test. If the input is not a -log10(p) volume, re-run with --no-adjust. New threshold is 2.698970 threshmin 3, threshminadj 2.69897 Using defalt ctab /autofs/space/topaz_001/users/ah221/test/freesurfer/FreeSurferColorLUT.txt INFO: loading mask volume: my-glm/mask.nii.gz INFO: MRIbinarize01(): nhits = 51000 Found 51000 voxels in mask INFO: subject = fsaverage Input volume FOV xfm Matrix: ---------------- -2.00000 0.00000 0.00000 76.00000; 0.00000 0.00000 2.00000 -93.00000; 0.00000 -2.00000 0.00000 76.00000; 0.00000 0.00000 0.00000 1.00000; Search Space = 408000 mm3 Using ctab /autofs/space/topaz_001/users/ah221/test/freesurfer/FreeSurferColorLUT.txt Computing voxel-wise significance CSDpvalMaxSigMap(): found 6755/51000 above 0, max=2.52331 INFO: Found 899 voxels in threhold range INFO: Found 26 clusters that meet threshold criteria INFO: Found 26 clusters that meet size criteria INFO: Found 26 final clusters Pruning by CW P-Value 0.5 INFO: writing summary to my-glm/osgm/perm.th30.pos.sig.cluster.summary Saving cluster pval my-glm/osgm/perm.th30.pos.sig.cluster.nii.gz INFO: writing OCN to my-glm/osgm/perm.th30.pos.sig.ocn.nii.gz mri_volcluster: done mri_segstats --seg my-glm/osgm/perm.th30.pos.sig.ocn.nii.gz --exclude 0 --i ces.nii.gz --avgwf my-glm/osgm/perm.th30.pos.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.23587 $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --seg my-glm/osgm/perm.th30.pos.sig.ocn.nii.gz --exclude 0 --i ces.nii.gz --avgwf my-glm/osgm/perm.th30.pos.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.23587 sysname Linux hostname topaz.nmr.mgh.harvard.edu machine x86_64 user ah221 UseRobust 0 Loading my-glm/osgm/perm.th30.pos.sig.ocn.nii.gz Loading ces.nii.gz Voxel Volume is 8 mm^3 Generating list of segmentation ids Found 16 segmentations Computing statistics for each segmentation Reporting on 15 segmentations Using PrintSegStat Computing spatial average of each frame 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 Writing to my-glm/osgm/perm.th30.pos.y.ocn.dat mri_segstats done mri_convert my-glm/osgm/perm.th30.pos.sig.cluster.nii.gz my-glm/osgm/perm.th30.pos.sig.cluster.nii.gz --frame 0 mri_convert.bin my-glm/osgm/perm.th30.pos.sig.cluster.nii.gz my-glm/osgm/perm.th30.pos.sig.cluster.nii.gz --frame 0 $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from my-glm/osgm/perm.th30.pos.sig.cluster.nii.gz... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) keeping frame 0 writing to my-glm/osgm/perm.th30.pos.sig.cluster.nii.gz... Sun Sep 30 20:41:32 EDT 2018 Sun Sep 30 20:46:31 EDT 2018 mri_glmfit-sim done