cd /autofs/cluster/freesurfer/tutorials/tutorial_data/fsfast-functional/group/workmem.sm05.lh/encode-v-base /autofs/space/topaz_001/users/ah221/test/freesurfer/bin/mri_glmfit-sim --glmdir my-glm --perm 1000 3 pos --cwp .05 --3spaces $Id: mri_glmfit-sim,v 1.66 2016/11/16 20:52:22 greve Exp $ Sun Sep 30 20:23:52 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 --surface fsaverage lh --glmdir my-glm --save-eres --nii.gz DoSim = 1 UseCache = 0 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 0 nSimPerJob = 1000 1/1 Sun Sep 30 20:23:52 EDT 2018 mri_glmfit --C my-glm/tmp.mri_glmfit-sim-19256/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 --surf fsaverage lh white simbase my-glm/csd/perm.th30.pos.j001 FWHM = 0.000000 Reading source surface /autofs/cluster/freesurfer/tutorials/tutorial_data/fsfast-tutorial.subjects/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65416.984375 AvgVtxArea 0.399269 AvgVtxDist 0.721953 StdVtxDist 0.195470 $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.lh/encode-v-base cmdline mri_glmfit.bin --C my-glm/tmp.mri_glmfit-sim-19256/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 --surf fsaverage lh white 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.lh/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.lh/encode-v-base/my-glm/eres.nii.gz ... done reading. Computing normalized matrix Normalized matrix condition is 1 Matrix condition is 1 Found 149925 voxels in mask Reshaping mriglm->mask... search space = 74598.200367 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 7.37413 Sun Sep 30 20:31:17 EDT 2018 mri_surfcluster --in my-glm/osgm/sig.nii.gz --mask my-glm/mask.nii.gz --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 --annot aparc --cwpvalthresh .05 --o my-glm/osgm/perm.th30.pos.sig.masked.nii.gz --no-fixmni --csd my-glm/csd/perm.th30.pos.j001-osgm.csd --csdpdf my-glm/osgm/perm.th30.pos.pdf.dat --vwsig my-glm/osgm/perm.th30.pos.sig.voxel.nii.gz --vwsigmax my-glm/osgm/perm.th30.pos.sig.voxel.max.dat --oannot my-glm/osgm/perm.th30.pos.sig.ocn.annot --bonferroni 3 --surf white Creating CDFs from CSD files csd->threshsign = 1 thsign = pos, id = 1 version $Id: mri_surfcluster.c,v 1.57.2.3 2016/11/17 18:19:42 zkaufman Exp $ hemi = lh srcid = my-glm/osgm/sig.nii.gz srcsubjid = fsaverage srcsurf = white srcframe = 0 thsign = pos thmin = 3 thmax = -1 fdr = -1 minarea = 0 Bonferroni = 3 xfmfile = talairach.xfm nth = -1 outid = my-glm/osgm/perm.th30.pos.sig.masked.nii.gz nii ocnid = my-glm/osgm/perm.th30.pos.sig.ocn.nii.gz nii sumfile = my-glm/osgm/perm.th30.pos.sig.cluster.summary subjectsdir = /autofs/cluster/freesurfer/tutorials/tutorial_data/fsfast-tutorial.subjects FixMNI = 0 Found 149925 vertices in mask Found 149925 vertices in mask Found 149925 points in clabel. ------------- XFM matrix (RAS2RAS) --------------- /autofs/cluster/freesurfer/tutorials/tutorial_data/fsfast-tutorial.subjects/fsaverage/mri/transforms/talairach.xfm 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; ---------------------------------------------------- Reading source surface /autofs/cluster/freesurfer/tutorials/tutorial_data/fsfast-tutorial.subjects/fsaverage/surf/lh.white Done reading source surface Reading annotation /autofs/cluster/freesurfer/tutorials/tutorial_data/fsfast-tutorial.subjects/fsaverage/label/lh.aparc.annot Computing metric properties Loading source values number of voxels in search space = 149925 Done loading source values (nvtxs = 163842) overall max = 12.7661 at vertex 129167 overall min = -6.41751 at vertex 74621 surface nvertices 163842 metric props tot surface area 65416.984375 group_avg_vtxarea_loaded 1 masked surface area 76451.875000 Computing voxel-wise significance CSDpvalMaxSigMap(): found 33164/163842 above 0, max=inf Adjusting threshold for 1-tailed test. If the input is not a -log10(p) volume, re-run with --no-adjust. thminadj = 2.69897 Searching for Clusters ... thmin=3.000000 (2.698970), thmax=-1.000000 (-1), thsignid=1, minarea=0.000000 Found 16 clusters Max cluster size 7602.349121 Pruning by CW P-Value 0.05 Saving thresholded output to my-glm/osgm/perm.th30.pos.sig.masked.nii.gz Saving cluster numbers to my-glm/osgm/perm.th30.pos.sig.ocn.nii.gz Saving cluster pval my-glm/osgm/perm.th30.pos.sig.cluster.nii.gz Constructing output annotation Writing annotation my-glm/osgm/perm.th30.pos.sig.ocn.annot 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.19256 $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.19256 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 1 mm^3 Generating list of segmentation ids Found 4 segmentations Computing statistics for each segmentation Reporting on 3 segmentations Using PrintSegStat Computing spatial average of each frame 0 1 2 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=0.00, 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 20:23:52 EDT 2018 Sun Sep 30 20:31:19 EDT 2018 mri_glmfit-sim done