cmdline mri_glmfit --y lh.meditation_age.thickness.10.mgh --fsgd meditation_age.fsgd dods --C Contrasts/g1g2.age.mtx --C Contrasts/g1g2.intercept.mtx --C Contrasts/diff.thickness.mtx --C Contrasts/group-x-age.mtx --surf ../../fsaverage lh --cortex --glmdir lh.meditation_age.glmdir SURFACE: ../../fsaverage lh log file is lh.meditation_age.glmdir/mc-z.positive.mri_glmfit-sim.log cd /media/TianYe/Freesurfer/Analysis/GLM/meditation_age /usr/local/freesurfer/bin/mri_glmfit-sim --glmdir lh.meditation_age.glmdir --sim mc-z 500 4 mc-z.positive --sim-sign pos --cwpvalthresh 0.05 --overwrite $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $ Tue Sep 24 19:47:19 EDT 2013 Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:41:14 UTC 2012 i686 i686 i386 GNU/Linux fsuser setenv SUBJECTS_DIR /media/TianYe/Freesurfer/Analysis/GLM/meditation_age FREESURFER_HOME /usr/local/freesurfer Original mri_glmfit command line: cmdline mri_glmfit --y lh.meditation_age.thickness.10.mgh --fsgd meditation_age.fsgd dods --C Contrasts/g1g2.age.mtx --C Contrasts/g1g2.intercept.mtx --C Contrasts/diff.thickness.mtx --C Contrasts/group-x-age.mtx --surf ../../fsaverage lh --cortex --glmdir lh.meditation_age.glmdir DoSim = 1 UseCache = 0 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 14.528221 nSimPerJob = 500 1/1 Tue Sep 24 19:47:19 EDT 2013 mri_glmfit --y /media/TianYe/Freesurfer/Analysis/GLM/meditation_age/lh.meditation_age.thickness.10.mgh --C lh.meditation_age.glmdir/tmp.mri_glmfit-sim-2017/diff.thickness.mtx --C lh.meditation_age.glmdir/tmp.mri_glmfit-sim-2017/g1g2.age.mtx --C lh.meditation_age.glmdir/tmp.mri_glmfit-sim-2017/g1g2.intercept.mtx --C lh.meditation_age.glmdir/tmp.mri_glmfit-sim-2017/group-x-age.mtx --mask lh.meditation_age.glmdir/mask.mgh --sim mc-z 500 4 lh.meditation_age.glmdir/csd/mc-z.positive.j001 --sim-sign pos --fwhm 14.528221 --fsgd lh.meditation_age.glmdir/y.fsgd dods --surf ../../fsaverage lh white simbase lh.meditation_age.glmdir/csd/mc-z.positive.j001 FWHM = 14.528221 gdfReadHeader: reading lh.meditation_age.glmdir/y.fsgd INFO: NOT demeaning continuous variables Continuous Variable Means (all subjects) 0 age 59.7778 5.94626 Class Means of each Continuous Variable 1 meditationNormal 58.9333 2 meditationTM 60.8333 INFO: gd2mtx_method is dods Reading source surface /media/TianYe/Freesurfer/Analysis/GLM/meditation_age/../../fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65416.648438 AvgVtxArea 0.399267 AvgVtxDist 0.721953 StdVtxDist 0.195470 Surface smoothing by fwhm=14.528221, niters=155.000000 $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /media/TianYe/Freesurfer/Analysis/GLM/meditation_age cmdline mri_glmfit --y /media/TianYe/Freesurfer/Analysis/GLM/meditation_age/lh.meditation_age.thickness.10.mgh --C lh.meditation_age.glmdir/tmp.mri_glmfit-sim-2017/diff.thickness.mtx --C lh.meditation_age.glmdir/tmp.mri_glmfit-sim-2017/g1g2.age.mtx --C lh.meditation_age.glmdir/tmp.mri_glmfit-sim-2017/g1g2.intercept.mtx --C lh.meditation_age.glmdir/tmp.mri_glmfit-sim-2017/group-x-age.mtx --mask lh.meditation_age.glmdir/mask.mgh --sim mc-z 500 4 lh.meditation_age.glmdir/csd/mc-z.positive.j001 --sim-sign pos --fwhm 14.528221 --fsgd lh.meditation_age.glmdir/y.fsgd dods --surf ../../fsaverage lh white sysname Linux hostname xubuntu-VirtualBox machine i686 user fsuser FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 fwhm 14.528221 niters 155.000000 OneSampleGroupMean 0 y /media/TianYe/Freesurfer/Analysis/GLM/meditation_age/lh.meditation_age.thickness.10.mgh logyflag 0 usedti 0 FSGD lh.meditation_age.glmdir/y.fsgd mask lh.meditation_age.glmdir/mask.mgh maskinv 0 glmdir (null) IllCondOK 0 ReScaleX 1 DoFFx 0 Loading y from /media/TianYe/Freesurfer/Analysis/GLM/meditation_age/lh.meditation_age.thickness.10.mgh INFO: gd2mtx_method is dods Normalized matrix condition is 655.899 Matrix condition is 722862 Found 149955 voxels in mask Reshaping mriglm->mask... search space = 74612.965197 DOF = 23 thresh = 4, threshadj = 3.69897 Starting simulation sim over 500 trials mri_glmfit simulation done Tue Sep 24 20:15:25 EDT 2013 mri_surfcluster --in lh.meditation_age.glmdir/diff.thickness/sig.mgh --csd lh.meditation_age.glmdir/csd/mc-z.positive.j001-diff.thickness.csd --mask lh.meditation_age.glmdir/mask.mgh --cwsig lh.meditation_age.glmdir/diff.thickness/mc-z.positive.sig.cluster.mgh --vwsig lh.meditation_age.glmdir/diff.thickness/mc-z.positive.sig.voxel.mgh --sum lh.meditation_age.glmdir/diff.thickness/mc-z.positive.sig.cluster.summary --ocn lh.meditation_age.glmdir/diff.thickness/mc-z.positive.sig.ocn.mgh --oannot lh.meditation_age.glmdir/diff.thickness/mc-z.positive.sig.ocn.annot --annot aparc --csdpdf lh.meditation_age.glmdir/diff.thickness/mc-z.positive.pdf.dat --cwpvalthresh 0.05 --o lh.meditation_age.glmdir/diff.thickness/mc-z.positive.sig.masked.mgh --no-fixmni --surf white Creating CDFs from CSD files csd->threshsign = 1 thsign = pos, id = 1 version $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $ hemi = lh srcid = lh.meditation_age.glmdir/diff.thickness/sig.mgh srcsubjid = ../../fsaverage srcsurf = white srcframe = 0 thsign = pos thmin = 4 thmax = -1 fdr = -1 minarea = 0 xfmfile = talairach.xfm nth = -1 outid = lh.meditation_age.glmdir/diff.thickness/mc-z.positive.sig.masked.mgh MGH ocnid = lh.meditation_age.glmdir/diff.thickness/mc-z.positive.sig.ocn.mgh MGH sumfile = lh.meditation_age.glmdir/diff.thickness/mc-z.positive.sig.cluster.summary subjectsdir = /media/TianYe/Freesurfer/Analysis/GLM/meditation_age FixMNI = 0 Found 149955 vertices in mask Found 149955 vertices in mask Found 149955 points in clabel. ------------- XFM matrix (RAS2RAS) --------------- /media/TianYe/Freesurfer/Analysis/GLM/meditation_age/../../fsaverage/mri/transforms/talairach.xfm 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; ---------------------------------------------------- Reading source surface /media/TianYe/Freesurfer/Analysis/GLM/meditation_age/../../fsaverage/surf/lh.white Done reading source surface Reading annotation /media/TianYe/Freesurfer/Analysis/GLM/meditation_age/../../fsaverage/label/lh.aparc.annot Computing metric properties Loading source values number of voxels in search space = 149955 Done loading source values (nvtxs = 163842) overall max = 2.64307 at vertex 7070 overall min = -3.06594 at vertex 156191 surface nvertices 163842 surface area 65417.097656 surface area 65416.648438 Computing voxel-wise significance CSDpvalMaxSigMap(): found 83/163842 above 0 Adjusting threshold for 1-tailed test. If the input is not a -log10(p) volume, re-run with --no-adjust. Searching for Clusters ... thmin=4.000000 (3.698970), thmax=-1.000000 (-1), thsignid=1, minarea=0.000000 Found 0 clusters Max cluster size 0.000000 Pruning by CW P-Value 0.05 Saving thresholded output to lh.meditation_age.glmdir/diff.thickness/mc-z.positive.sig.masked.mgh Saving cluster numbers to lh.meditation_age.glmdir/diff.thickness/mc-z.positive.sig.ocn.mgh Saving cluster pval lh.meditation_age.glmdir/diff.thickness/mc-z.positive.sig.cluster.mgh Constructing output annotation Writing annotation lh.meditation_age.glmdir/diff.thickness/mc-z.positive.sig.ocn.annot mri_segstats --seg lh.meditation_age.glmdir/diff.thickness/mc-z.positive.sig.ocn.mgh --exclude 0 --i /media/TianYe/Freesurfer/Analysis/GLM/meditation_age/lh.meditation_age.thickness.10.mgh --avgwf lh.meditation_age.glmdir/diff.thickness/mc-z.positive.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.2017 $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg lh.meditation_age.glmdir/diff.thickness/mc-z.positive.sig.ocn.mgh --exclude 0 --i /media/TianYe/Freesurfer/Analysis/GLM/meditation_age/lh.meditation_age.thickness.10.mgh --avgwf lh.meditation_age.glmdir/diff.thickness/mc-z.positive.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.2017 sysname Linux hostname xubuntu-VirtualBox machine i686 user fsuser UseRobust 0 Loading lh.meditation_age.glmdir/diff.thickness/mc-z.positive.sig.ocn.mgh Loading /media/TianYe/Freesurfer/Analysis/GLM/meditation_age/lh.meditation_age.thickness.10.mgh Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 0 segmentations Computing spatial average of each frame Writing to lh.meditation_age.glmdir/diff.thickness/mc-z.positive.y.ocn.dat mri_segstats done mri_convert lh.meditation_age.glmdir/diff.thickness/mc-z.positive.sig.cluster.mgh lh.meditation_age.glmdir/diff.thickness/mc-z.positive.sig.cluster.mgh --frame 0 mri_convert lh.meditation_age.glmdir/diff.thickness/mc-z.positive.sig.cluster.mgh lh.meditation_age.glmdir/diff.thickness/mc-z.positive.sig.cluster.mgh --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from lh.meditation_age.glmdir/diff.thickness/mc-z.positive.sig.cluster.mgh... 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 lh.meditation_age.glmdir/diff.thickness/mc-z.positive.sig.cluster.mgh... mri_surfcluster --in lh.meditation_age.glmdir/g1g2.age/sig.mgh --csd lh.meditation_age.glmdir/csd/mc-z.positive.j001-g1g2.age.csd --mask lh.meditation_age.glmdir/mask.mgh --cwsig lh.meditation_age.glmdir/g1g2.age/mc-z.positive.sig.cluster.mgh --vwsig lh.meditation_age.glmdir/g1g2.age/mc-z.positive.sig.voxel.mgh --sum lh.meditation_age.glmdir/g1g2.age/mc-z.positive.sig.cluster.summary --ocn lh.meditation_age.glmdir/g1g2.age/mc-z.positive.sig.ocn.mgh --oannot lh.meditation_age.glmdir/g1g2.age/mc-z.positive.sig.ocn.annot --annot aparc --csdpdf lh.meditation_age.glmdir/g1g2.age/mc-z.positive.pdf.dat --cwpvalthresh 0.05 --o lh.meditation_age.glmdir/g1g2.age/mc-z.positive.sig.masked.mgh --no-fixmni --surf white Creating CDFs from CSD files csd->threshsign = 1 thsign = pos, id = 1 version $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $ hemi = lh srcid = lh.meditation_age.glmdir/g1g2.age/sig.mgh srcsubjid = ../../fsaverage srcsurf = white srcframe = 0 thsign = pos thmin = 4 thmax = -1 fdr = -1 minarea = 0 xfmfile = talairach.xfm nth = -1 outid = lh.meditation_age.glmdir/g1g2.age/mc-z.positive.sig.masked.mgh MGH ocnid = lh.meditation_age.glmdir/g1g2.age/mc-z.positive.sig.ocn.mgh MGH sumfile = lh.meditation_age.glmdir/g1g2.age/mc-z.positive.sig.cluster.summary subjectsdir = /media/TianYe/Freesurfer/Analysis/GLM/meditation_age FixMNI = 0 Found 149955 vertices in mask Found 149955 vertices in mask Found 149955 points in clabel. ------------- XFM matrix (RAS2RAS) --------------- /media/TianYe/Freesurfer/Analysis/GLM/meditation_age/../../fsaverage/mri/transforms/talairach.xfm 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; ---------------------------------------------------- Reading source surface /media/TianYe/Freesurfer/Analysis/GLM/meditation_age/../../fsaverage/surf/lh.white Done reading source surface Reading annotation /media/TianYe/Freesurfer/Analysis/GLM/meditation_age/../../fsaverage/label/lh.aparc.annot Computing metric properties Loading source values number of voxels in search space = 149955 Done loading source values (nvtxs = 163842) overall max = 3.53411 at vertex 68827 overall min = -3.54169 at vertex 53376 surface nvertices 163842 surface area 65417.097656 surface area 65416.648438 Computing voxel-wise significance CSDpvalMaxSigMap(): found 97/163842 above 0 Adjusting threshold for 1-tailed test. If the input is not a -log10(p) volume, re-run with --no-adjust. Searching for Clusters ... thmin=4.000000 (3.698970), thmax=-1.000000 (-1), thsignid=1, minarea=0.000000 Found 0 clusters Max cluster size 0.000000 Pruning by CW P-Value 0.05 Saving thresholded output to lh.meditation_age.glmdir/g1g2.age/mc-z.positive.sig.masked.mgh Saving cluster numbers to lh.meditation_age.glmdir/g1g2.age/mc-z.positive.sig.ocn.mgh Saving cluster pval lh.meditation_age.glmdir/g1g2.age/mc-z.positive.sig.cluster.mgh Constructing output annotation Writing annotation lh.meditation_age.glmdir/g1g2.age/mc-z.positive.sig.ocn.annot mri_segstats --seg lh.meditation_age.glmdir/g1g2.age/mc-z.positive.sig.ocn.mgh --exclude 0 --i /media/TianYe/Freesurfer/Analysis/GLM/meditation_age/lh.meditation_age.thickness.10.mgh --avgwf lh.meditation_age.glmdir/g1g2.age/mc-z.positive.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.2017 $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg lh.meditation_age.glmdir/g1g2.age/mc-z.positive.sig.ocn.mgh --exclude 0 --i /media/TianYe/Freesurfer/Analysis/GLM/meditation_age/lh.meditation_age.thickness.10.mgh --avgwf lh.meditation_age.glmdir/g1g2.age/mc-z.positive.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.2017 sysname Linux hostname xubuntu-VirtualBox machine i686 user fsuser UseRobust 0 Loading lh.meditation_age.glmdir/g1g2.age/mc-z.positive.sig.ocn.mgh Loading /media/TianYe/Freesurfer/Analysis/GLM/meditation_age/lh.meditation_age.thickness.10.mgh Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 0 segmentations Computing spatial average of each frame Writing to lh.meditation_age.glmdir/g1g2.age/mc-z.positive.y.ocn.dat mri_segstats done mri_convert lh.meditation_age.glmdir/g1g2.age/mc-z.positive.sig.cluster.mgh lh.meditation_age.glmdir/g1g2.age/mc-z.positive.sig.cluster.mgh --frame 0 mri_convert lh.meditation_age.glmdir/g1g2.age/mc-z.positive.sig.cluster.mgh lh.meditation_age.glmdir/g1g2.age/mc-z.positive.sig.cluster.mgh --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from lh.meditation_age.glmdir/g1g2.age/mc-z.positive.sig.cluster.mgh... 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 lh.meditation_age.glmdir/g1g2.age/mc-z.positive.sig.cluster.mgh... mri_surfcluster --in lh.meditation_age.glmdir/g1g2.intercept/sig.mgh --csd lh.meditation_age.glmdir/csd/mc-z.positive.j001-g1g2.intercept.csd --mask lh.meditation_age.glmdir/mask.mgh --cwsig lh.meditation_age.glmdir/g1g2.intercept/mc-z.positive.sig.cluster.mgh --vwsig lh.meditation_age.glmdir/g1g2.intercept/mc-z.positive.sig.voxel.mgh --sum lh.meditation_age.glmdir/g1g2.intercept/mc-z.positive.sig.cluster.summary --ocn lh.meditation_age.glmdir/g1g2.intercept/mc-z.positive.sig.ocn.mgh --oannot lh.meditation_age.glmdir/g1g2.intercept/mc-z.positive.sig.ocn.annot --annot aparc --csdpdf lh.meditation_age.glmdir/g1g2.intercept/mc-z.positive.pdf.dat --cwpvalthresh 0.05 --o lh.meditation_age.glmdir/g1g2.intercept/mc-z.positive.sig.masked.mgh --no-fixmni --surf white Creating CDFs from CSD files csd->threshsign = 1 thsign = pos, id = 1 version $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $ hemi = lh srcid = lh.meditation_age.glmdir/g1g2.intercept/sig.mgh srcsubjid = ../../fsaverage srcsurf = white srcframe = 0 thsign = pos thmin = 4 thmax = -1 fdr = -1 minarea = 0 xfmfile = talairach.xfm nth = -1 outid = lh.meditation_age.glmdir/g1g2.intercept/mc-z.positive.sig.masked.mgh MGH ocnid = lh.meditation_age.glmdir/g1g2.intercept/mc-z.positive.sig.ocn.mgh MGH sumfile = lh.meditation_age.glmdir/g1g2.intercept/mc-z.positive.sig.cluster.summary subjectsdir = /media/TianYe/Freesurfer/Analysis/GLM/meditation_age FixMNI = 0 Found 149955 vertices in mask Found 149955 vertices in mask Found 149955 points in clabel. ------------- XFM matrix (RAS2RAS) --------------- /media/TianYe/Freesurfer/Analysis/GLM/meditation_age/../../fsaverage/mri/transforms/talairach.xfm 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; ---------------------------------------------------- Reading source surface /media/TianYe/Freesurfer/Analysis/GLM/meditation_age/../../fsaverage/surf/lh.white Done reading source surface Reading annotation /media/TianYe/Freesurfer/Analysis/GLM/meditation_age/../../fsaverage/label/lh.aparc.annot Computing metric properties Loading source values number of voxels in search space = 149955 Done loading source values (nvtxs = 163842) overall max = 10.0396 at vertex 7414 overall min = -0.30465 at vertex 83216 surface nvertices 163842 surface area 65417.097656 surface area 65416.648438 Computing voxel-wise significance CSDpvalMaxSigMap(): found 138260/163842 above 0 Adjusting threshold for 1-tailed test. If the input is not a -log10(p) volume, re-run with --no-adjust. Searching for Clusters ... thmin=4.000000 (3.698970), thmax=-1.000000 (-1), thsignid=1, minarea=0.000000 Found 11 clusters Max cluster size 42201.789062 Pruning by CW P-Value 0.05 Saving thresholded output to lh.meditation_age.glmdir/g1g2.intercept/mc-z.positive.sig.masked.mgh Saving cluster numbers to lh.meditation_age.glmdir/g1g2.intercept/mc-z.positive.sig.ocn.mgh Saving cluster pval lh.meditation_age.glmdir/g1g2.intercept/mc-z.positive.sig.cluster.mgh Constructing output annotation Writing annotation lh.meditation_age.glmdir/g1g2.intercept/mc-z.positive.sig.ocn.annot mri_segstats --seg lh.meditation_age.glmdir/g1g2.intercept/mc-z.positive.sig.ocn.mgh --exclude 0 --i /media/TianYe/Freesurfer/Analysis/GLM/meditation_age/lh.meditation_age.thickness.10.mgh --avgwf lh.meditation_age.glmdir/g1g2.intercept/mc-z.positive.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.2017 $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg lh.meditation_age.glmdir/g1g2.intercept/mc-z.positive.sig.ocn.mgh --exclude 0 --i /media/TianYe/Freesurfer/Analysis/GLM/meditation_age/lh.meditation_age.thickness.10.mgh --avgwf lh.meditation_age.glmdir/g1g2.intercept/mc-z.positive.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.2017 sysname Linux hostname xubuntu-VirtualBox machine i686 user fsuser UseRobust 0 Loading lh.meditation_age.glmdir/g1g2.intercept/mc-z.positive.sig.ocn.mgh Loading /media/TianYe/Freesurfer/Analysis/GLM/meditation_age/lh.meditation_age.thickness.10.mgh Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 5 segmentations Computing statistics for each segmentation 1 1 83733 83733.000 2 2 1742 1742.000 3 3 330 330.000 4 4 111 111.000 Reporting on 4 segmentations Computing spatial average of each frame 0 1 2 3