cmdline mri_glmfit --y lh.AD_CN_NO_COVARIATE.thickness.15.mgh --fsgd AD_CN_NO_COVARIATE.fsgd dods --C group.diff.mtx --surf fsaverage lh --cortex --glmdir lh.AD_CN_NO_COVARIATE.glmdir SURFACE: fsaverage lh log file is lh.AD_CN_NO_COVARIATE.glmdir/cache.mri_glmfit-sim.log cd /aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/glm/AD_CN_NO_COVARIATE /aramis/dartagnan2/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos/bin/mri_glmfit-sim --glmdir lh.AD_CN_NO_COVARIATE.glmdir --cache 3 pos --cwp 0.05 $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $ Fri May 27 10:21:48 CEST 2016 Linux HP1973 3.11.0-26-generic #45~precise1-Ubuntu SMP Tue Jul 15 04:02:35 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux wen setenv SUBJECTS_DIR /aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/ FREESURFER_HOME /aramis/dartagnan2/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos Original mri_glmfit command line: cmdline mri_glmfit --y lh.AD_CN_NO_COVARIATE.thickness.15.mgh --fsgd AD_CN_NO_COVARIATE.fsgd dods --C group.diff.mtx --surf fsaverage lh --cortex --glmdir lh.AD_CN_NO_COVARIATE.glmdir DoSim = 0 UseCache = 1 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 22.776285 CSD /aramis/dartagnan2/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos/average/mult-comp-cor/fsaverage/lh/cortex/fwhm23/pos/th30/mc-z.csd mri_surfcluster --in lh.AD_CN_NO_COVARIATE.glmdir/group.diff/sig.mgh --csd /aramis/dartagnan2/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos/average/mult-comp-cor/fsaverage/lh/cortex/fwhm23/pos/th30/mc-z.csd --mask lh.AD_CN_NO_COVARIATE.glmdir/mask.mgh --cwsig lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th30.pos.sig.cluster.mgh --vwsig lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th30.pos.sig.voxel.mgh --sum lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th30.pos.sig.cluster.summary --ocn lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th30.pos.sig.ocn.mgh --oannot lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th30.pos.sig.ocn.annot --annot aparc --csdpdf lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th30.pos.pdf.dat --cwpvalthresh 0.05 --o lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th30.pos.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.AD_CN_NO_COVARIATE.glmdir/group.diff/sig.mgh srcsubjid = fsaverage srcsurf = white srcframe = 0 thsign = pos thmin = 3 thmax = -1 fdr = -1 minarea = 0 xfmfile = talairach.xfm nth = -1 outid = lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th30.pos.sig.masked.mgh MGH ocnid = lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th30.pos.sig.ocn.mgh MGH sumfile = lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th30.pos.sig.cluster.summary subjectsdir = /aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/ FixMNI = 0 Found 149955 vertices in mask Found 149955 vertices in mask Found 149955 points in clabel. ------------- XFM matrix (RAS2RAS) --------------- /aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//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 /aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//fsaverage/surf/lh.white Done reading source surface Reading annotation /aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//fsaverage/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Computing metric properties Loading source values number of voxels in search space = 149955 Done loading source values (nvtxs = 163842) overall max = 8.58718 at vertex 22205 overall min = -1.57802 at vertex 24019 surface nvertices 163842 surface area 65417.097656 surface area 65416.648438 Computing voxel-wise significance CSDpvalMaxSigMap(): found 76162/163842 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=3.000000 (2.698970), thmax=-1.000000 (-1), thsignid=1, minarea=0.000000 Found 15 clusters Max cluster size 12517.508789 Pruning by CW P-Value 0.05 Saving thresholded output to lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th30.pos.sig.masked.mgh Saving cluster numbers to lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th30.pos.sig.ocn.mgh Saving cluster pval lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th30.pos.sig.cluster.mgh Constructing output annotation Writing annotation lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th30.pos.sig.ocn.annot mri_segstats --seg lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th30.pos.sig.ocn.mgh --exclude 0 --i /aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/glm/AD_CN_NO_COVARIATE/lh.AD_CN_NO_COVARIATE.thickness.15.mgh --avgwf lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th30.pos.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.27760 $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th30.pos.sig.ocn.mgh --exclude 0 --i /aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/glm/AD_CN_NO_COVARIATE/lh.AD_CN_NO_COVARIATE.thickness.15.mgh --avgwf lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th30.pos.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.27760 sysname Linux hostname HP1973 machine x86_64 user wen UseRobust 0 Loading lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th30.pos.sig.ocn.mgh Loading /aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/glm/AD_CN_NO_COVARIATE/lh.AD_CN_NO_COVARIATE.thickness.15.mgh Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 6 segmentations Computing statistics for each segmentation 1 1 24017 24017.000 2 2 5270 5270.000 3 3 2632 2632.000 4 4 2776 2776.000 5 5 1100 1100.000 Reporting on 5 segmentations Computing spatial average of each frame 0 1 2 3 4 Writing to lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th30.pos.y.ocn.dat mri_segstats done mri_convert lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th30.pos.sig.cluster.mgh lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th30.pos.sig.cluster.mgh --frame 0 mri_convert lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th30.pos.sig.cluster.mgh lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th30.pos.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.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th30.pos.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.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th30.pos.sig.cluster.mgh... Fri May 27 10:21:48 CEST 2016 Fri May 27 10:21:58 CEST 2016 mri_glmfit-sim done ./cluster_wise_correction_for_multiple_comparisons.sh: line 25: --bonferroni: command not found wen@HP1973:/aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/glm/AD_CN_NO_COVARIATE$ Did not find any volume geometry information in the surface p��Breading colortable from annotation file... colortable with 6 entries read (originally none) colortable with 6 entries read (originally none)