cd /autofs/cluster/birn/LEGACY/45/users/BWH/buckner_data/tutorial_subjs/group_analysis_tutorial/glm /usr/local/freesurfer/dev/bin/mri_glmfit-sim --glmdir lh.gender_age.glmdir --sim mc-z 5 4 mc-z.negative --sim-sign neg --cwpvalthresh 0.4 --overwrite $Id: mri_glmfit-sim,v 1.48 2013/06/05 16:59:32 greve Exp $ Fri Nov 1 09:10:30 EDT 2013 Linux sangwoo 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux maritza setenv SUBJECTS_DIR /autofs/cluster/birn/LEGACY/45/users/BWH/buckner_data/tutorial_subjs/group_analysis_tutorial FREESURFER_HOME /usr/local/freesurfer/dev Original mri_glmfit command line: cmdline mri_glmfit --y lh.gender_age.thickness.10.mgh --fsgd gender_age.fsgd dods --C lh-Avg-thickness-age-Cor.mtx --surf fsaverage lh --cortex --glmdir lh.gender_age.glmdir DoSim = 1 UseCache = 0 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 13.914377 nSimPerJob = 5 1/1 Fri Nov 1 09:10:30 EDT 2013 mri_glmfit --C lh.gender_age.glmdir/tmp.mri_glmfit-sim-18726/lh-Avg-thickness-age-Cor.mtx --sim mc-z 5 4 lh.gender_age.glmdir/csd/mc-z.negative.j001 --y lh.gender_age.thickness.10.mgh --mask lh.gender_age.glmdir/mask.mgh --sim-sign neg --fwhm 13.914377 --fsgd lh.gender_age.glmdir/y.fsgd dods --surf fsaverage lh white simbase lh.gender_age.glmdir/csd/mc-z.negative.j001 FWHM = 13.914377 gdfReadHeader: reading lh.gender_age.glmdir/y.fsgd INFO: NOT demeaning continuous variables Continuous Variable Means (all subjects) 0 age 57.175 26.6006 Class Means of each Continuous Variable 1 genderFemale 59.1429 2 genderMale 55.0000 INFO: gd2mtx_method is dods Reading source surface /autofs/cluster/birn/LEGACY/45/users/BWH/buckner_data/tutorial_subjs/group_analysis_tutorial/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=13.914377, niters=142.000000 $Id: mri_glmfit.c,v 1.225 2013/10/29 18:58:02 greve Exp $ cwd /autofs/cluster/birn/LEGACY/45/users/BWH/buckner_data/tutorial_subjs/group_analysis_tutorial/glm cmdline mri_glmfit --C lh.gender_age.glmdir/tmp.mri_glmfit-sim-18726/lh-Avg-thickness-age-Cor.mtx --sim mc-z 5 4 lh.gender_age.glmdir/csd/mc-z.negative.j001 --y lh.gender_age.thickness.10.mgh --mask lh.gender_age.glmdir/mask.mgh --sim-sign neg --fwhm 13.914377 --fsgd lh.gender_age.glmdir/y.fsgd dods --surf fsaverage lh white sysname Linux hostname sangwoo machine x86_64 user maritza FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 fwhm 13.914377 niters 142.000000 OneSampleGroupMean 0 y /autofs/cluster/birn/LEGACY/45/users/BWH/buckner_data/tutorial_subjs/group_analysis_tutorial/glm/lh.gender_age.thickness.10.mgh logyflag 0 usedti 0 FSGD lh.gender_age.glmdir/y.fsgd mask lh.gender_age.glmdir/mask.mgh maskinv 0 glmdir (null) IllCondOK 0 ReScaleX 1 DoFFx 0 Loading y from /autofs/cluster/birn/LEGACY/45/users/BWH/buckner_data/tutorial_subjs/group_analysis_tutorial/glm/lh.gender_age.thickness.10.mgh ... done reading. INFO: gd2mtx_method is dods Computing normalized matrix Normalized matrix condition is 22.1063 Matrix condition is 25322.5 Found 149953 voxels in mask Reshaping mriglm->mask... search space = 74612.446501 DOF = 36 thresh = 4, threshadj = 3.69897 Starting simulation sim over 5 trials mri_glmfit simulation done Fri Nov 1 09:10:40 EDT 2013 mri_surfcluster --in lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh --csd lh.gender_age.glmdir/csd/mc-z.negative.j001-lh-Avg-thickness-age-Cor.csd --mask lh.gender_age.glmdir/mask.mgh --cwsig lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.cluster.mgh --vwsig lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.voxel.mgh --sum lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.cluster.summary --ocn lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.ocn.mgh --oannot lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.ocn.annot --annot aparc --csdpdf lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.pdf.dat --cwpvalthresh 0.4 --o lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.masked.mgh --no-fixmni --surf white Creating CDFs from CSD files csd->threshsign = -1 thsign = neg, id = -1 version $Id: mri_surfcluster.c,v 1.56 2012/05/31 22:08:59 greve Exp $ hemi = lh srcid = lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh srcsubjid = fsaverage srcsurf = white srcframe = 0 thsign = neg thmin = 4 thmax = -1 fdr = -1 minarea = 0 xfmfile = talairach.xfm nth = -1 outid = lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.masked.mgh MGH ocnid = lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.ocn.mgh MGH sumfile = lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.cluster.summary subjectsdir = /autofs/cluster/birn/LEGACY/45/users/BWH/buckner_data/tutorial_subjs/group_analysis_tutorial FixMNI = 0 Found 149953 vertices in mask Found 149953 vertices in mask Found 149953 points in clabel. ------------- XFM matrix (RAS2RAS) --------------- /autofs/cluster/birn/LEGACY/45/users/BWH/buckner_data/tutorial_subjs/group_analysis_tutorial/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 /autofs/cluster/birn/LEGACY/45/users/BWH/buckner_data/tutorial_subjs/group_analysis_tutorial/fsaverage/surf/lh.white Done reading source surface Reading annotation /autofs/cluster/birn/LEGACY/45/users/BWH/buckner_data/tutorial_subjs/group_analysis_tutorial/fsaverage/label/lh.aparc.annot Computing metric properties Loading source values number of voxels in search space = 149953 Done loading source values (nvtxs = 163842) overall max = 3.62548 at vertex 153106 overall min = -11.4482 at vertex 134036 surface nvertices 163842 surface area 65417.097656 surface area 65416.648438 Computing voxel-wise significance CSDpvalMaxSigMap(): found 73475/163842 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 32 clusters Max cluster size 7917.266602 Pruning by CW P-Value 0.4 Saving thresholded output to lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.masked.mgh Saving cluster numbers to lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.ocn.mgh Saving cluster pval lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.cluster.mgh Constructing output annotation Writing annotation lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.ocn.annot mri_segstats --seg lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.ocn.mgh --exclude 0 --i lh.gender_age.thickness.10.mgh --avgwf lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.18726 $Id: mri_segstats.c,v 1.101 2013/08/20 15:52:54 greve Exp $ cwd cmdline mri_segstats --seg lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.ocn.mgh --exclude 0 --i lh.gender_age.thickness.10.mgh --avgwf lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.18726 sysname Linux hostname sangwoo machine x86_64 user maritza UseRobust 0 Loading lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.ocn.mgh Loading lh.gender_age.thickness.10.mgh Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 33 segmentations Computing statistics for each segmentation 1 1 8074 8074.000 2 2 17658 17658.000 3 3 3247 3247.000 4 4 388 388.000 5 5 2404 2404.000 6 6 1596 1596.000 7 7 911 911.000 8 8 937 937.000 9 9 450 450.000 10 10 1002 1002.000 11 11 1084 1084.000 12 12 1010 1010.000 13 13 451 451.000 14 14 483 483.000 15 15 440 440.000 16 16 565 565.000 17 17 246 246.000 18 18 184 184.000 19 19 123 123.000 20 20 134 134.000 21 21 235 235.000 22 22 104 104.000 23 23 56 56.000 24 24 386 386.000 25 25 106 106.000 26 26 203 203.000 27 27 59 59.000 28 28 56 56.000 29 29 27 27.000 30 30 9 9.000 31 31 10 10.000 32 32 1 1.000 Reporting on 32 segmentations Computing spatial average of each frame 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 Writing to lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.y.ocn.dat mri_segstats done mri_convert lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.cluster.mgh lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.cluster.mgh --frame 0 mri_convert lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.cluster.mgh lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.cluster.mgh --frame 0 $Id: mri_convert.c,v 1.205 2013/10/04 18:33:25 greve Exp $ reading from lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.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.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.cluster.mgh...