cd /autofs/cluster/freesurfer/tutorials/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial_perm/glm /autofs/space/topaz_001/users/ah221/test/freesurfer/bin/mri_glmfit-sim --glmdir lh.gender_age.glmdir --perm 1000 4.0 abs --cwp 0.05 --2spaces --bg 1 --overwrite $Id: mri_glmfit-sim,v 1.66 2016/11/16 20:52:22 greve Exp $ Mon Oct 1 17:43:32 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/buckner_data/tutorial_subjs/group_analysis_tutorial_perm FREESURFER_HOME /autofs/space/topaz_001/users/ah221/test/freesurfer Original mri_glmfit command line: cmdline mri_glmfit.bin --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 --eres-save DoSim = 1 UseCache = 0 DoPoll = 1 DoPBSubmit = 0 DoBackground = 1 DiagCluster = 0 gd2mtx = dods fwhm = 0 nSimPerJob = 1000 1/1 Mon Oct 1 17:43:32 EDT 2018 mri_glmfit --C lh.gender_age.glmdir/tmp.mri_glmfit-sim-3637/lh-Avg-thickness-age-Cor.mtx --sim perm 1000 4.0 lh.gender_age.glmdir/csd/perm.th40.abs.j001 --sim-sign abs --fwhm 0 --fsgd lh.gender_age.glmdir/y.fsgd dods --mask lh.gender_age.glmdir/mask.mgh --y lh.gender_age.glmdir/eres.mgh --perm-force --surf fsaverage lh white --sim-done lh.gender_age.glmdir/csd/poll/done.perm.th40.abs.j001 Polling Poll 1 job 1 Mon Oct 1 17:43:32 EDT 2018 INFO: ignoring tag Creator INFO: ignoring tag SUBJECTS_DIR INFO: ignoring tag SynthSeed simbase lh.gender_age.glmdir/csd/perm.th40.abs.j001 FWHM = 0.000000 gdfRead(): 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/freesurfer/tutorials/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial_perm/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/buckner_data/tutorial_subjs/group_analysis_tutorial_perm/glm cmdline mri_glmfit.bin --C lh.gender_age.glmdir/tmp.mri_glmfit-sim-3637/lh-Avg-thickness-age-Cor.mtx --sim perm 1000 4.0 lh.gender_age.glmdir/csd/perm.th40.abs.j001 --sim-sign abs --fwhm 0 --fsgd lh.gender_age.glmdir/y.fsgd dods --mask lh.gender_age.glmdir/mask.mgh --y lh.gender_age.glmdir/eres.mgh --perm-force --surf fsaverage lh white --sim-done lh.gender_age.glmdir/csd/poll/done.perm.th40.abs.j001 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/buckner_data/tutorial_subjs/group_analysis_tutorial_perm/glm/lh.gender_age.glmdir/eres.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/freesurfer/tutorials/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial_perm/glm/lh.gender_age.glmdir/eres.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 = 74612.064358 INFO: design matrix is not orthogonal, but perm forced DOF = 36 thresh = 4, threshadj = 3.69897 Starting simulation sim over 1000 trials Poll 2 job 1 Mon Oct 1 17:43:42 EDT 2018 Poll 3 job 1 Mon Oct 1 17:43:52 EDT 2018 Poll 4 job 1 Mon Oct 1 17:44:02 EDT 2018 Poll 5 job 1 Mon Oct 1 17:44:12 EDT 2018 Poll 6 job 1 Mon Oct 1 17:44:22 EDT 2018 Poll 7 job 1 Mon Oct 1 17:44:32 EDT 2018 Poll 8 job 1 Mon Oct 1 17:44:42 EDT 2018 Poll 9 job 1 Mon Oct 1 17:44:52 EDT 2018 Poll 10 job 1 Mon Oct 1 17:45:02 EDT 2018 Poll 11 job 1 Mon Oct 1 17:45:12 EDT 2018 Poll 12 job 1 Mon Oct 1 17:45:22 EDT 2018 Poll 13 job 1 Mon Oct 1 17:45:32 EDT 2018 Poll 14 job 1 Mon Oct 1 17:45:42 EDT 2018 Poll 15 job 1 Mon Oct 1 17:45:52 EDT 2018 Poll 16 job 1 Mon Oct 1 17:46:02 EDT 2018 Poll 17 job 1 Mon Oct 1 17:46:12 EDT 2018 Poll 18 job 1 Mon Oct 1 17:46:22 EDT 2018 Poll 19 job 1 Mon Oct 1 17:46:32 EDT 2018 Poll 20 job 1 Mon Oct 1 17:46:42 EDT 2018 Poll 21 job 1 Mon Oct 1 17:46:52 EDT 2018 Poll 22 job 1 Mon Oct 1 17:47:02 EDT 2018 Poll 23 job 1 Mon Oct 1 17:47:12 EDT 2018 Poll 24 job 1 Mon Oct 1 17:47:22 EDT 2018 Poll 25 job 1 Mon Oct 1 17:47:32 EDT 2018 Poll 26 job 1 Mon Oct 1 17:47:42 EDT 2018 Poll 27 job 1 Mon Oct 1 17:47:52 EDT 2018 Poll 28 job 1 Mon Oct 1 17:48:02 EDT 2018 Poll 29 job 1 Mon Oct 1 17:48:12 EDT 2018 Poll 30 job 1 Mon Oct 1 17:48:22 EDT 2018 Poll 31 job 1 Mon Oct 1 17:48:32 EDT 2018 Poll 32 job 1 Mon Oct 1 17:48:42 EDT 2018 Poll 33 job 1 Mon Oct 1 17:48:52 EDT 2018 Poll 34 job 1 Mon Oct 1 17:49:02 EDT 2018 Poll 35 job 1 Mon Oct 1 17:49:12 EDT 2018 Poll 36 job 1 Mon Oct 1 17:49:22 EDT 2018 Poll 37 job 1 Mon Oct 1 17:49:32 EDT 2018 Poll 38 job 1 Mon Oct 1 17:49:42 EDT 2018 Poll 39 job 1 Mon Oct 1 17:49:52 EDT 2018 Poll 40 job 1 Mon Oct 1 17:50:02 EDT 2018 Poll 41 job 1 Mon Oct 1 17:50:12 EDT 2018 Poll 42 job 1 Mon Oct 1 17:50:22 EDT 2018 Poll 43 job 1 Mon Oct 1 17:50:33 EDT 2018 Poll 44 job 1 Mon Oct 1 17:50:43 EDT 2018 Poll 45 job 1 Mon Oct 1 17:50:53 EDT 2018 Poll 46 job 1 Mon Oct 1 17:51:03 EDT 2018 Poll 47 job 1 Mon Oct 1 17:51:13 EDT 2018 Poll 48 job 1 Mon Oct 1 17:51:23 EDT 2018 Poll 49 job 1 Mon Oct 1 17:51:33 EDT 2018 Poll 50 job 1 Mon Oct 1 17:51:43 EDT 2018 Poll 51 job 1 Mon Oct 1 17:51:53 EDT 2018 Poll 52 job 1 Mon Oct 1 17:52:03 EDT 2018 Poll 53 job 1 Mon Oct 1 17:52:13 EDT 2018 Poll 54 job 1 Mon Oct 1 17:52:23 EDT 2018 Poll 55 job 1 Mon Oct 1 17:52:33 EDT 2018 Poll 56 job 1 Mon Oct 1 17:52:43 EDT 2018 Poll 57 job 1 Mon Oct 1 17:52:53 EDT 2018 Poll 58 job 1 Mon Oct 1 17:53:03 EDT 2018 Poll 59 job 1 Mon Oct 1 17:53:13 EDT 2018 Poll 60 job 1 Mon Oct 1 17:53:23 EDT 2018 Poll 61 job 1 Mon Oct 1 17:53:33 EDT 2018 Poll 62 job 1 Mon Oct 1 17:53:43 EDT 2018 Poll 63 job 1 Mon Oct 1 17:53:53 EDT 2018 Poll 64 job 1 Mon Oct 1 17:54:03 EDT 2018 Poll 65 job 1 Mon Oct 1 17:54:13 EDT 2018 Poll 66 job 1 Mon Oct 1 17:54:23 EDT 2018 Poll 67 job 1 Mon Oct 1 17:54:33 EDT 2018 Poll 68 job 1 Mon Oct 1 17:54:43 EDT 2018 Poll 69 job 1 Mon Oct 1 17:54:53 EDT 2018 Poll 70 job 1 Mon Oct 1 17:55:03 EDT 2018 Poll 71 job 1 Mon Oct 1 17:55:13 EDT 2018 Poll 72 job 1 Mon Oct 1 17:55:23 EDT 2018 Poll 73 job 1 Mon Oct 1 17:55:33 EDT 2018 Poll 74 job 1 Mon Oct 1 17:55:43 EDT 2018 Poll 75 job 1 Mon Oct 1 17:55:53 EDT 2018 Poll 76 job 1 Mon Oct 1 17:56:03 EDT 2018 Poll 77 job 1 Mon Oct 1 17:56:13 EDT 2018 Poll 78 job 1 Mon Oct 1 17:56:23 EDT 2018 Poll 79 job 1 Mon Oct 1 17:56:33 EDT 2018 Poll 80 job 1 Mon Oct 1 17:56:43 EDT 2018 Poll 81 job 1 Mon Oct 1 17:56:53 EDT 2018 Poll 82 job 1 Mon Oct 1 17:57:03 EDT 2018 Poll 83 job 1 Mon Oct 1 17:57:13 EDT 2018 Poll 84 job 1 Mon Oct 1 17:57:23 EDT 2018 Poll 85 job 1 Mon Oct 1 17:57:33 EDT 2018 Poll 86 job 1 Mon Oct 1 17:57:43 EDT 2018 Poll 87 job 1 Mon Oct 1 17:57:53 EDT 2018 Poll 88 job 1 Mon Oct 1 17:58:03 EDT 2018 Poll 89 job 1 Mon Oct 1 17:58:13 EDT 2018 Poll 90 job 1 Mon Oct 1 17:58:23 EDT 2018 Poll 91 job 1 Mon Oct 1 17:58:33 EDT 2018 Poll 92 job 1 Mon Oct 1 17:58:43 EDT 2018 Poll 93 job 1 Mon Oct 1 17:58:53 EDT 2018 Poll 94 job 1 Mon Oct 1 17:59:03 EDT 2018 Poll 95 job 1 Mon Oct 1 17:59:13 EDT 2018 Poll 96 job 1 Mon Oct 1 17:59:23 EDT 2018 Poll 97 job 1 Mon Oct 1 17:59:33 EDT 2018 Poll 98 job 1 Mon Oct 1 17:59:43 EDT 2018 Poll 99 job 1 Mon Oct 1 17:59:53 EDT 2018 mri_glmfit simulation done 16.3381 mri_surfcluster --in lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh --mask lh.gender_age.glmdir/mask.mgh --cwsig lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/perm.th40.abs.sig.cluster.mgh --sum lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/perm.th40.abs.sig.cluster.summary --ocn lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/perm.th40.abs.sig.ocn.mgh --annot aparc --cwpvalthresh 0.05 --o lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/perm.th40.abs.sig.masked.mgh --no-fixmni --csd lh.gender_age.glmdir/csd/perm.th40.abs.j001-lh-Avg-thickness-age-Cor.csd --csdpdf lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/perm.th40.abs.pdf.dat --vwsig lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/perm.th40.abs.sig.voxel.mgh --vwsigmax lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/perm.th40.abs.sig.voxel.max.dat --oannot lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/perm.th40.abs.sig.ocn.annot --bonferroni 2 --surf white Creating CDFs from CSD files csd->threshsign = 0 thsign = abs, id = 0 version $Id: mri_surfcluster.c,v 1.57.2.3 2016/11/17 18:19:42 zkaufman Exp $ hemi = lh srcid = lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh srcsubjid = fsaverage srcsurf = white srcframe = 0 thsign = abs thmin = 4 thmax = -1 fdr = -1 minarea = 0 Bonferroni = 2 xfmfile = talairach.xfm nth = -1 outid = lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/perm.th40.abs.sig.masked.mgh MGH ocnid = lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/perm.th40.abs.sig.ocn.mgh MGH sumfile = lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/perm.th40.abs.sig.cluster.summary subjectsdir = /autofs/cluster/freesurfer/tutorials/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial_perm FixMNI = 0 Found 149953 vertices in mask Found 149953 vertices in mask Found 149953 points in clabel. ------------- XFM matrix (RAS2RAS) --------------- /autofs/cluster/freesurfer/tutorials/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial_perm/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/buckner_data/tutorial_subjs/group_analysis_tutorial_perm/fsaverage/surf/lh.white Done reading source surface Reading annotation /autofs/cluster/freesurfer/tutorials/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial_perm/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 = 3.62549 at vertex 153106 overall min = -11.4481 at vertex 134036 surface nvertices 163842 metric props tot surface area 65416.984375 group_avg_vtxarea_loaded 1 masked surface area 76467.078125 Computing voxel-wise significance CSDpvalMaxSigMap(): found 96240/163842 above 0, max=-inf NOT Adjusting threshold for 1-tailed test thminadj = 4 Searching for Clusters ... thmin=4.000000 (4.000000), thmax=-1.000000 (-1), thsignid=0, minarea=0.000000 Found 38 clusters Max cluster size 5238.312988 Pruning by CW P-Value 0.05 Saving thresholded output to lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/perm.th40.abs.sig.masked.mgh Saving cluster numbers to lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/perm.th40.abs.sig.ocn.mgh Saving cluster pval lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/perm.th40.abs.sig.cluster.mgh Constructing output annotation Writing annotation lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/perm.th40.abs.sig.ocn.annot mri_segstats --seg lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/perm.th40.abs.sig.ocn.mgh --exclude 0 --i lh.gender_age.thickness.10.mgh --avgwf lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/perm.th40.abs.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.3637 $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --seg lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/perm.th40.abs.sig.ocn.mgh --exclude 0 --i lh.gender_age.thickness.10.mgh --avgwf lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/perm.th40.abs.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.3637 sysname Linux hostname topaz.nmr.mgh.harvard.edu machine x86_64 user ah221 UseRobust 0 Loading lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/perm.th40.abs.sig.ocn.mgh Loading lh.gender_age.thickness.10.mgh Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 26 segmentations Computing statistics for each segmentation Reporting on 25 segmentations Using PrintSegStat 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 Writing to lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/perm.th40.abs.y.ocn.dat mri_segstats done mri_convert lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/perm.th40.abs.sig.cluster.mgh lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/perm.th40.abs.sig.cluster.mgh --frame 0 mri_convert.bin lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/perm.th40.abs.sig.cluster.mgh lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/perm.th40.abs.sig.cluster.mgh --frame 0 $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/perm.th40.abs.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/perm.th40.abs.sig.cluster.mgh... Mon Oct 1 17:43:32 EDT 2018 Mon Oct 1 18:00:16 EDT 2018 mri_glmfit-sim done