cd /media/sda1/nmrclass/tutorial_data_Sep_2019_rev3/buckner_data/tutorial_subjs/group_analysis_tutorial_perm/glm /media/sda1/nmrclass/freesurfer/bin/mri_glmfit-sim --glmdir glm_challenge --perm 10 4.0 abs --cwp 0.05 --2spaces --bg 1 $Id: mri_glmfit-sim,v 1.66 2016/11/16 20:52:22 greve Exp $ Tue Sep 10 18:30:20 EDT 2019 Linux fsuser3-G5-5587 4.15.0-47-generic #50-Ubuntu SMP Wed Mar 13 10:44:52 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux nmrclass setenv SUBJECTS_DIR /media/sda1/nmrclass/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial_perm FREESURFER_HOME /media/sda1/nmrclass/freesurfer Original mri_glmfit command line: cmdline mri_glmfit.bin --y lh.gender_age.thickness.10.mgh --fsgd gender_age.fsgd dods --C challenge-Cor.mtx --surf fsaverage lh --cortex --glmdir glm_challenge --eres-save DoSim = 1 UseCache = 0 DoPoll = 1 DoPBSubmit = 0 DoBackground = 1 DiagCluster = 0 gd2mtx = dods fwhm = 0 nSimPerJob = 10 1/1 Tue Sep 10 18:30:20 EDT 2019 mri_glmfit --C glm_challenge/tmp.mri_glmfit-sim-8515/challenge-Cor.mtx --sim perm 10 4.0 glm_challenge/csd/perm.th40.abs.j001 --sim-sign abs --fwhm 0 --fsgd glm_challenge/y.fsgd dods --mask glm_challenge/mask.mgh --y glm_challenge/eres.mgh --perm-force --surf fsaverage lh white --sim-done glm_challenge/csd/poll/done.perm.th40.abs.j001 Polling Poll 1 job 1 Tue Sep 10 18:30:20 EDT 2019 INFO: ignoring tag Creator INFO: ignoring tag SUBJECTS_DIR INFO: ignoring tag SynthSeed simbase glm_challenge/csd/perm.th40.abs.j001 FWHM = 0.000000 gdfRead(): reading glm_challenge/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 /media/sda1/nmrclass/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 /media/sda1/nmrclass/tutorial_data_Sep_2019_rev3/buckner_data/tutorial_subjs/group_analysis_tutorial_perm/glm cmdline mri_glmfit.bin --C glm_challenge/tmp.mri_glmfit-sim-8515/challenge-Cor.mtx --sim perm 10 4.0 glm_challenge/csd/perm.th40.abs.j001 --sim-sign abs --fwhm 0 --fsgd glm_challenge/y.fsgd dods --mask glm_challenge/mask.mgh --y glm_challenge/eres.mgh --perm-force --surf fsaverage lh white --sim-done glm_challenge/csd/poll/done.perm.th40.abs.j001 sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /media/sda1/nmrclass/tutorial_data_Sep_2019_rev3/buckner_data/tutorial_subjs/group_analysis_tutorial_perm/glm/glm_challenge/eres.mgh logyflag 0 usedti 0 FSGD glm_challenge/y.fsgd mask glm_challenge/mask.mgh maskinv 0 glmdir (null) IllCondOK 0 ReScaleX 1 DoFFx 0 Loading y from /media/sda1/nmrclass/tutorial_data_Sep_2019_rev3/buckner_data/tutorial_subjs/group_analysis_tutorial_perm/glm/glm_challenge/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 10 trials mri_glmfit simulation done 0.123017 mri_surfcluster --in glm_challenge/challenge-Cor/sig.mgh --mask glm_challenge/mask.mgh --cwsig glm_challenge/challenge-Cor/perm.th40.abs.sig.cluster.mgh --sum glm_challenge/challenge-Cor/perm.th40.abs.sig.cluster.summary --ocn glm_challenge/challenge-Cor/perm.th40.abs.sig.ocn.mgh --annot aparc --cwpvalthresh 0.05 --o glm_challenge/challenge-Cor/perm.th40.abs.sig.masked.mgh --no-fixmni --csd glm_challenge/csd/perm.th40.abs.j001-challenge-Cor.csd --csdpdf glm_challenge/challenge-Cor/perm.th40.abs.pdf.dat --vwsig glm_challenge/challenge-Cor/perm.th40.abs.sig.voxel.mgh --vwsigmax glm_challenge/challenge-Cor/perm.th40.abs.sig.voxel.max.dat --oannot glm_challenge/challenge-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 = glm_challenge/challenge-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 = glm_challenge/challenge-Cor/perm.th40.abs.sig.masked.mgh MGH ocnid = glm_challenge/challenge-Cor/perm.th40.abs.sig.ocn.mgh MGH sumfile = glm_challenge/challenge-Cor/perm.th40.abs.sig.cluster.summary subjectsdir = /media/sda1/nmrclass/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) --------------- /media/sda1/nmrclass/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 /media/sda1/nmrclass/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial_perm/fsaverage/surf/lh.white Done reading source surface Reading annotation /media/sda1/nmrclass/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 = 3.51717 at vertex 53253 overall min = -2.97287 at vertex 16888 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 320/163842 above 0, max=0.19382 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 0 clusters Max cluster size 0.000000 Pruning by CW P-Value 0.05 Saving thresholded output to glm_challenge/challenge-Cor/perm.th40.abs.sig.masked.mgh Saving cluster numbers to glm_challenge/challenge-Cor/perm.th40.abs.sig.ocn.mgh Saving cluster pval glm_challenge/challenge-Cor/perm.th40.abs.sig.cluster.mgh Constructing output annotation Writing annotation glm_challenge/challenge-Cor/perm.th40.abs.sig.ocn.annot mri_segstats --seg glm_challenge/challenge-Cor/perm.th40.abs.sig.ocn.mgh --exclude 0 --i lh.gender_age.thickness.10.mgh --avgwf glm_challenge/challenge-Cor/perm.th40.abs.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.8515 $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --seg glm_challenge/challenge-Cor/perm.th40.abs.sig.ocn.mgh --exclude 0 --i lh.gender_age.thickness.10.mgh --avgwf glm_challenge/challenge-Cor/perm.th40.abs.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.8515 sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass UseRobust 0 Loading glm_challenge/challenge-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 1 segmentations Computing statistics for each segmentation Reporting on 0 segmentations Using PrintSegStat Computing spatial average of each frame Writing to glm_challenge/challenge-Cor/perm.th40.abs.y.ocn.dat mri_segstats done mri_convert glm_challenge/challenge-Cor/perm.th40.abs.sig.cluster.mgh glm_challenge/challenge-Cor/perm.th40.abs.sig.cluster.mgh --frame 0 mri_convert.bin glm_challenge/challenge-Cor/perm.th40.abs.sig.cluster.mgh glm_challenge/challenge-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 glm_challenge/challenge-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 glm_challenge/challenge-Cor/perm.th40.abs.sig.cluster.mgh... Tue Sep 10 18:30:20 EDT 2019 Tue Sep 10 18:30:42 EDT 2019 mri_glmfit-sim done