cd /home1/am2359/fs6_data/fpeb_app_fs /home1/am2359/freesurfer_6/bin/mri_glmfit-sim --glmdir lh.sv2a_group.glmdir.10 --perm 1000 2 abs $Id: mri_glmfit-sim,v 1.60.2.4 2016/11/17 18:01:28 zkaufman Exp $ Fri Mar 2 03:23:25 EST 2018 Linux tauruspet.med.yale.edu 2.6.32-696.el6.x86_64 #1 SMP Tue Mar 21 19:29:05 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux am2359 setenv SUBJECTS_DIR /home1/am2359/fs6_data/fpeb_app_fs FREESURFER_HOME /home1/am2359/freesurfer_6 Original mri_glmfit command line: cmdline mri_glmfit.bin --y lh.sv2a.group.thickness.10.mgh --fsgd dx_sv2a.fsgd --C sv2a_thickness_group.mtx --surf fsaverage lh --cortex --glmdir lh.sv2a_group.glmdir.10 DoSim = 1 UseCache = 0 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 0 nSimPerJob = 1000 1/1 Fri Mar 2 03:23:25 EST 2018 mri_glmfit --C lh.sv2a_group.glmdir.10/tmp.mri_glmfit-sim-13158/sv2a_thickness_group.mtx --sim perm 1000 2 lh.sv2a_group.glmdir.10/csd/perm.th20.abs.j001 --sim-sign abs --fwhm 0 --fsgd lh.sv2a_group.glmdir.10/y.fsgd dods --y lh.sv2a.group.thickness.10.mgh --mask lh.sv2a_group.glmdir.10/mask.mgh --surf fsaverage lh white simbase lh.sv2a_group.glmdir.10/csd/perm.th20.abs.j001 FWHM = 0.000000 gdfRead(): reading lh.sv2a_group.glmdir.10/y.fsgd INFO: gd2mtx_method is dods Reading source surface /home1/am2359/fs6_data/fpeb_app_fs/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 /home1/am2359/fs6_data/fpeb_app_fs cmdline mri_glmfit.bin --C lh.sv2a_group.glmdir.10/tmp.mri_glmfit-sim-13158/sv2a_thickness_group.mtx --sim perm 1000 2 lh.sv2a_group.glmdir.10/csd/perm.th20.abs.j001 --sim-sign abs --fwhm 0 --fsgd lh.sv2a_group.glmdir.10/y.fsgd dods --y lh.sv2a.group.thickness.10.mgh --mask lh.sv2a_group.glmdir.10/mask.mgh --surf fsaverage lh white sysname Linux hostname tauruspet.med.yale.edu machine x86_64 user am2359 FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /home1/am2359/fs6_data/fpeb_app_fs/lh.sv2a.group.thickness.10.mgh logyflag 0 usedti 0 FSGD lh.sv2a_group.glmdir.10/y.fsgd mask lh.sv2a_group.glmdir.10/mask.mgh maskinv 0 glmdir (null) IllCondOK 0 ReScaleX 1 DoFFx 0 Loading y from /home1/am2359/fs6_data/fpeb_app_fs/lh.sv2a.group.thickness.10.mgh ... done reading. INFO: gd2mtx_method is dods Computing normalized matrix Normalized matrix condition is 1 Matrix condition is 1.1 Found 149953 voxels in mask Reshaping mriglm->mask... search space = 74612.064358 DOF = 19 thresh = 2, threshadj = 1.69897 Starting simulation sim over 1000 trials mri_glmfit simulation done 20.274 Fri Mar 2 03:43:45 EST 2018 mri_surfcluster --in lh.sv2a_group.glmdir.10/sv2a_thickness_group/sig.mgh --mask lh.sv2a_group.glmdir.10/mask.mgh --cwsig lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.sig.cluster.mgh --sum lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.sig.cluster.summary --ocn lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.sig.ocn.mgh --annot aparc --cwpvalthresh .05 --o lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.sig.masked.mgh --no-fixmni --csd lh.sv2a_group.glmdir.10/csd/perm.th20.abs.j001-sv2a_thickness_group.csd --csdpdf lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.pdf.dat --vwsig lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.sig.voxel.mgh --vwsigmax lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.sig.voxel.max.dat --oannot lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.sig.ocn.annot --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.sv2a_group.glmdir.10/sv2a_thickness_group/sig.mgh srcsubjid = fsaverage srcsurf = white srcframe = 0 thsign = abs thmin = 2 thmax = -1 fdr = -1 minarea = 0 xfmfile = talairach.xfm nth = -1 outid = lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.sig.masked.mgh MGH ocnid = lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.sig.ocn.mgh MGH sumfile = lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.sig.cluster.summary subjectsdir = /home1/am2359/fs6_data/fpeb_app_fs FixMNI = 0 Found 149953 vertices in mask Found 149953 vertices in mask Found 149953 points in clabel. ------------- XFM matrix (RAS2RAS) --------------- /home1/am2359/fs6_data/fpeb_app_fs/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 /home1/am2359/fs6_data/fpeb_app_fs/fsaverage/surf/lh.white Done reading source surface Reading annotation /home1/am2359/fs6_data/fpeb_app_fs/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 = 5.13607 at vertex 42693 overall min = -1.32724 at vertex 100014 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 4903/163842 above 0, max=1.35655 NOT Adjusting threshold for 1-tailed test thminadj = 2 Searching for Clusters ... thmin=2.000000 (2.000000), thmax=-1.000000 (-1), thsignid=0, minarea=0.000000 Found 27 clusters Max cluster size 470.815887 Pruning by CW P-Value 0.05 Saving thresholded output to lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.sig.masked.mgh Saving cluster numbers to lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.sig.ocn.mgh Saving cluster pval lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.sig.cluster.mgh Constructing output annotation Writing annotation lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.sig.ocn.annot mri_segstats --seg lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.sig.ocn.mgh --exclude 0 --i lh.sv2a.group.thickness.10.mgh --avgwf lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.13158 $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --seg lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.sig.ocn.mgh --exclude 0 --i lh.sv2a.group.thickness.10.mgh --avgwf lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.13158 sysname Linux hostname tauruspet.med.yale.edu machine x86_64 user am2359 UseRobust 0 Loading lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.sig.ocn.mgh Loading lh.sv2a.group.thickness.10.mgh Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 2 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.y.ocn.dat mri_segstats done mri_convert lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.sig.cluster.mgh lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.sig.cluster.mgh --frame 0 mri_convert.bin lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.sig.cluster.mgh lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.sig.cluster.mgh --frame 0 $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.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.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.sig.cluster.mgh... Fri Mar 2 03:23:25 EST 2018 Fri Mar 2 03:43:50 EST 2018 mri_glmfit-sim done