mri_glmfit-sim --glmdir ./rh.38sb_score.dods.glmdir --no-sim mc-z.neg.3 --cwpvalthresh 0.1 cmdline mri_glmfit --y rh.38sb_score.10.mgh --fsgd 38sb_score.fsgd dods --C 38sb_score-dods.mtx --surf fsaverage rh --cortex --glmdir rh.38sb_score.dods.glmdir SURFACE: fsaverage rh log file is ./rh.38sb_score.dods.glmdir/mc-z.neg.3.mri_glmfit-sim.log cd /mnt/sdb1/psylab16/BACKUP/freesurfer/freesurfer/subjects/glm /mnt/sdb1/psylab16/BACKUP/freesurfer/freesurfer/bin/mri_glmfit-sim --glmdir ./rh.38sb_score.dods.glmdir --no-sim mc-z.neg.3 --cwpvalthresh 0.1 $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $ Wed Feb 26 14:36:27 CST 2014 Linux centos2 2.6.18-308.20.1.el5xen #1 SMP Tue Nov 13 11:03:56 EST 2012 x86_64 x86_64 x86_64 GNU/Linux psylab16 setenv SUBJECTS_DIR /mnt/sdb1/psylab16/BACKUP/freesurfer/freesurfer/subjects FREESURFER_HOME /mnt/sdb1/psylab16/BACKUP/freesurfer/freesurfer Original mri_glmfit command line: cmdline mri_glmfit --y rh.38sb_score.10.mgh --fsgd 38sb_score.fsgd dods --C 38sb_score-dods.mtx --surf fsaverage rh --cortex --glmdir rh.38sb_score.dods.glmdir DoSim = 0 UseCache = 0 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 14.015189 mri_surfcluster --in ./rh.38sb_score.dods.glmdir/38sb_score-dods/sig.mgh --csd ./rh.38sb_score.dods.glmdir/csd/mc-z.neg.3.j001-38sb_score-dods.csd --csd ./rh.38sb_score.dods.glmdir/csd/mc-z.neg.3.j002-38sb_score-dods.csd --csd ./rh.38sb_score.dods.glmdir/csd/mc-z.neg.3.j003-38sb_score-dods.csd --csd ./rh.38sb_score.dods.glmdir/csd/mc-z.neg.3.j004-38sb_score-dods.csd --csd ./rh.38sb_score.dods.glmdir/csd/mc-z.neg.3.j005-38sb_score-dods.csd --csd ./rh.38sb_score.dods.glmdir/csd/mc-z.neg.3.j006-38sb_score-dods.csd --csd ./rh.38sb_score.dods.glmdir/csd/mc-z.neg.3.j007-38sb_score-dods.csd --csd ./rh.38sb_score.dods.glmdir/csd/mc-z.neg.3.j008-38sb_score-dods.csd --csd ./rh.38sb_score.dods.glmdir/csd/mc-z.neg.3.j009-38sb_score-dods.csd --csd ./rh.38sb_score.dods.glmdir/csd/mc-z.neg.3.j010-38sb_score-dods.csd --csd ./rh.38sb_score.dods.glmdir/csd/mc-z.neg.3.j011-38sb_score-dods.csd --csd ./rh.38sb_score.dods.glmdir/csd/mc-z.neg.3.j012-38sb_score-dods.csd --csd ./rh.38sb_score.dods.glmdir/csd/mc-z.neg.3.j013-38sb_score-dods.csd --csd ./rh.38sb_score.dods.glmdir/csd/mc-z.neg.3.j014-38sb_score-dods.csd --csd ./rh.38sb_score.dods.glmdir/csd/mc-z.neg.3.j015-38sb_score-dods.csd --csd ./rh.38sb_score.dods.glmdir/csd/mc-z.neg.3.j016-38sb_score-dods.csd --csd ./rh.38sb_score.dods.glmdir/csd/mc-z.neg.3.j017-38sb_score-dods.csd --csd ./rh.38sb_score.dods.glmdir/csd/mc-z.neg.3.j018-38sb_score-dods.csd --csd ./rh.38sb_score.dods.glmdir/csd/mc-z.neg.3.j019-38sb_score-dods.csd --csd ./rh.38sb_score.dods.glmdir/csd/mc-z.neg.3.j020-38sb_score-dods.csd --mask ./rh.38sb_score.dods.glmdir/mask.mgh --cwsig ./rh.38sb_score.dods.glmdir/38sb_score-dods/mc-z.neg.3.sig.cluster.mgh --vwsig ./rh.38sb_score.dods.glmdir/38sb_score-dods/mc-z.neg.3.sig.voxel.mgh --sum ./rh.38sb_score.dods.glmdir/38sb_score-dods/mc-z.neg.3.sig.cluster.summary --ocn ./rh.38sb_score.dods.glmdir/38sb_score-dods/mc-z.neg.3.sig.ocn.mgh --oannot ./rh.38sb_score.dods.glmdir/38sb_score-dods/mc-z.neg.3.sig.ocn.annot --annot aparc --csdpdf ./rh.38sb_score.dods.glmdir/38sb_score-dods/mc-z.neg.3.pdf.dat --cwpvalthresh 0.1 --o ./rh.38sb_score.dods.glmdir/38sb_score-dods/mc-z.neg.3.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 1.51.2.3 2012/05/31 22:10:05 greve Exp $ hemi = rh srcid = ./rh.38sb_score.dods.glmdir/38sb_score-dods/sig.mgh srcsubjid = fsaverage srcsurf = white srcframe = 0 thsign = neg thmin = 3 thmax = -1 fdr = -1 minarea = 0 xfmfile = talairach.xfm nth = -1 outid = ./rh.38sb_score.dods.glmdir/38sb_score-dods/mc-z.neg.3.sig.masked.mgh MGH ocnid = ./rh.38sb_score.dods.glmdir/38sb_score-dods/mc-z.neg.3.sig.ocn.mgh MGH sumfile = ./rh.38sb_score.dods.glmdir/38sb_score-dods/mc-z.neg.3.sig.cluster.summary subjectsdir = /mnt/sdb1/psylab16/BACKUP/freesurfer/freesurfer/subjects FixMNI = 0 Found 149926 vertices in mask Found 149926 vertices in mask Found 149926 points in clabel. ------------- XFM matrix (RAS2RAS) --------------- /mnt/sdb1/psylab16/BACKUP/freesurfer/freesurfer/subjects/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 /mnt/sdb1/psylab16/BACKUP/freesurfer/freesurfer/subjects/fsaverage/surf/rh.white Done reading source surface Reading annotation /mnt/sdb1/psylab16/BACKUP/freesurfer/freesurfer/subjects/fsaverage/label/rh.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 = 149926 Done loading source values (nvtxs = 163842) overall max = 2.41955 at vertex 93589 overall min = -5.2195 at vertex 4418 surface nvertices 163842 surface area 65020.929688 surface area 65020.765625 Computing voxel-wise significance CSDpvalMaxSigMap(): found 2222/163842 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 9 clusters Max cluster size 123.432686 Pruning by CW P-Value 0.1 Saving thresholded output to ./rh.38sb_score.dods.glmdir/38sb_score-dods/mc-z.neg.3.sig.masked.mgh Saving cluster numbers to ./rh.38sb_score.dods.glmdir/38sb_score-dods/mc-z.neg.3.sig.ocn.mgh Saving cluster pval ./rh.38sb_score.dods.glmdir/38sb_score-dods/mc-z.neg.3.sig.cluster.mgh Constructing output annotation Writing annotation ./rh.38sb_score.dods.glmdir/38sb_score-dods/mc-z.neg.3.sig.ocn.annot mri_segstats --seg ./rh.38sb_score.dods.glmdir/38sb_score-dods/mc-z.neg.3.sig.ocn.mgh --exclude 0 --i /mnt/sdb1/psylab16/BACKUP/freesurfer/freesurfer/subjects/glm/rh.38sb_score.10.mgh --avgwf ./rh.38sb_score.dods.glmdir/38sb_score-dods/mc-z.neg.3.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.1113 $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg ./rh.38sb_score.dods.glmdir/38sb_score-dods/mc-z.neg.3.sig.ocn.mgh --exclude 0 --i /mnt/sdb1/psylab16/BACKUP/freesurfer/freesurfer/subjects/glm/rh.38sb_score.10.mgh --avgwf ./rh.38sb_score.dods.glmdir/38sb_score-dods/mc-z.neg.3.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.1113 sysname Linux hostname centos2 machine x86_64 user psylab16 UseRobust 0 Loading ./rh.38sb_score.dods.glmdir/38sb_score-dods/mc-z.neg.3.sig.ocn.mgh Loading /mnt/sdb1/psylab16/BACKUP/freesurfer/freesurfer/subjects/glm/rh.38sb_score.10.mgh Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 2 segmentations Computing statistics for each segmentation 1 1 226 226.000 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./rh.38sb_score.dods.glmdir/38sb_score-dods/mc-z.neg.3.y.ocn.dat mri_segstats done mri_convert ./rh.38sb_score.dods.glmdir/38sb_score-dods/mc-z.neg.3.sig.cluster.mgh ./rh.38sb_score.dods.glmdir/38sb_score-dods/mc-z.neg.3.sig.cluster.mgh --frame 0 mri_convert ./rh.38sb_score.dods.glmdir/38sb_score-dods/mc-z.neg.3.sig.cluster.mgh ./rh.38sb_score.dods.glmdir/38sb_score-dods/mc-z.neg.3.sig.cluster.mgh --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from ./rh.38sb_score.dods.glmdir/38sb_score-dods/mc-z.neg.3.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 ./rh.38sb_score.dods.glmdir/38sb_score-dods/mc-z.neg.3.sig.cluster.mgh... Wed Feb 26 14:36:27 CST 2014 Wed Feb 26 14:36:32 CST 2014 mri_glmfit-sim done