dhcp-10-240-197-124:NIMROD_DTI MacPro$ mri_glmfit-sim --glmdir tau_lh_ad_hc.glmdir --cache 2 neg --cwp 0.05 --2spaces cmdline mri_glmfit --y concat_ad_hc_lh_tau_sm2.mgh --fsgd tau_ad_control_fsgd --C tau_hc_ad.mtx --glmdir tau_lh_ad_hc.glmdir --surf fsaverage lh --cortex SURFACE: fsaverage lh log file is tau_lh_ad_hc.glmdir/cache.mri_glmfit-sim.log cd /Users/MacPro/Documents/NIMROD_DTI /Applications/freesurfer6beta/bin/mri_glmfit-sim --glmdir tau_lh_ad_hc.glmdir --cache 2 neg --cwp 0.05 --2spaces $Id: mri_glmfit-sim,v 1.53.2.2 2015/08/28 19:00:13 greve Exp $ Sat Apr 16 01:22:12 BST 2016 Darwin dhcp-10-240-197-124.cp.wireless.private.cam.ac.uk 14.0.0 Darwin Kernel Version 14.0.0: Fri Sep 19 00:26:44 PDT 2014; root:xnu-2782.1.97~2/RELEASE_X86_64 x86_64 MacPro setenv SUBJECTS_DIR /Users/MacPro/Documents/NIMROD_DTI/ FREESURFER_HOME /Applications/freesurfer6beta Original mri_glmfit command line: cmdline mri_glmfit --y concat_ad_hc_lh_tau_sm2.mgh --fsgd tau_ad_control_fsgd --C tau_hc_ad.mtx --glmdir tau_lh_ad_hc.glmdir --surf fsaverage lh --cortex DoSim = 0 UseCache = 1 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 12.549009 CSD /Applications/freesurfer6beta/average/mult-comp-cor/fsaverage/lh/cortex/fwhm13/neg/th20/mc-z.csd mri_surfcluster --in tau_lh_ad_hc.glmdir/tau_hc_ad/sig.mgh --csd /Applications/freesurfer6beta/average/mult-comp-cor/fsaverage/lh/cortex/fwhm13/neg/th20/mc-z.csd --mask tau_lh_ad_hc.glmdir/mask.mgh --cwsig tau_lh_ad_hc.glmdir/tau_hc_ad/cache.th20.neg.sig.cluster.mgh --vwsig tau_lh_ad_hc.glmdir/tau_hc_ad/cache.th20.neg.sig.voxel.mgh --sum tau_lh_ad_hc.glmdir/tau_hc_ad/cache.th20.neg.sig.cluster.summary --ocn tau_lh_ad_hc.glmdir/tau_hc_ad/cache.th20.neg.sig.ocn.mgh --oannot tau_lh_ad_hc.glmdir/tau_hc_ad/cache.th20.neg.sig.ocn.annot --annot aparc --csdpdf tau_lh_ad_hc.glmdir/tau_hc_ad/cache.th20.neg.pdf.dat --cwpvalthresh 0.05 --o tau_lh_ad_hc.glmdir/tau_hc_ad/cache.th20.neg.sig.masked.mgh --no-fixmni --bonferroni 2 --surf white Creating CDFs from CSD files csd->threshsign = -1 thsign = neg, id = -1 version $Id: mri_surfcluster.c,v 1.57 2014/03/06 17:02:46 greve Exp $ hemi = lh srcid = tau_lh_ad_hc.glmdir/tau_hc_ad/sig.mgh srcsubjid = fsaverage srcsurf = white srcframe = 0 thsign = neg thmin = 2 thmax = -1 fdr = -1 minarea = 0 Bonferroni = 2 xfmfile = talairach.xfm nth = -1 outid = tau_lh_ad_hc.glmdir/tau_hc_ad/cache.th20.neg.sig.masked.mgh MGH ocnid = tau_lh_ad_hc.glmdir/tau_hc_ad/cache.th20.neg.sig.ocn.mgh MGH sumfile = tau_lh_ad_hc.glmdir/tau_hc_ad/cache.th20.neg.sig.cluster.summary subjectsdir = /Users/MacPro/Documents/NIMROD_DTI/ FixMNI = 0 Found 146238 vertices in mask Found 146238 vertices in mask Found 146238 points in clabel. ------------- XFM matrix (RAS2RAS) --------------- /Users/MacPro/Documents/NIMROD_DTI//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 /Users/MacPro/Documents/NIMROD_DTI//fsaverage/surf/lh.white Done reading source surface Reading annotation /Users/MacPro/Documents/NIMROD_DTI//fsaverage/label/lh.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 = 146238 Done loading source values (nvtxs = 163842) overall max = 1.15204 at vertex 83208 overall min = -5.52419 at vertex 49465 surface nvertices 163842 surface area 65417.097656 surface area 65416.648438 Computing voxel-wise significance CSDpvalMaxSigMap(): found 50849/163842 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=2.000000 (1.698970), thmax=-1.000000 (-1), thsignid=-1, minarea=0.000000 Found 74 clusters Max cluster size 18149.767578 Pruning by CW P-Value 0.05 Saving thresholded output to tau_lh_ad_hc.glmdir/tau_hc_ad/cache.th20.neg.sig.masked.mgh Saving cluster numbers to tau_lh_ad_hc.glmdir/tau_hc_ad/cache.th20.neg.sig.ocn.mgh Saving cluster pval tau_lh_ad_hc.glmdir/tau_hc_ad/cache.th20.neg.sig.cluster.mgh Constructing output annotation Writing annotation tau_lh_ad_hc.glmdir/tau_hc_ad/cache.th20.neg.sig.ocn.annot mri_segstats --seg tau_lh_ad_hc.glmdir/tau_hc_ad/cache.th20.neg.sig.ocn.mgh --exclude 0 --i concat_ad_hc_lh_tau_sm2.mgh --avgwf tau_lh_ad_hc.glmdir/tau_hc_ad/cache.th20.neg.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.92380 $Id: mri_segstats.c,v 1.110.2.5 2015/10/06 18:46:28 greve Exp $ cwd cmdline mri_segstats --seg tau_lh_ad_hc.glmdir/tau_hc_ad/cache.th20.neg.sig.ocn.mgh --exclude 0 --i concat_ad_hc_lh_tau_sm2.mgh --avgwf tau_lh_ad_hc.glmdir/tau_hc_ad/cache.th20.neg.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.92380 sysname Darwin hostname dhcp-10-240-197-124.cp.wireless.private.cam.ac.uk machine x86_64 user MacPro UseRobust 0 Loading tau_lh_ad_hc.glmdir/tau_hc_ad/cache.th20.neg.sig.ocn.mgh Loading concat_ad_hc_lh_tau_sm2.mgh Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 5 segmentations Computing statistics for each segmentation Reporting on 4 segmentations Using PrintSegStat Computing spatial average of each frame 0 1 2 3 Writing to tau_lh_ad_hc.glmdir/tau_hc_ad/cache.th20.neg.y.ocn.dat mri_segstats done mri_convert tau_lh_ad_hc.glmdir/tau_hc_ad/cache.th20.neg.sig.cluster.mgh tau_lh_ad_hc.glmdir/tau_hc_ad/cache.th20.neg.sig.cluster.mgh --frame 0 mri_convert tau_lh_ad_hc.glmdir/tau_hc_ad/cache.th20.neg.sig.cluster.mgh tau_lh_ad_hc.glmdir/tau_hc_ad/cache.th20.neg.sig.cluster.mgh --frame 0 $Id: mri_convert.c,v 1.221.2.2 2015/10/02 16:39:36 zkaufman Exp $ reading from tau_lh_ad_hc.glmdir/tau_hc_ad/cache.th20.neg.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 tau_lh_ad_hc.glmdir/tau_hc_ad/cache.th20.neg.sig.cluster.mgh... Sat Apr 16 01:22:12 BST 2016 Sat Apr 16 01:22:16 BST 2016 mri_glmfit-sim done