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 01:20:20 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)
Segmentation fault