cd /autofs/space/sand_001/users/zkaufman/tutorial_data/fsfast-functional/group/workmem.sm05.rh/encode-v-base
/usr/local/freesurfer/dev/bin/mri_glmfit-sim
--glmdir my-glm.wls --cache 3 pos --cwpvalthresh .0166

$Id: mri_glmfit-sim,v 1.52 2014/12/18 17:16:41 greve Exp $
Tue Dec 23 11:57:58 EST 2014
Linux sand 2.6.32-504.1.3.el6.x86_64 #1 SMP Tue Nov 11 17:57:25 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
zkaufman
setenv SUBJECTS_DIR /space/sand/1/users/zkaufman/tutorial_data/fsfast-tutorial.subjects
FREESURFER_HOME /usr/local/freesurfer/dev

Original mri_glmfit command line:
cmdline mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --surface fsaverage rh --glmdir my-glm.wls --nii.gz

DoSim = 0
UseCache = 1
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = dods
fwhm = 10.513341
CSD /usr/local/freesurfer/dev/average/mult-comp-cor/fsaverage/rh/cortex/fwhm11/pos/th30/mc-z.csd
mri_surfcluster --in my-glm.wls/osgm/sig.nii.gz --csd /usr/local/freesurfer/dev/average/mult-comp-cor/fsaverage/rh/cortex/fwhm11/pos/th30/mc-z.csd --mask my-glm.wls/mask.nii.gz --cwsig my-glm.wls/osgm/cache.th30.pos.sig.cluster.nii.gz --vwsig my-glm.wls/osgm/cache.th30.pos.sig.voxel.nii.gz --sum my-glm.wls/osgm/cache.th30.pos.sig.cluster.summary --ocn my-glm.wls/osgm/cache.th30.pos.sig.ocn.nii.gz --oannot my-glm.wls/osgm/cache.th30.pos.sig.ocn.annot --annot aparc --csdpdf my-glm.wls/osgm/cache.th30.pos.pdf.dat --cwpvalthresh .0166 --o my-glm.wls/osgm/cache.th30.pos.sig.masked.nii.gz --no-fixmni --surf white
Creating CDFs from CSD files
csd->threshsign = 1
thsign = pos, id = 1
version $Id: mri_surfcluster.c,v 1.57 2014/03/06 17:02:46 greve Exp $
hemi           = rh
srcid          = my-glm.wls/osgm/sig.nii.gz 
srcsubjid      = fsaverage
srcsurf        = white
srcframe       = 0
thsign         = pos
thmin          = 3
thmax          = -1
fdr            = -1
minarea        = 0
xfmfile        = talairach.xfm
nth         = -1
outid    = my-glm.wls/osgm/cache.th30.pos.sig.masked.nii.gz nii
ocnid    = my-glm.wls/osgm/cache.th30.pos.sig.ocn.nii.gz nii
sumfile  = my-glm.wls/osgm/cache.th30.pos.sig.cluster.summary
subjectsdir    = /space/sand/1/users/zkaufman/tutorial_data/fsfast-tutorial.subjects
FixMNI = 0
Found 149477 vertices in mask
Found 149477 vertices in mask
Found 149477 points in clabel.
------------- XFM matrix (RAS2RAS) ---------------
/space/sand/1/users/zkaufman/tutorial_data/fsfast-tutorial.subjects/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 /space/sand/1/users/zkaufman/tutorial_data/fsfast-tutorial.subjects/fsaverage/surf/rh.white
Done reading source surface
Reading annotation /space/sand/1/users/zkaufman/tutorial_data/fsfast-tutorial.subjects/fsaverage/label/rh.aparc.annot
Computing metric properties
Loading source values
number of voxels in search space = 149477
Done loading source values (nvtxs = 163842)
overall max = 11.715 at vertex 49595
overall min = -8.62222 at vertex 29967
surface nvertices 163842
surface area 65020.929688
surface area 65020.765625
Computing voxel-wise significance
CSDpvalMaxSigMap(): found 13983/163842 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 18 clusters
Max cluster size 6662.818848
Pruning by CW P-Value 0.0166
Saving thresholded output to  my-glm.wls/osgm/cache.th30.pos.sig.masked.nii.gz
Saving cluster numbers to my-glm.wls/osgm/cache.th30.pos.sig.ocn.nii.gz
Saving cluster pval my-glm.wls/osgm/cache.th30.pos.sig.cluster.nii.gz
Constructing output annotation
Writing annotation my-glm.wls/osgm/cache.th30.pos.sig.ocn.annot
mri_segstats --seg my-glm.wls/osgm/cache.th30.pos.sig.ocn.nii.gz --exclude 0 --i ces.nii.gz --sum /tmp/mri_glmfit-sim.junk.55554

$Id: mri_segstats.c,v 1.109 2014/10/17 19:31:46 greve Exp $
cwd 
cmdline mri_segstats --seg my-glm.wls/osgm/cache.th30.pos.sig.ocn.nii.gz --exclude 0 --i ces.nii.gz --sum /tmp/mri_glmfit-sim.junk.55554 
sysname  Linux
hostname sand
machine  x86_64
user     zkaufman
UseRobust  0
Loading my-glm.wls/osgm/cache.th30.pos.sig.ocn.nii.gz
Loading ces.nii.gz
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
mri_segstats done
mri_convert my-glm.wls/osgm/cache.th30.pos.sig.cluster.nii.gz my-glm.wls/osgm/cache.th30.pos.sig.cluster.nii.gz --frame 0
mri_convert my-glm.wls/osgm/cache.th30.pos.sig.cluster.nii.gz my-glm.wls/osgm/cache.th30.pos.sig.cluster.nii.gz --frame 0 
$Id: mri_convert.c,v 1.215 2014/12/17 00:09:19 greve Exp $
reading from my-glm.wls/osgm/cache.th30.pos.sig.cluster.nii.gz...
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 my-glm.wls/osgm/cache.th30.pos.sig.cluster.nii.gz...