I guess the better term would be to say that I'm not sure if the cluster correction is using the monte-carlo I made from the label file correctly.

I see on the wiki and in the mailing list you can use a different directory and then spec that folder using mri_glmfit-sim with the --cache-dir flag.  When I run it like that, I get this output
mri_glmfit-sim --glmdir rh.ALESocial__agevolume.glmdir --cache-dir /media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/ --cwp 0.05 --2spaces --sim
ERROR: flag --sim requires four arguments

When I specify the sim (which I'm not sure I need since I ran the simulation already) and sim-sign abs, and run either of the following, I get these as outputs:

mri_glmfit-sim --glmdir rh.ALESocial__agevolume.glmdir --sim mc-z 10000 2 /media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/ --sim-sign abs --2spacescmdline mri_glmfit --y rh.diagnosisxageICVslopetest.volume.10.mgh --fsgd SBM_glmVolumeNOGENDER.fsgd dods --C diagnosisnonlGIICmeas.mtx --C agesxdiagnosisnonlGI.mtx --C diagnosisnonxagexICmeas.mtx --C ICmeasurexdiagnosisnonlGI.mtx --surf fsaverage rh --label /media/rkbatch/gyrification/fsaverage/label/rh.SocialBrainMask --glmdir rh.ALESocial__agevolume.glmdir
SURFACE: fsaverage rh
log file is rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log
tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory

tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory
cd /media/rkbatch/gyrification
tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory
/usr/local/freesurfer/bin/mri_glmfit-sim
tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory
--glmdir rh.ALESocial__agevolume.glmdir --sim mc-z 10000 2 /media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/ --sim-sign abs --2spaces
tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory

tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory
$Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $
tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory
Mon Oct 20 15:06:19 CDT 2014
tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory
Linux waffle 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:39:51 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux
tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory
tderamus
tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory
setenv SUBJECTS_DIR /media/rkbatch/gyrification
tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory
FREESURFER_HOME /usr/local/freesurfer
tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory

tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory
Original mri_glmfit command line:
tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory
cmdline mri_glmfit --y rh.diagnosisxageICVslopetest.volume.10.mgh --fsgd SBM_glmVolumeNOGENDER.fsgd dods --C diagnosisnonlGIICmeas.mtx --C agesxdiagnosisnonlGI.mtx --C diagnosisnonxagexICmeas.mtx --C ICmeasurexdiagnosisnonlGI.mtx --surf fsaverage rh --label /media/rkbatch/gyrification/fsaverage/label/rh.SocialBrainMask --glmdir rh.ALESocial__agevolume.glmdir
tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory

tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory
DoSim = 1
tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory
UseCache = 0
tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory
DoPoll = 0
tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory
DoPBSubmit = 0
tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory
DoBackground = 0
tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory
DiagCluster = 0
tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory
gd2mtx = dods
tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory
tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory
fwhm = 14.594354
tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory
nSimPerJob = 10000
tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory
1/1 Mon Oct 20 15:06:19 CDT 2014
tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory
mri_glmfit --y /media/rkbatch/gyrification/rh.diagnosisxageICVslopetest.volume.10.mgh --C rh.ALESocial__agevolume.glmdir/tmp.mri_glmfit-sim-20978/agesxdiagnosisnonlGI.mtx --C rh.ALESocial__agevolume.glmdir/tmp.mri_glmfit-sim-20978/diagnosisnonlGIICmeas.mtx --C rh.ALESocial__agevolume.glmdir/tmp.mri_glmfit-sim-20978/diagnosisnonxagexICmeas.mtx --C rh.ALESocial__agevolume.glmdir/tmp.mri_glmfit-sim-20978/ICmeasurexdiagnosisnonlGI.mtx --mask rh.ALESocial__agevolume.glmdir/mask.mgh --sim mc-z 10000 2 rh.ALESocial__agevolume.glmdir/csd//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.j001 --sim-sign abs --fwhm 14.594354 --fsgd rh.ALESocial__agevolume.glmdir/y.fsgd dods --label /media/rkbatch/gyrification/fsaverage/label/rh.SocialBrainMask --surf fsaverage rh white
tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.mri_glmfit-sim.log: No such file or directory
INFO: ignoring tag Creator
INFO: ignoring tag SUBJECTS_DIR
INFO: ignoring tag SynthSeed
MatrixMultiply: m1 is null!

No such file or directory
simbase rh.ALESocial__agevolume.glmdir/csd//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/.j001
FWHM = 14.594354
gdfReadHeader: reading rh.ALESocial__agevolume.glmdir/y.fsgd
INFO: NOT demeaning continuous variables
Continuous Variable Means (all subjects)
0 Age 18.4329 6.76585
1 tICV 1.67822e+06 146117
Class Means of each Continuous Variable
1 CTRL  18.2315 1690205.3333
2 ASD  18.6525 1665138.7273

mri_glmfit-sim --glmdir rh.ALESocial__agevolume.glmdir --sim mc-z 10000 2 /media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd --sim-sign abs --2spaces
cmdline mri_glmfit --y rh.diagnosisxageICVslopetest.volume.10.mgh --fsgd SBM_glmVolumeNOGENDER.fsgd dods --C diagnosisnonlGIICmeas.mtx --C agesxdiagnosisnonlGI.mtx --C diagnosisnonxagexICmeas.mtx --C ICmeasurexdiagnosisnonlGI.mtx --surf fsaverage rh --label /media/rkbatch/gyrification/fsaverage/label/rh.SocialBrainMask --glmdir rh.ALESocial__agevolume.glmdir
SURFACE: fsaverage rh
log file is rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log
tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log: No such file or directory

tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log: No such file or directory
cd /media/rkbatch/gyrification
tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log: No such file or directory
/usr/local/freesurfer/bin/mri_glmfit-sim
tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log: No such file or directory
--glmdir rh.ALESocial__agevolume.glmdir --sim mc-z 10000 2 /media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd --sim-sign abs --2spaces
tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log: No such file or directory

tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log: No such file or directory
$Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $
tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log: No such file or directory
Mon Oct 20 15:04:37 CDT 2014
tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log: No such file or directory
Linux waffle 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:39:51 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux
tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log: No such file or directory
tderamus
tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log: No such file or directory
setenv SUBJECTS_DIR /media/rkbatch/gyrification
tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log: No such file or directory
FREESURFER_HOME /usr/local/freesurfer
tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log: No such file or directory

tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log: No such file or directory
Original mri_glmfit command line:
tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log: No such file or directory
cmdline mri_glmfit --y rh.diagnosisxageICVslopetest.volume.10.mgh --fsgd SBM_glmVolumeNOGENDER.fsgd dods --C diagnosisnonlGIICmeas.mtx --C agesxdiagnosisnonlGI.mtx --C diagnosisnonxagexICmeas.mtx --C ICmeasurexdiagnosisnonlGI.mtx --surf fsaverage rh --label /media/rkbatch/gyrification/fsaverage/label/rh.SocialBrainMask --glmdir rh.ALESocial__agevolume.glmdir
tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log: No such file or directory

tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log: No such file or directory
DoSim = 1
tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log: No such file or directory
UseCache = 0
tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log: No such file or directory
DoPoll = 0
tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log: No such file or directory
DoPBSubmit = 0
tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log: No such file or directory
DoBackground = 0
tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log: No such file or directory
DiagCluster = 0
tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log: No such file or directory
gd2mtx = dods
tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log: No such file or directory
tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log: No such file or directory
fwhm = 14.594354
tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log: No such file or directory
nSimPerJob = 10000
tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log: No such file or directory
1/1 Mon Oct 20 15:04:37 CDT 2014
tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log: No such file or directory
mri_glmfit --y /media/rkbatch/gyrification/rh.diagnosisxageICVslopetest.volume.10.mgh --C rh.ALESocial__agevolume.glmdir/tmp.mri_glmfit-sim-20856/agesxdiagnosisnonlGI.mtx --C rh.ALESocial__agevolume.glmdir/tmp.mri_glmfit-sim-20856/diagnosisnonlGIICmeas.mtx --C rh.ALESocial__agevolume.glmdir/tmp.mri_glmfit-sim-20856/diagnosisnonxagexICmeas.mtx --C rh.ALESocial__agevolume.glmdir/tmp.mri_glmfit-sim-20856/ICmeasurexdiagnosisnonlGI.mtx --mask rh.ALESocial__agevolume.glmdir/mask.mgh --sim mc-z 10000 2 rh.ALESocial__agevolume.glmdir/csd//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.j001 --sim-sign abs --fwhm 14.594354 --fsgd rh.ALESocial__agevolume.glmdir/y.fsgd dods --label /media/rkbatch/gyrification/fsaverage/label/rh.SocialBrainMask --surf fsaverage rh white
tee: rh.ALESocial__agevolume.glmdir//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.mri_glmfit-sim.log: No such file or directory
INFO: ignoring tag Creator
INFO: ignoring tag SUBJECTS_DIR
INFO: ignoring tag SynthSeed
MatrixMultiply: m1 is null!

No such file or directory
simbase rh.ALESocial__agevolume.glmdir/csd//media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/fwhm13/abs/th20/mc-z.csd.j001
FWHM = 14.594354
gdfReadHeader: reading rh.ALESocial__agevolume.glmdir/y.fsgd
INFO: NOT demeaning continuous variables
Continuous Variable Means (all subjects)
0 Age 18.4329 6.76585
1 tICV 1.67822e+06 146117
Class Means of each Continuous Variable
1 CTRL  18.2315 1690205.3333
2 ASD  18.6525 1665138.7273

Since the directory and flags are returning errors, I'm assuming I'm just inputing everything incorrectly or its a path issue. Does that help?

On Mon, Oct 20, 2014 at 2:53 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

what do you mean it has trouble understanding? What is your command line
and terminal output. Also, are you following these instructions?

https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo


On 10/20/2014 03:50 PM, Thomas DeRamus wrote:
> Dear Freesurfer Experts,
>
> I have a label file of a number of ROI's I've made based on a mask.
> I'm trying to get an idea of what cluster are significant within a
> focused region of the label file.
>
> To make the correction a little less sever, I pre-computed some
> monte-carlo values using mri_mcsim
>
> mri_mcsim --o
> /media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain
> --base mc-z --surface fsaverage rh --nreps 10000 --label
> /media/rkbatch/gyrification/fsaverage/label/rh.SocialBrainMask
>
> mri_mcsim --o
> $SUBJECTS_DIR/fsaverage/mult-comp-cor/fsaverage/lh/Socialbrain --base
> mc-z --surface fsaverage lh --nreps 10000 --label
> $SUBJECTS_DIR/fsaverage/label/lh.SocialBrainMask
>
> Respectively for each surface (the labels are different on each
> hemisphere).
>
> I've run mri_glmfit and have the uncorrected outputs and results
> (there are actually 6 of these, one for volume, thickness, and surface
> area for each hemi):
>
> mri_glmfit --y rh.diagnosisxagexrightThickslopetest.thickness.10.mgh
> --fsgd SBM_glmRightthickNOGENDER.fsgd dods --C
> diagnosisnonlGIICmeas.mtx --C agesxdiagnosisnonlGI.mtx --C
> diagnosisnonxagexICmeas.mtx --C ICmeasurexdiagnosisnonlGI.mtx --surf
> fsaverage rh --label
> /media/rkbatch/gyrification/fsaverage/label/rh.SocialBrainMask
> --glmdir rh.ALESocial__agethickness.glmdir
>
> But when I try to do the mri_glmfit-sim, I am having trouble getting
> it to read in the corrected csd file.
>
> I'm wanting to run it at cwp of 0.05 at a threshold of 2 (0.01), with
> a correction for two hemispheres. However, when I try to run it with
> --cache-dir
> /media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/lh/Socialbrain
> , it has trouble understanding the --cwp .05, --2spaces and 2 abs
> (after cache dir) flags. Additionally, it wants a --sim and --sim-sign
> value like it wants to compute a monte-carlo from scratch.
>
> Could I get an example on how best to direct it to the simulation I've
> run on it?
>
> Thanks much.
> -Thomas
>
>
> --
> *Thomas DeRamus*
> UAB Department of Psychology, Behavioral Neuroscience
> Graduate Research Trainee
> Civitan International Research Center
> 1719 6th Ave S, Suite 235J, Birmingham, AL 35233
> _Phone_: 205-934-0971 <tel:205-934-0971> _Email:_ tpderamus@gmail.com
> <mailto:tpderamus@gmail.com>, faustus@uab.edu <mailto:faustus@uab.edu>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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--
Thomas DeRamus
UAB Department of Psychology, Behavioral Neuroscience
Graduate Research Trainee
Civitan International Research Center
1719 6th Ave S, Suite 235J, Birmingham, AL 35233
Phone: 205-934-0971 Email: tpderamus@gmail.com, faustus@uab.edu