New subject: Running mri_glmfit-sim with pre-computed Monte-Carlo

20 Oct 2014

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> <tel:205-934-0971
<tel:205-934-0971>> _Email:_ tpderamus@gmail.com
<mailto:tpderamus@gmail.com>
> <mailto:tpderamus@gmail.com <mailto:tpderamus@gmail.com>>,
faustus@uab.edu <mailto:faustus@uab.edu> <mailto:faustus@uab.edu
<mailto:faustus@uab.edu>>
>
>
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