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

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