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