Hello Freesurfer Experts,

I am trying to plot the ${meas} values at the maximum vertex in a significant cluster found by the group analysis pipeline (mri_glmfit).

I created an .mgh file with mris_preproc, rh.cbd7.area.10.mgh.  I read this file into matlab using MRIread.  (mgh=MRIread(${path}/rh.cbd7.area.10.mgh);)  After running mri_glmfit and mri_glmfit-sim, I found a significant cluster with maximum at vertex 53263.  I read the values at this vertex using matlab again (values=mgh.vol(1,53263,1,:)).  I then tried to duplicate the p value that mri_glmfit gave me at that vertex in R, and was unsuccessful (the p values did not match, and were actually quite different). 

I had assumed that mri_glmfit ran a glm at every vertex of the smoothed mgh file created by mris_preproc, and that the p values of that glm were assembled into sig.mgh.  Was this assumption wrong?

Thanks,

-Eric