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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