This is partially a follow-up question to another thread related to the mask.mgh generated by mri_glmfit (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50691.html).

We would like to use the mri_surfcluster tool on a log10p map.  I’m wondering — for vertex-wise analyses that use freesurfer-specific output (e.g., thickness, surface area, lgi, etc, not FMRI or DTI data)….can we rely on a single mask image for each hemisphere that comes from the fsaverage ?h.cortex.label? Or, should we be creating a mask that is specific to a given analysis/dataset, as is done with mri_glmfit?

If the latter, is there a way to create this mask outside of mri_glmfit?

Thank you in advance for your time and help! 

Best,

Ryan