You can use mri_segstats with either the --sum option (for an input with one time point) or --avgwf (for multiple). Pass your mask with --seg. By default it will give you both outside the mask (first column) and inside the mask (second column).

Hi Freesurfer Team,

I have previously used mri_binarize to derive the mask.mgh from the sig.mgh after a first-level group comparison of cortical thickness. Now, I would like to extract the vertex data from from another modality surface within and outside the mask in individual subjects. Is there an nice workflow to do that?

Thanks a lot. I hope my question made sense!

Best Wishes,

Elijah 

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