Hi Doug, Thank you for the information about the matlab method.
Since asking the question, I found a way to do this with the help of tksurfer and freesurfer commands, and wanted to share with the community, in case someone will find this useful in the future. Basically, after the desired regions are saved as labels (using one of the desired methods in tksurfer), geometric overlap (and other regional interactions) can be calculated using the "mris_label_calc" function. Best, Arkadiy
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