Working with ROIs (Freesurfer)
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Joining and Intersecting .label Files
The .label files created during autorecon3, or by saving an overlay are plaintext lists of vertices. It should be straightforward to find the intersection or union of the vertices in two or more .label files using common Unix shell commands.
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2009-August/011743.html