Hello, In FS v4.0.1 the Aseg Stats stage now occurs toward the end of the recon-all script, and is designed to use the "--surf-wm-vol" flag if both the lh.white and rh.white surfaces exist.
Just wanted to point out that if any subsequent edits are made resulting in changes to either lh.white or rh.white (e.g. as a consequence of making edits and then running either -autorecon2-cp, -autorecon2-wm, or -autorecon2-pial), the values for "cerebral-white-matter" volume contained in aseg.stats will no longer reflect the true volume for the current ?h.white surfaces, since Aseg Stats is not automatically rerun as part of those flags.
Perhaps "set DoSegStats = 1" should be included as part of any flag that results in new ?h.white surfaces?
cheers, Mike H .