Have you tried control points seeding, I usually place the control points right behind the surface in trouble areas so seeded points would push the surfaces forward.
-------- Original message --------
From: Saturne Fox <saturne.fox@gmail.com>
Date: 2016-05-31 1:20 AM (GMT-08:00)
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Manual segmentation issues