Try fixing the aseg and running from there forward
On Dec 28, 2011, at 9:05 PM, David Groppe david.m.groppe@gmail.com wrote:
Thanks for the speedy response Bruce. I'm running: $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $
-David
On Wed, Dec 28, 2011 at 7:44 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi David
what version are you running?
Bruce
On Wed, 28 Dec 2011, David Groppe wrote:
Hi FreeSurfers, I'm trying to fix FreeSurfer's pial and white matter surface boundary estimates on a brain missing a large part of the right hemisphere. I've manually filled in the greatly expanded ventricles in the damaged hemisphere as white matter (see attached) and tried rerunning recon-all with -autorecon2-wm and -autorecon3 flags. This fails to help. Is there sometime else I can do? thanks in advance, -David
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