Hi Gabriel
I would run recon-all and see whether the remaining non-brain is included in the surfaces or cerebellum. If not you should be set. I would worry about shaving of gray matter though, which can be difficult to see.
cheers Bruce
On Tue, 12 Feb 2013, Gabriel Obregon wrote:
Hi,
I'm using the -gcut flag for the first time and I've noticed that the
skull stripping process is still leaving small fragments of dura behind. Will this affect my surfaces? Should I manually edit the brainmask volume to remove as much of these fragments as I can?
Also, should I only be concerned about the GM and cerebellum edges when
checking for over-aggressive cutting, or are other brain structures important as well, e.g. optic chiasm?
Thanks,
--G
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