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

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer