On Tue, Feb 19, 2013 at 11:44 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

Hi Eric

yes, the bits of dura left around (your red circles) will make the thickness incorrect in those regions. If you want to fix it you can try the graph cuts skull stripping, or if you have a hires T2 or FLAIR we can typically refine the surfaces to avoid dura. As for the yellow arrow, I can't tell from a single slice if that is an error. Certainly the intensities look like gray matter, but it could be damaged white matter instead.

cheers
Bruce

On Tue, 19 Feb 2013, Eric Cunningham wrote:

hello freesurfer experts,

attached is an image drawn from the tutorial page.
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits
i have circled 3 examples of what i am asking about

sometimes the gray matter surface (the red line) appears to include an area
of membrane or something else that isn't brain. will this adversely affect
the any of the measures in the region? what, if anything, should be done
about it?

thank you,
-eric cunningham

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