Hi Eric

there's a flag in the always-soon-to-be-released 5.2 that will run it

cheers Bruce On Tue, 19 Feb 2013, Eric Cunningham wrote:

oh interesting! i'm not sure if it will apply to me, but how would one go about the hires T2 / FLAIR based refinement? thanks, -eric

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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