is the WM in those regions already close to 110? No, there is no way to normalize GM intensity (it has too much biological variability over the brain)

On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote:

Thanks, Bruce. The problem is fairly extensive. There is no way to do
normalize grey matter intensity (the white surface looks pretty good)?Caspar

On Thursday, October 3, 2013, Bruce Fischl wrote:
      Hi Caspar

      try putting control points in the white matter where the pial
      surface doesn't get out far enough.

      cheers
      Bruce
      On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote:

            Hi Freesurfer Experts,
            I am working on a fairly noisy and inhomogeneous
            MPRAGE T1 and I am having
            trouble getting the pial surface to go all the way
            through the grey matter.
            Please see screenshot attached. These data were
            acquired with a surface coil
            and the grey matter varies a lot in intensity.
            Interestingly, the pial
            surface growing process fails where the grey matter
            is fairly dark. I have
            tried several rounds of normalizing using the N3
            tool but that didn't change
            anything.
            Thanks for any advice on this, Caspar




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