Re: [Freesurfer] trouble with pial surface in v5.1

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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