This was a fairly regular MPRAGE, unfortunately not very well optimized for contrast. However, the main issue seems to be that the data were acquired with a surface coil here. That made some of the brain extremely bright (close to the coil) and some of the brain pretty dark (far away from the coil). In the screenshot that I sent you, there is some gray matter that has values between 95-100, which is well captured by the pial surface, while the grey matter in the more medial areas has values between 70 and 80. The transition where the pial surface starts to fail is when the gray matter values drop from above 90 to below 90.
Caspar


2013/10/3 Bruce Fischl <fischl@nmr.mgh.harvard.edu>
hmmmm. Can you tell us more about the acquisition?

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

the white matter is mostly between 100 and 110 in these regions. at least in
the center of the wm, the voxels are almost all 110.
caspar


2013/10/3 Bruce Fischl <fischl@nmr.mgh.harvard.edu>
      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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