what resolution?

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

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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