Hi Bruce,

sorry, I meant to say that data is conformed.

It is primate data. I am having trouble with this particular data set only; the other ones are at the same resolution and worked fine.

I am attaching another screenshot to show that the control points unfortunately do not solve the problem. See occipital lobe.
Caspar

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

Hi Caspar,

that's probably part of the problem. Is this human data? If you actually run it at 1mm (conforming it) does it work better?

Bruce


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

It is originally 0.5x0.5x0.5 mm but we are pretending it's 1x1x1 mm.
Caspar


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