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

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