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
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.