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 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/**complianceline<http://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.