Hello,
I've been banging my head against the wall and keyboard to get mris_make_surfaces generate correct pial surfaces. While the white matter surface looks okay for the most part, the pial matter surfaces almost never actually reach the pial surface, but rather stop very close to the white matter surface. I was able to get it pushed out a bit by setting MIN_GRAY_AT_CSF_BORDER and MAX of that same parameter to really low numbers, but then it makes the error of putting the pial surface somewhere in the csf. Is there a list of parameters that I can play with to correct this problem?
I should note that I'm working with macaque MRI's acquired at 0.35mm iso that have been made to look like they were acquired at 1mm in order to make freesurfer happy. If there is a thickness limit to gray matter, then this may fail at some locations because of the incorrect voxel size. Is there such a limit set in mris_make_surfaces?
Many thanks in advance for your help,
Reza