Hi Freesurfers-
I was trying to run freesurfer on a study template and was having major problems with pial surface generation. Orig and Main surfaces seem to be ok, but there are major missing chinks in pial surface. Just to give some background, the template was being using for Diffeomorphic Image Registration, so it is a very unique volume.I know it is likely it is an intensity value issue.I wondered what folks have done previously to correct similar issues?
It appears to be across a massive proportion of the brain, so correcting by hand (by altering intensity values seems a bit labor intensive and perhaps questionable in terms of reliability). I also thought of trying to rerun some of the initial preprocessing (autorecon1 + 2) with some more 'expert settings'. Initially, I was running with no skull strip and no n3 flag (b/c the template has already been skull-stripped and massive preprocessed), but was looking for some additional advice and guidance.
Any thoughts or suggestions would be greatly appreciated.
Best, jamie.