this is because the aseg doesn't show any white matter, and so the pial surface is "frozen", since it is adjacent to a noncortical gray matter structure and assumed not to be part of cortex. What version are you running? We did have some fixes for this, but it may be that you need to draw a bit of white matter in lateral to basal ganglia
cheers Bruce
On Mon, 19 Nov 2012, ?? ? wrote:
Dear Freesurfer experts, I met a problem as shown in the appended figuer. You can see that in the insula, the pial surface abnormally curves in but the parcellation seems recognize the boundary of gray and white matter quite well. The tutorial tells us how to correct pial problem which generally incorporates dural as gray matter. However, in my case, the pial is too conservative in that region, ignores the gray matter, and nearly overlaps with white matter boundary. I cannot get help from the tutorial/manual. Could you please guide me how to correct this problem? Thanks in advance, JoJo