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
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