[Freesurfer] Pial Surfaces Cutting off Gyri

Hello brilliant and generous FS people,

I have introduced a problem I cannot solve. I am simply trying to capture as much gray matter as possible. We have some very bad constrast images (ghostly edeges where the gray matter should be). I'm adding control points to try to capture - however, now when I run AR2-cp, the pial surfaces go haywire on the superior borders of the slices.

Attached are two images displaying the problem.

I have edited wm.mgz to fill in the ventricles because I was getting islands, and I manually edited the brainmask to remove some vasculature that was being included in the pial surfaces.

Can you tell me where I introduced this instability?

Best Regards, Sherri