Hi all,

I have a few subjects who have angled cutting planes. I ran talairach <subjid> and rerun the mri_fill and there is a very angled cut. A reason for this may be that the pons have been removed during white matter segmentation. The brain images have the pons intact but the wm images don’t. I’ve run recon-all stage1, segment_subject, and process volume from the csurf interface. They all remove the pons. I’ve also tracked the coordinates of the pons in the brain volumes and used those in the mri_fill command (-P <x> <y> <z>). Is there a reason for this and a way to fix it?

Thank you,

Thang Nguyen