[Freesurfer] Fixing incorrect segmentation and pial surface

Hi,

I have a file where the pial surface is excluding some of the gray matter.

I edited wm.mgz and added control points to brainmask.mgz, this fixed some of the pial surface errors but not all. After looking at the aseg closer there is a section of incorrectly labeled wm near the pial surface errors. Voxels which look like they should be labeled at wm are labeled as left-putamen in the aseg. Is there a way to fix this other than manual edits to the aseg?

I'm using v5.0.0 and the aim is to run mri_segstats with the segmented brain and a matched PIB scan, so I do need the segmentation and the pial surface to be quite correct.

I've attached some screenshots of the problematic area, it runs through coronal slices 96-106 and 118-124.

Thanks for any help you can give. Regards,

Brenna

[image: Inline image 1][image: Inline image 2][image: Inline image 3]