Hi Brenna
that's a bit strange. Yes, you will want to correct the aseg in either tkmedit or freeview as the presence of the putamen causes the surfaces to be clamped.
cheers Bruce
On Tue, 3 Sep 2013, Brenna Day wrote:
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
Inline image 1 Inline image 2 Inline image 3