External Email - Use Caution
Hi Freesurfer Developers,
I was hoping to get some advice on fixing pial surface error so we can calculate cortical thickness. In several patients, although the aseg is fine, the red outline for the pial surface is missing parts of the cortex (not the subcortical areas, those are alright). Unfortunately, we cannot use control points to edit the pial surface because there is no white matter in those parts of the brain. Is it possible to manually extend the pial surface to include the excluded cortex?
Also, I looked through the archive and found a similar question and read that overriding the intensity statistics that mris_make_surfaces computes automatically may solve my issue. If this is possible could I have some advice on how to do this?
Otherwise, if you have any advice to fix this problem we would greatly appreciate it.
Thanks, Monica