Dear Freesurfer Experts,
This might be a very basic question, and sorry for posting again, but I would be grateful for any advice.
I have read the advice on the wiki regarding what to do when pial surfaces extend into the cerebellum. I had a few questions to clairfy things:
1) If I have made other (non-cerebellar) edits to the brainmask.mgz, and added control points can I simply do
cp brainmask.mgz brain.finalsurfs.manedit.mgz edit the cerebellum voxels out on the brain.finalsurfs.manedit.mgz run recon-all -autorecon2-cp -autorecon3 -subjid name
Will this then apply non-cerebellar and cerebellar edits (as well as control points) and give appropriate subcortical segmentations ?
OR
Do I have to
make non-cerbellar edits to brainmask.mgz cp brain.finalsurfs.mgz brain.finalsurfs.manedit.mgz make cerebellar edits to brain.finalsurfs.manedit.mgz run recon-all -autorecon2-cp -autorecon3 -subjid name
Thanks.
Mahinda