Hi Mahinda,
I believe that the intent of the brain.finalsurfs.mgz is to allow you to make edits that are only for the ?h.white/?h.pial surface placement, so you should be able to erase the whole cerebellum with no impact on the measures.
cheers Bruce
On Sat, 21 Jan 2012, Mahinda Yogarajah wrote:
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:
- 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