Re: [Freesurfer] Large part of brain missing from wm.mgz and surfs

Hi Nicole

do you want to upload an example subject directory tarred and gzipped? We almost never see this, so it sounds like something is wrong.

cheers Bruce On Tue, 7 Feb 2012, Nicole Senecal wrote:

Hi all, My lab is just starting to use Freesurfer, and are finding that a lot of our recon-all jobs are needing a fair amount of editing. We've run into a problem that we can't figure out how to address - on several of our brains, a large chunk (up to 2/3 of the brain) is missing from the wm.mgz file and from surfs, although it IS present in the brainmask.mgz volume. Do we need to add control points manually to the entire brain? Why would this happen on multiple files?

thanks, Nicole