Hi Deirdre, It looks like your skullstrip failed and left a lot of the neck which was mistaken for the cerebellum. The actual cerebellum was incorporated into your surfaces. Take a look at the wiki page below for how you might go about fixing this case.
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix
-Louis
On Tue, 19 Feb 2013, Deirdre O Shea wrote:
Dear FreeSurfer community,
After running FreeSurfer on almost a hundred subjects, I have encountered just two that have strange surface reconstructions. I have re-ran them from scratch hoping it would rectify this problem but to no avail. I have not done anything different with these subjects and the rest turned out okay. I have attached an image to show you what I mean. Any suggestions about why this happens and how it can be fixed would be great!
Thanks in advance,
Deirdre