Hi all,
I think that there is a bug in mris_flatten of freesurfer version 4.0.0. It took more than 1000 iterations for each occiput patch of a subject, and they are getting flattened incorrectly. I went back to version 3.0.5, and the exact same patches are flattened correctly withing 200 - 300 iterations. I can upload pictures of the patches if you would like.
Best,
Valentin