We're experiencing some difficulties with editing several of our control subjects' wm.mgz volumes. For many of them the ventricle space was not filled during the recon-all process (some subjs have enlarged ventricles, while others do not). Re-running with the - bigventricles flag did not correct the problem, and we subsequently filled the space manually by added new voxels (255 value) in the wm.mgz volume. After running them again under -autorecon2-wm, we discovered that the wm.mgz volumes now appear without any of our edits (as if they had been run with a -clean-wm flag). We edited and reran again, but with the exact same result for a second time, but only for a subset of the original (edits worked on some, didn't on others). Any thoughts as to why this is occurring? We are pretty confident that the volumes are saved each time edits are made, and we are not running with any -clean flags. If all else fails, is it permissible to using the subjects as is (see attached pics) if the surfaces being affected are only the 'unknown' regions? FS 4.1.0 is the version that is being used, thanks.
-Derin