We're taking a look at using FreeSurfer for our lab's analysis of cortical thickness...just ran a fully automated recon-all on one of our lab's brains that generated no error messages and looks good in the "Inspection of Freesurfer Output" exercise from your tutorial. However, I noticed while moving through this exercise that the curvature file button, pial surface button, and the thickness map button are grayed out (not available for use) in the tksurfer toolbox. If this means there was some subtle error in the output - any ideas where to begin troubleshooting? Perhaps automatic topology defect correction? Not sure how obvious the topology defects you refer to would be on inspection; there were no holes or handles that I could see in the inflated surface, though ours was more lumpy than the tutorial's...Some dura was left in and was designated cortex, lying outside of the pial surface generated. Could this be the issue? If so, would the solution be an adjustment of the watershed parameters fix it, or is that really intended for large over-inclusions of skull?
Thanks - Jennifer