[Freesurfer] tksurfer buttons grayed out

[hranilovich]

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
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