In the attached picture, the green line is the orig surface, not the wm surface. To get the wm outline:
tkmedit <subj> orig.mgz lh.white
and the lh.white surface outline will be yellow.
It may still be necessary to correct inaccuracies. See:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FixingGeomInaccuracies
On Fri, 2006-04-28 at 13:02 -0400, rhaynes@neuro.gatech.edu wrote:
After running the final processing stage of recon-all, I viewed the results in tkmedit and noticed several places where the wm and pial surfaces intersect (see attachment). This mostly happens on the medial and temporal areas, but I have seen it elsewhere. Doesn't this cause problems with the cortical thickness estimation? Is there anything else I should be doing to correct this? Thanks.
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