Hi Brendan if you send us the sample we can take a look, but in general the thickness is the average of the distance from the white to the pial with the distance from the pial to the white. Sometimes things can seem like a knot or tangle, but really it's just that the surface is almost parallel to a viewing plane (so it crosses back and forth over it lots of times in a short distance). Try looking at it in a different orientation and see if it loooks better.
Bruce On Wed, 3 Feb 2010, Brendan Robert Ansell wrote:
Hi, I have a set of fairly old MRIs which have been run on freesurfer. Occasionally scans have scrambled pial or white matter boundaries - a knot-like appearance especially in sulci. I am wondering how freesurfer estimates cortical thickness in these regions. For example, does it take the pial boundary closest to the white boundary i.e. the outer surface of the 'pial knot'? Are the encapsulated GM voxels included in the overall cortical thickness measurement?
Thanks-
Brendan Ansell MNC
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