hmmm, that's pretty bad ringing in your data. You could try editing the
wm to remove incorrect segmentations in these regions (if the orig surface
also extends out too far).
On Fri, 5
Sep 2008, Christian Scheel wrote:
Dear FS-Experts,
While checking the results of the autorecon2 process and editing the
brainmask.mgz and wm.mgz I regularly encounter quite a few spots per brain
where - in my eyes - the red pial line seems to get far too close to the yellow
line making the calculated cortex appear too thin in these regions (see the
three examples attached). Sometimes the lines get so close that hardly any room
for the cortex is left.
I wonder what might be the best way to deal with these spots. Can I simply
ignore them or should I try to remove some parts of the white matter in the
wm.mgz (which will of course add another subjective factor into the analysis)
or is there another way of handling them that i did not think of?
Any help is greatly appreciated.
Best wishes,
Christian Scheel
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