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
