Hello,
Occasionally I run into a problem with lower quality, noisy T1 images (1.5mmx1mmx1mm) where almost all of the tissue is classified as white matter. Upon inspecting these images (attached), I can understand why it would make this mistake; the white-gray matter border in them is very difficult to identify, and tissue intensity is almost homogenous, except for areas of partial voluming at the very outer edge (which is the only tissue contained by the pial surface - the white surface on these images).
Is there any way I can force the white matter segmentation step to be more conservative with some of its settings? For example, could I modify the intensity "threshold" for the wm segmentation step? Since this isn't an error described in the wiki, I'm guessing control points won't do me much good. Any suggestions would be great.
Victor Laluz : Imaging Coordinator : UCSF Memory and Aging Center