[Freesurfer] Original Brain Surface Transparent

Hi Everyone Again,

I thought I'd re-state my question more clearly:

I managed to make an annotation with 2 parts: one, of interest, and the other, not. On the color table file, the "not of interest" part has 0 0 0 0 for Red, Green, Blue, and Opacity.

However, when I load the annotation in TkSurfer, the "not of interest" part of the brain is the original grey.

So, here is my question: is there a way to make the original brain surface transparent? If not, then it is pointless for me to have the "not of interest" part in my annotation at all.

Thanks very much,

Allie Rosen, MSc Graduate Student, Department of Neurosurgery Toronto Western Hospital 14-327 399 Bathurst St. University of Toronto