afni.nimh.nih.gov

You don't say what that image is, but it looks like one of beta weights, not of a significance volume (t-/F-stat). But what is actually wrong with this? Note that afni_proc.py does not mask by default, since we would rather see what is happening outside the brain than simply hide it.

If you display the thresholded Full F-stat, and apply some threshold, how does that look?

- rick