Thanks Daniel! I didn't realize the release date of that document was older than the others. Now, what I did is I ran the @auto_tlrc command to automatically transform my anat and func images from +orig to +tlrc/Talairach space, so I believe the 3dSkullstrip was automatically applied because my images now have no skull - just the brain. By your suggestion, I ran the Automask separately and came up with a pretty nice mask for the images. It may need a bit touching up, but overall it's better than anything I could display before. The dilemma I have now is that I cannot apply a correlational value to the mask, so the when the mask is selected as an overlay, it just displays at p=1 in all red and covers most of the brain. I want to get it to show activation (neg. and pos.) at p<0.5. AFNI doesn't allow me to compute a fit correlation using an ideal for the mask, as it does for the func files, so how would I go about doing that?

Thanks again!
-Dmitry