Thanks Bob. To be honest, I intended to add to that post that there was probably a way to do it in AFNI that I was just unaware of, but then I forgot to write that. It certainly didn't come as a surprise that AFNI was one step ahead of me.
In any case, since we're on a roll here, there is one other thing I was wondering about. It would be great to have a way to automatically mask the overlay on the basis of the underlay. As things stand, if I run a second-level analysis I wind up making two copies, one of the original analysis and one masked by the intersection mask of the normalized data of the participants. But I don't really need both these files. Ideally, there would be some way that the AFNI viewer could on-the-fly mask the overlay by something like the 3dAutomasked underlay resampled into the grid of the overlay. That way I could see all the blobs outside of the brain but if I wanted to not see them I could also do that, without making a new masked output file on disk (not that this is a big deal from a storage standpoint, it's just an extra step that I have to do for every analysis).
Anyway, maybe there is a way to do something like this that I am unaware of, but in any case I thought I'd mention it. Thanks a lot either way.
James
