I recently finished doing 3rd level analysis in FSL. Now, I am interested in using AFNI to extract activation data in my regions of interest.

I just started using AFNI on Monday and have gotten a lot of functionality out of it in just a few day with little effort. So, first off, thanks for a great program that is letting me do powerful things without an awful lot of effort.

Poking around in AFNI, I have found that I cannot use the "See TT Atlas Regions" options with my FSL datasets which were aligned to FSL's standard space. My understanding is that this is due to the fact that the FSL coordinates don't match AFNI ones. Is this correct? If so, what is the easiest way to get FSL files totally in line with AFNI, so I can use all its functionality.

Furthermore, I looked at the "Draw Dataset" plugin for AFNI and again found some very cool TT Atlas options, namely the ability to load regions in. How do I get my FSL files into a format so that I can use the AFNI tools to extract data from FSL according to region of interest? Is there some other way to use AFNI defined ROI's to extract data from FSL files?

Darren