Hello, thanks for your response, your suggestions helped! We have a few more questions so here is a more in depth explanation of what our original issue was what we decided to do based off of your suggestions.

"We are trying to compare the raw fmri data for 6 runs (about 1400 TRs) of multi echo multiband data, averaged over the dorsal ACC region, to the fitted data generated from afni_proc. We thought the simplest thing to do would be to take our output fitts file, use 3dmaskave afni function to generate the average over the dorsal ACC for all 1400 TRs, use the same function on our residuals file, load it all into matlab and add the residuals to the fits to give us the 'raw' then plot this reconstructed 'raw' on top of the 'fits' to see how good the fits are in AFNI. Is this method valid or are we missing something? We tried to use the pb.04.combine data file in afni originally to look at 'raw' data, but it was scaled to extremely different values and we couldn't figure out how to get everything on the same scale. If you have tips, let us know."

Thanks!
Aidan Blankenship