Hi Rick,
Thanks for your help! I tried using 3dWarp on the afni dataset, with the matrix from my .mat file, but the warp file it produced still cuts off a lot of the brain; the image produced is basically a small box in the afni window. I also tried using 3dfractionize with the -template and -vote options and 3dresample with the -master option on the afni dataset but none of it seems to work properly. Could you please take a look at the dataset for me?