Hi Babak - 

Thank you very much for getting back to me!

You were correct. The aberations appear to have been caused by trying to use files that I first processed with AFNI and then further processed with ART. To compensate for this, I have now run just files that have been run in ART alone using the -A command, but the final registerd brain appears to have more badly warped areas than it had been using my previous pipeline. I cannot remember the numbers offhand, but I belive it is 3 out of 25 of my brains had a major 3D warping aberation while the previous version had had 0 out of 25 with a major problem.

I haven't yet had a chance to try using the applywarp3d command, but it is certainly worth a shot. Thank you very much for the suggestion. 

Thank you again for your help!

Matt