Hello again Paul,

I was hoping to check-in one more time about this. I originally found the solution to this problem from the @auto_tlrc help page. Specifically, here:

"1- Oh my God! The brain is horribly distorted (by Jason Stein):
The probable cause is a failure of 3dWarpDrive to converge.
In that case, rerun the script with the option
-xform shift_rotate_scale. That usually takes care of it.
Update:
The script now has a mechanism for detecting cases
where convergence is not reached and it will automatically
change -xform to fix the problem. So you should see very
few such cases. If you do, check the skull stripping
step for major errors and if none are found send the
authors a copy of the command you used, the input and base
data and they'll look into it."

But, it also says here that the script is automatically supposed to change -xform when convergence isn't reached. However, it ends up providing the terminal output from my initial message, and I then always have to reprocess the subject after adding "-xform shift_rotate_scale" manually in the script. I made sure I am using the latest AFNI version and that everything else is up to date, in case that was the problem. This is part of our standard preprocessing pipeline, so it would be super useful if the script automatically changed -xform without having to re-run the entire script. Please let me know if I'm misunderstanding something here, and thanks so much for your help!

Sincerely,
Ian