Same issue here.

We notice that it might ART issue for motion. We test on one subject with a lot of motion. It was chopped off. For the other subject with minimum motion, no chop-off happening. Did not know how to solve the issue. Take the volumes out before preprocessing, or etc. 

If it is bounding box issue. How shall we fix that? How big shall we use? it didn't seem to me the chop-off is cubed.