Thanks for your reply.
As to A: I performed the first-2dreg-then-3dreg order and first-3dreg-then-2dreg order in my data, yet found the same results. Anything wrong here?
B: By "really move to be alligned" I mean I want to know whether the position of volumes (as in 3dreg) really changed to be alligned after 3dreg.
For example: volume 1 is the reg target and volume 2 is 2 mm left to the volume 1. After 3dreg, does the volume 2 move 2 mm right?