Hi @LiuYuchen,
Firstly, I should note that the original question in this thread from @Yixin_Ma was explicitly about testing the efficacy of different acquisition / concatenation / averaging strategies, and wanting to perform the pre-processing in such a manner as to best facilitate such comparisons. In your case however it sounds like you simply want to process the data that you have acquired in the best manner possible.
As such, I would suggest firstly looking at the dwicat command, which aims to address the question of whether or not there are global signal intensity fluctuations between acquisitions. It may or may not be required for your data, but it’s worth running once to see whether the intensity balancing factors it derives deviate substantially from unity.
Secondly, when it comes to utilisation of repeated scans, I would refer to my recent response in another thread; note in particular the comment on concatenating rather than averaging data (which also “improves SNR” as far as the overall reconstruction is concerned, even if it doesn’t involve “increasing SNR” in individual DWI volumes through explicit averaging).
Cheers
Rob