Thank you for your reply. I did initially run eddy being aware that it can correct motion artifacts. Then checked the motion visually with the movie loop. The DWIs seem to still shift. Afterwards, I tried running mcflirt on the b0s and separately on the rest of DWIs. However, the DWIs, do not seem to be coregistered with much improvement.
The only other solution that I can think of is registering each DWI volume to my reference DWI with flirt, having a weight volume that basically tells to ignore the regions that are varying a lot from one volume to another.
Best,
Maria
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