Hi Matt,
thanks for your answer. I did this before, I mean run eddy_current first, and then split up the 4D image and average the corresponding acquisitions and then put the averaged volumes back together to a 4D image. Just wanted to make sure that this is common practice.
Regarding my 2nd question: I am doing the BET after eddy_current correction at the moment - I am just not sure whether it is wise thinking eddy_current correction may give better results using the brain only, but then the BET results may not be the same for each volume (using 1st volume, ie b0, as reference) in case the subject has moved.
Would you use BET before or after eddy_current correction?
Thanks,
Torsten
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