> What you loose in that case is the possibility to do pairwise least-squares restoration. Ok, I acknowledge I'm late to the game on this thread, but it's the only one that relates to the problem I'm having. We're collecting identical acquisitions (each 145 volumes) with reversed PE direction, then using topup to create the "field map", and feeding all 290 volumes into eddy. This, not surprisingly, spits out 290 corrected volumes. While it's great to do all the corrections in a single step, what I really want is 145 images that are corrected AND weighted based on blip a la applytopup. So the question is: How do I get pairwise least-squares restoration using eddy? It does not appear to be the default or immediately obvious to invoke. Do I need to do it in a separate step? Any help is appreciated.