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Dear Megan, > Can you please advise me on how to deal with slice drop outs when using eddy? I'm not using a blip-up blip-down sequence but my diffusion encoding directions span the entire sphere. I have found that compared to eddy_correct, eddy works much better for my data - no "tremor" at all (side note, Jesper have you thought about naming it "steddy"?). I quite like that idea. Can you come up with a suggestion for what that is an abbreviation for? > > I saw in a previous post that in the future eddy may be able to perform the QC but will that be for blip-up blip-down sequences only? I think I might have been unclear then. There is no reason why that would require blippie sequences. We are currently working on getting the QC in place and that will definitely be part of the next release of eddy. I'm afraid I can't really give a time frame for that though. > > In the meantime, should I exclude the volumes with the slice drop out and amend the bvecs, bvals, index and acqp files accordingly? Yes, for volumes with bad drop-out that is the best option. Note also that if you get drop-out in a large proportion of your volumes it might be a sign that you are using a too severe partial k-space acquisition. My personal experience is for example that 5/8 is to severe and that 3/4 is better for reducing drop-out. Hope that helps Jesper