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Jesper, Really appreciate the quick response! Just to confirm, the acquisition should be: 1) blip-down b0 (just 1 volume) 2) 96 direction 3000 bvalue blip-up scan (first volume is b0 => 97 total volumes) 3) 96 direction 2500 bvalue blip-up scan (first volume is b0 => 97 total volumes) 4) 96 direction 2000 bvalue blip-up scan (first volume is b0 => 97 total volumes) 5) 96 direction 1500 bvalue blip-up scan (first volume is b0 => 97 total volumes) 6) 96 direction 1000 bvalue blip-up scan (first volume is b0 => 97 total volumes) I'm a little confused as to what the inputs to topup/eddy should be: --- 1) all_b0s = [blip-down b0, blip-up b0 (from bvalue = 3000), blip-up b0 (from bvalue = 2500), blip-up b0 (from bvalue = 2000), blip-up b0 (from bvalue = 1500), blip-up b0 (from bvalue = 1000)] ? and all_dwmri = [scan 2); scan 3); scan 4); scan 5); scan 6]; (total length = 5*96) index = [2...2 3...3 4...4 5...5 6...6]; (total length = 5*96) (or is it ok to keep the blip-down b0 in the all_dwmri and add a 1 to the front of "index"?) OR 2) all_b0s = [blip-up b0 (from bvalue = 3000), blip-down b0, blip-up b0 (from bvalue = 2500), blip-up b0 (from bvalue = 2000), blip-up b0 (from bvalue = 1500), blip-up b0 (from bvalue = 1000)] ? all_dwmri = [scan 2); scan 3); scan 4); scan 5); scan 6]; index = [1...1 3...3 4...4 5...5 6...6]; (total length = 5*96) --- I was under the impression that the first b0 in topup needs to correspond to the first b0 in eddy? Is that incorrect? The only requirement is that the first b0 in topup needs to be collected close in time to the first dwmri volume given to eddy? Thanks! -Justin