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Dear Miguel, I have a dataset with two diffusion acquisitions for 40 directions and reverse polarity. The problem is that they have different TEs: - 1st dataset: TE = 77 ms, blip down - 2nd dataset: TE = 110ms, blip up Do you know if there is any configuration parameter I can tune, or any preprocessing that I can apply to my data for topup to work? I already tried scaling the second dataset, slice-wise, to match the first one by the result still shows misalignment. I don’t have a good feel for how different the contrast is between TE77 and TE110. I would have thought that if they were not massively different topup would still be able to improve on things. Though I suspect it would always struggle to do a perfect job on data with different echo time. One thing you might consider trying could be “histogram matching”. It is an image processing trick, and I _think_ there are Matlab tools for doing that, though I am not sure if it is part of Matlab or one of the toolboxes. Jesper Thank you for your help. Best regards, Miguel.