Dear Jesper,
Sorry for the inconsistency topup command line on the previous email. I used ID on the command line instead of MMU45976_6M.
Thank you for your suggestions that solved my problem. But I got two questions for you. 1) Why does topup work better on unswaped b0 images? I assume sphinx position scans from head to foot on Z axial, therefore, we need to swap original b0 image x y z to swapped Rb0 image x z y. Then, topup will be applied on Rb0. 2) When I applied topup results, applytopup parameter topup should be rubbestad_field_coef.nii.gz, right? Thank you again!
Best wishes,
Joyce
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