FSL - TBSS: how to handle topup and eddy correction for data that's already distortion corrected at the MRI scanner?


I am trying to do TBSS on a population of MS-patients. My DTI images are distortion corrected during scanning and therefore I assume topup is not necessary. However, if I skip topup, then I am missing an output that’s needed for the next step, eddy correction (using “eddy” command). Anyone that can recommend a solution for this? Should I just use eddy_cuda? “eddy_correct” could be an alternative but I’ve read that it should be avoided.

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Have you tried running ‘eddy’ without topup i.e omitting the --topup parameter?

If you run eddy without topup it will correct for eddy current distortions and movement (sounds like you’ve already corrected for susceptibility distortion).

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