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Matt, Thank you for the response! The field of view between our DTI acquisition and field map acquisition match (read=210mm, phase=100%), and both cover whole brain. Our field maps are SE EPI images collected in opposite phase encoding directions, A>P and P>A. Forgive me if this is still too vague, if you would like more detail I would be happy to share more of our acquisition privately. Based on your response, it would seem that we can run topup with our fieldmaps and feed that into eddy, rather than using fsl_prepare_fieldmap and fugue/feat to register our field maps to our eddy-corrected b0, correct? Your guidance is much appreciated. Best, Josh ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1