Hello FSL Diffusion Imaging Community,
I am currently collecting pilot multishell diffusion data and trying to establish a good processing pipeline. I will be using FSL's topup tool to correct for susceptibility induced distortions, but I am having some difficulty deciding whether it is necessary to run eddy (not eddy_correct). Initially, I collected data using a monpolar acquisition, so running eddy was necessary; however, through my reading, I came across a few papers, albeit somewhat older papers (e.g., http://mriquestions.com/uploads/3/4/5/7/34572113/reese.pdf, http://mriquestions.com/uploads/3/4/5/7/34572113/alexander_bipolar_diff_mrm_1997.pdf), that appear to imply that if a bipolar acquisition is used, eddy current correction is not necessary. Overall, I interpreted the papers to mean that eddy currents are significantly decreased when a bipolar acquisition is used, but would this mean that it is still prudent to run eddy to ensure that the data is in good shape or is only topup necessary?
Any information or wisdom you can provide on this topic would be greatly appreciated!
Thank you in advance for your help and wisdom!
Cristina
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