I used dcm2niix to generate .json files of my DTI data. The first (P--A) has a phase encoding direction of "j", and the second (A--P) has a phase encoding direction of "j-". I'm now trying to coregister my anatomical to my DTI data (I've already performed topup and eddy correction). For the eddy step I combined the two DTI scans, but for epi_reg, I'm not sure what I'm supposed to specify for --pedir
Thank you for the help.
Dan
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