I have a rather basic question about how to properly use eddy. I have two DTI scans (one was run in the P-A phase encoding direction, and the other was A-P). I've already run topup with the combined b0 volumes. For the eddy section though, does the --imain option need to be a merged file of the two DTI scans? So something like fslmerge -t DTI_combine_all.nii.gz DTI_PA.nii.gz DTI_AP.nii.gz
If this is the case, then do I also need to combine the .bval and .bvec files as well?
Thanks for the help.
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