Dear Daniel,
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> 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
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> If this is the case, then do I also need to combine the .bval and .bvec files as well?
yes, you need to concatenate both the image files and the bvals and the bvecs. Use fslmerge (as you have indicated) for the image files and paste (a bash command) for the bvals/bvecs.
Jesper
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> Thanks for the help.
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