eddy combo makes the assumption that the third axis corresponds to slices, particularly now with
eddy's slice-to-volume motion correction. Therefore phase encoding can’t possibly occur along that axis.
What needs to be done is to permute the image axes so that the direction in which phase encoding was applied appears as one of the first two axes, perform the distortion correction, and then permute the axes back to their original order. This can be done using the
-axes option in
I did make an attempt at doing so seamlessly within
dwipreproc, but IIRC I got too frustrated because that script is a nightmare. So you’re stuck doing it on your own