I'm trying to use topup on pairs of scans that were acquired with coronal slices with F>>H phase encode.  My data are in RPI orientation and the size is 200x84x156 (84 slices).

If i say "0 0 -1 1" and "0 0 1 1" for the acquisition params, I get an error saying the 3rd column must be 0.  If I try 1 0 0 1, or 0 1 0 1, I get warping in the LR or AP axes, as expected.  I also tried fslswapdim <input> z x y <input>_swapped, followed by topup with "1 0 0 1" and "-1 0 0 1", but I still end up with warping in the LR direction.