In the meantime, incase anyone else has this problem, here is a workaround that uses FSL. [url=https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Orientation%20Explained]It isn't the most elegant solution[/url]:

fslorient -deleteorient dwi_QCed.nii.gz
fslswapdim dwi_QCed.nii.gz -x y z dwi_reorient.nii.gz #WHETHER X Y AND Z ARE POSITIVE OR NEGATIVE DEPENDS ON THE ORIENTATION OF YOUR BRAIN
fslorient -setqformcode 1 dwi_reorient.nii.gz