Hi you could use fslhd to tell the orientation of your data.
For example, my following data has an LPS orientation.
fslhd MRI. nii
qform_xorient Right-to-Left
qform_yorient Anterior-to-Posterior
qform_zorient Inferior-to-Superior
Assuming you have a direct b0 map collected just as my case, then what you want to do is to make sure function data is in the same orientation as the b0 fieldmap. And you may also want to change the phase encoding direction if a flipping is made in the phase encoding direction.
Re how to change the orientation, I use fslreorient2std or nipype:
from nipype.interfaces.image import Reorient
I hope it helps.