desphinxify is intended for datasets that are some variation of sphinx position to start. Left-right is assumed to be correct, but A-P and I-S are swapped. If you have the more general case, then you may want to follow a procedure like this one or one of the other ones mentioned in that thread. If you ALWAYS have the same orientation for acquisition (and anyone who uses your script in the distant future has the same one too), then you can then use just a 3drefit -orient ... command to reorient your data.