Problems in use .nrrd format from 3d slicer in python.

[pieper (Steve Pieper (Isomics, Inc.))]

This is normal - Slicer shows patient coordinates and it looks like your images are slightly rotated with respect to patient.

https://www.slicer.org/wiki/Coordinate_systems

You can change this in slicer with the button labelled 4 in this image.