Test more MRtrix3 functionalities

[Lestropie]

Any command that involves a spatial transformation of data should ideally be applying that same transformation to any metadata that relates to orientation. Whether or not a particular transformation necessitates a modification to metadata will depend on whether that metadata is defined with respect to image axes or realspace coordinates.

Likely not an exhaustive list:

• [ ] Permuting axes
• [ ] Flipping an axis
• [ ] Applying an affine transformation