This is a set of tools that I have created to fit my needs when processing MRIs.
reorient_RAS.py reorients a nifti input so its axes are in RAS orientation (left to Right, posterior to Anterior, inferior to Superior). It uses as_closest_canonical while saving the reorientation matrix so the reorientation can be undone.
reorient_nifti.py
It is a routine of MRtrix3 commands to align (linear registration), interpolate, and combine (average) a set of images.