The terminology of orientation in AFNI is different from other libraries.
RAI in AFNI means that origin is right, anterior, inferior. (See here and here).
RAI in this program (which I don't know) is like in AFNI: aliza doc
RAI in MRTRIX means the opposite: going towards right, anterior, inferior (See here)
RAI in this forum, in nipy/nibabel are like in MRTRIX.
When going from, say, AFNI to MRTRIX, do we break our images?
This discrepancy in terminology should probably be at least acknowledged in your doc I believe.
We are very much aware of this issue, and we try to include this information in our classes. This confusion is about nomenclature and not the underlying data, so our "RAI" is others' "LPS", but the data formats from NIFTI and AFNI define the storage order, so software won't "break" because of that naming. We generally recommend when reporting coordinates to identify the direction of the coordinate, 10R, 5P, 7S. Unfortunately, confusion about orientation is deeper than that, but we make an effort to make users aware of what right and left are.