[ENH] Handling of different coordinate systems

[kaitj]

Describe the feature you'd like to see
At some version of Slicer, I believe the coordinate system either switched or could be toggled to be LPS or RAS. We had previously implemented something to handle this in the afids-validator, reading in the coordinate system and flipping the coordinates as needed when reading in files.

We should probably implement it here too.

[kaitj]

As is, there are methods to read in / save AFIDs of different coordinate systems, but no way of transforming between the two if needed.

[kaitj]

One thing I just came across in the nibabel documentation is that they assume RAS. Not sure if this affects the accuracy of applying the affine that is grabbed from the image and applied to an afid coordinate that is potentially in LPS.

@ataha24, do you have any thoughts or experience with this?

[ataha24]

good catch! We keep all analyses in RAS (and afids-data is in RAS) -- slicer moved to LPS convention so if someone is annotating AFIDs using a lastest version of slicer we may need to handle that. Now whenever I apply a transform (specifically talking non-linear warps) I do a LPS conversion because most software packages are configured that way. However for an affine, it is ok to keep in RAS.

[kaitj]

Other way around I think. Thought slicer always defaulted to LPS until a recent version. In any case, I wouldn't be opposed to doing something similar to nibabel and always setting everything to RAS upon loading - I thought most packages assume RAS.