Are aligners correct for non-cube shapes when align_in_real_world_coords = False ?

[etienne87]

I have a doubt that it makes sense to compute the closed-form affine/rigid/tps in align_in_real_world_coords=False.

EDIT:

in fact the transform you compute is correct for non-cube shapes if align_in_real_world_coords=True, because before fitting you:

• denormalize coordinates
• then apply affine
  in here:

So if one wants KM to work fine with non-cube shapes but does not have affine matrices, he can just set align_in_real_world_coords=True, and then feed identity affines.