BUG when reading mha file with AnatomicalOrientation

@lassoan in the other thread linked above, you mention that the TransforMatrix (is that different from the Orientation field?) is a rotation from ijk to RAS. However, when saved as a NRRD, the transformation matrix is the same, but in LPS, as shown above. So either:

  1. the actual transform is IJKtoRAS but IJKtoLPS
  2. is is IJKtoRAS but we read it as IJKtoLPS

Would you agree?

Also, I’m currently updating those readers & writers in VTK. What do you suggest I do for MetaIO?

  1. Same as NRRD (use the AnatomicalOrientation as the target coordinate system)
  2. enforce as LPS (do nothing)
  3. enforce as RAS (flip I and J)