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Downstream medical application code needs to correctly handle image spacing, image orientation, and unusual image origins correctly – in particular, landmarks, volume and size measurements, and mesh data are always in physical coordinates.
If we try to manually handle this metadata by, for each downstream task, manually scaling, transposing, and shifting deformation fields, we will make mistakes and spend a lot of time. Instead, we need to use a metadata-aware representation of image registration results at application boundaries. I propose that itk.Transform objects are the current best option.