Elastix is a very powerful registration toolbox with lots of advantages over stock ITK registration tools - it has many more metrics, transformation methods, constraints, optimizers, and it comes with a large registration parameter set database, which contains optimized settings for a wide range of registration tasks.
This toolbox is now available in Slicer, through the SlicerElastix extension, in the latest nightly builds.
Even the default settings work really well for simple (same patient, same modality) and difficult cases (different modality, different field of view, even different patient), as shown in this 1-minute demo video here: https://youtu.be/cU0pWhn0-3o
Limitations: Masking will be available in tomorrow’s nightly build. Multi-label, landmark, 4D volumes, and multi-metric inputs are not supported yet (can be added quite easily if the community needs it). Parameter set editing is manual (edit files in a directory).
Any feedback and suggestions are welcome.