elastix
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Elastix is a toolbox for rigid and nonrigid registration of (medical) images.
Elastix is based on the ITK library, and provides additional algorithms for image registration.
The software can be run as a single-line command, making it easy to include in larger scripts or workflows. The user needs to edit a configuration file that contains all relevant parameters for registration: transformation model, metric used to comapre images, optimization algorithm, mutliscale pyramidal representation of images...