simpleElastix

quote:

Elastix cite{Klein2010} is an open source, command-line program for intensity-based registration of medical images that allows the user to quickly configure, test, and compare different registration methods. SimpleElastix is an extension of SimpleITK cite{Lowekamp2013} that allows you to configure and run Elastix entirely in Python, Java, R, Octave, Ruby, Lua, Tcl and C# on Linux, Mac and Windows. The goal is to bring robust registration algorithms to a wider audience and make it easier to use elastix, e.g. for Java-based enterprise applications or rapid Python prototyping.

Python example

import SimpleITK as sitk
resultImage = sitk.Elastix(sitk.ReadImage("fixedImage.nii"), sitk.ReadImage("movingImage.nii"))