The Ezys image registration software performs both affine and elastic 3D image registration of medical images.

We have recently compared Ezys with the performance found by Klein et al. "Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration" (2009) and a more recent version of the ANTS-SyN program and found Ezys performs well.

The source code of Ezys 1.0.22 can be found here.

Audrunas also has Ezys web pages here and on sourceforge.