DRAMMS
A Deformable Medical Image Registration Toolbox
... development, etc);
-- Registration under missing correspondences (e.g., vascular lesions, tumors, histological cuts).
DRAMMS runs in command line in UNIX/Mac OS, It accepts Nifti/ANALYZE/MetaImage image formats. It is fully-automatic --- takes two input images, and generates a registered image and (optionally) the deformation field.
More information (installation, tutorial, manual, demonstration, FAQ, etc) can be found at http://www.rad.upenn.edu/sbia/software/dramms/ .