cmtk binary package in Ubuntu Precise i386

 A software toolkit for computational morphometry of biomedical
 images, CMTK comprises a set of command line tools and a back-end
 general-purpose library for processing and I/O.
 .
 The command line tools primarily provide the following functionality:
 registration (affine and nonrigid; single and multi-channel; pairwise
 and groupwise), image correction (MR bias field estimation;
 interleaved image artifact correction), processing (filters;
 combination of segmentations via voting and STAPLE; shape-based
 averaging), statistics (t-tests; general linear regression).

Source package