Plastimatch is not the only choice for deformable image registration. Please try out some of these other great software, and use the ones which fit your needs.
Open source toolkits
The following software are available under open source licenses.
http://www.picsl.upenn.edu/ANTS/
License: BSD
http://www.nitrc.org/projects/multimodereg/
License: BSD
http://code.google.com/p/dirart/
License: GPL 3
License: BSD
License: BSD
http://www.fil.ion.ucl.ac.uk/spm/software/
License: GPL
Restricted use toolkits
The following software are available at no cost, but carry restrictions on how they can be used.
http://bishopw.loni.ucla.edu/AIR5/
License: Research use only
License: The software is GPL, but the download link is password protected.
http://www.mrf-registration.net
License: Non-commercial use only
http://www.fmrib.ox.ac.uk/fsl/fsl/downloading.html
License: Non-commercial use only
http://surfer.nmr.mgh.harvard.edu/
License: Non-commercial use only
http://www.nitrc.org/projects/hammer/
License: Non-commercial use only
http://www.doc.ic.ac.uk/~dr/software/
License: Research use only