Updated getXfms in old_MBM_interface_functions to correctly handle lsq12 option.
Updated command line options in pairwise_nlin.py and registration_chain.py accordingly. (Also, to add consistency/clarity in how they are used.)
Unrelated to above: modification in pairwise_nlin.py to use full displacement instead of pure nlin component. (This may be removed later.)
Comment in stats class regarding calculation of scaled jacobian--will likely need to change handling later.