First pass at NLIN module and related changes.
This code is still being tested.
1. NonlinearRegistration application that can be run on the command line + standard MBM 3 generation ANTS registration
2. Misc changes:
2a. moved addMBMGroup to MBM.py
2b. added comments and additional directory creation in MBM.py, fixed file handler initialization to include mask dir
2c. added mincAverage atom
2d. Added pipeline_dir to general registration option group.