Addition of pairwise_nlin.py and some general minc_tools/framework changes:

1. Addition of pairwise_nlin.py to do pairwise nonlinear calculations. Relevant change made to setup.py.
2. Moved setup_logger() to application class. Can be overwritten, but I wanted to have a base function defined to avoid so much duplication.
	a. Existing files impacted: application.py, MAGeT.py, MBM.py
3. Created option groups to avoid duplication of command line options. Addition of option_groups.py file
	a. Existing files impacted: MBM.py, registration_chain.py, stats_tools.py
	b. NOTE: stats specific options defined in stats_tools.py. This will be the general paradigm we use going forward. (Options defined in classes where they are needed/used.)
4. Moved temporary MBM interface functions, previously in registration_chain.py, to their own file: old_MBM_interface_functions.py
5. Modified getLsq6AndXfms to getXfms only. getLsq6Files now its own functions.
6. Updated CalcStats class so calculations not done automatically in __init__. Now down in fullStatsCalc() function. Additional changes forthcoming that will further modularize this code.