Added ability to update minctracc parameters for non-linear registration. Issue #59.
Format/parsing similar to previous check in 15941835d92357d for mincANTS.

Minor changes:
1. Removed unused imports from NLIN.py
2. Added optimization parameter for minctracc atom (-use_simplex as default)
3. Added -tol 0.0001 as default for all minctracc calls.