Added ability to change registration parameters in MAGeT and registration chain. (Issue #84.)

Major changes:
1. HierarchicalMinctracc, LSQ12ANTSNlin, MAGeTMask and MAGeTRegister now take registration protocols (aka a command line specified csv file) as arguments. For HM and LSQ12ANTSNlin, this means that individual registration parameters are no longer specified. Default for all is if no protocols are specified, the default registration parameters are used.
2. HM and LSQ12ANTSNlin also take subject_matter as an argument, in preparation for addressing Issue #88, but nothing is currently done with it.
3. HM takes includeLinear=True as an argument. Default is that LSQ12 HM is run prior to non-linear generations. If includeLinear=False is specified, only non-linear registrations are run.
4. Another option group has been added to minc_parameters, so that LSQ12 and non-linear protocols only may be specified. Not sure if this is overkill, but since this is what is needed for registration chain and MAGeT (and likely others down the road), adding it for now.

Minor changes:
1. Added a comment to the top of pairwise nlin to indicate that it is deprecated and may be combined in the future with the registration chain code because it is so similar. This is in part because I have not updated this module in a while, and did not make the above changes to the code.
2. In MAGeTRegister, changed method to regMethod for clarity and to be consistent with MAGeTMask.