Modified twolevel and registration chain code to move reading files from csv and creation of subject hash to a function.

Removed unused import statement from twolevel code that was causing a crash.
Added setInitialTarget function in registration functions, so that initModel and/or initial target for LSQ6 registration are set here.

This makes the high level code more streamlined and easier to read.

Note that this was done in the reg-chain-updates branch because I need to add LSQ6 to the registration chain code, but wanted to accomplish this first, so adding it will be more seamless.
Misc updates to code, related in part to Issue #80.

1. Added LSQ6NUCInorm class to wrap LSQ6 alignment and subsequent NUC and intensity normalization into a single call. This class is now called in MBM and LSQ6, as before, and now in registration_chain as well. This reduces duplicate code without eliminating any functionality.
2. Added function to retrieve the currentGroupIndex for a hash of file handlers. This is used in the registration_chain code so the appropriate index (and therefore last base volume) can be set prior to the chain alignment. This gives the correct value regardless of the input_space (native or LSQ6) or the whether or not a groupwise registration is run.
3. Fixed bug in one instance (no common space is created or existing) where nlinFH was referenced prior to assignment.
More changes related to Issue #80. Specifically: for build model run outside of registration_chain.py, transforms retrieved now using pydpiper naming conventions.

1. Moved getXfms to registration_functions.py and deleted old_MBM_interface_functions.py.
2. Modified import statements in pairwise_nlin.py, registration_chain.py and twolevel_model_building.py
3. Updated description in getXfms.
Updated description of LongitudinalStatsConcatAndResample to include absolute and relative jacobians nomenclature instead of scaled jacobians and jacobians.
Wrapped LSQ12 and NLIN calls into module FullIterativeLSQ12Nlin to make registration_chain.py code easier to read and write.

May eventually want to put this in MBM.py as well?
This commit (e8bda50c133a on the reg-chain-updates branch) will likely be reverted when we wrap all of MBM into its own class, as we (MF, MVE, JPL) discussed this morning. Leaving for now to keep code cleaner while I address other issues.
Updated help message for --MBM-directory option.
Merge branch 'reg-chain-updates' into develop