Merge branch 'release-1.1' into develop
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?
Merge branch 'master' of github.com:mfriedel/pydpiper into develop
Added the possibility for an executor to kill itself if it has been asleep/idle for a specified number of minutes (seppuku)
Merge branch 'seppuku' into develop
Added the ability for an executor to stop accepting jobs after a certain amount of time. When all jobs that are running finish, and this time is up, the executor will kill itself.
Merge branch 'job_acceptance_limit' into develop
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
* added functionality to the server that allows it to (re)launch executors. For this to happen, the server needs to keep track of how many executors are launched but potentially waiting in the queue, and how many are registered and active. When executors kill themselves, they report back to the server so it can take them out of the pool of active executors.
Merge branch 'server_launching_executors' into develop
This check-in closes Issue #57.

pipeline executor options now in a single option group, so they are not separately defined in pipeline_executor.py and AbstractApplication.

This will make it easier (and less error-prone!) to add and update options.

Command line options that are unique to AbstractApplication only are also in an option group.
Merge branch 'develop' into pre-1.2-misc-fixes
Updated defaults for executor options:

--num-executors = 0 (Otherwise, due to new launching/killing executor functionality), server would automatically launch an executor even if --num-executors was not specified.
--proc = 1
--mem = 6
--time-to-seppuku=15 minutes
--time-to-accept-jobs=180 minutes (3 hours)

The last two defaults were agreed upon by Matthijs and myself yesterday. They will potentially change as we get more people using this code and we continue to optimize parameters.