ENH: Use a new default parameters set for LBFGSBoptv4
Merge pull request #143 from aghayoor/bfitSlicer_final

ENH: Use a new default parameters set for LBFGSBoptv4
COMP: Updated ITK tag to BRAINSiaITK

I updated the ITK tag to use the current version of BRAINSia/ITK
in a branch called NewParallelizedMattesMetricv4.

New performance improvements to the
MattesMutualInformationImageToImageMetricv4 are included in the above
branch.

We can revert the BRAINSia/ITK repository to the main repository as soon as
the following gerrit patch is merged to ITK:
http://review.source.kitware.com/#/c/16839
Merge pull request #144 from aghayoor/bfitSlicer_final

COMP: Updated ITK tag to BRAINSiaITK
COMP: Allow BRAINSTransformConvert without output transform file
ENH: Modified atlas xml name
ENH: Added print statement to diagnose missing sentinal file
COMP: Remove global declarations from GenericTransformImage.h
BUG: Uniformly apply modify_qsub_args for configuring qsub_args.

There was a wide array of options for the modify_qsub_args that were
not uniformly applied or implemented.  By using modify_qsub_args
consistently and uniformly we can simplify testing and reduce
problems with running these experiments.
ENH: Allow template building to only do new files

It is desirable to simply skip sessions that are
completed so that the cluster is not bombarded with
unnecessary qsub jobs.
ENH: Add code for identifying the brain stem

This is an initial step toward robustly identifying the brain
stem from a set of images.
BUG: ATLAS_DIRECTORY to ATLAS_INSTALLING_DIRECTORY
BUG: Fixed logic for set notation.

The logic for identifying jobs that need to be done
was not correct.
PERF: Fixed job submission logic to speed job start.

The SGE job submission criteria was too comples and was causing
the cluster manager to take too much time in submitting new
jobs that were ready to run.  This patch makes the defaults
simple to identify if they can run (i.e. specify only 1 thread
by default, rather than a range) so that the small jobs get
started quickly.
BUG: Add consistent use-sentinal file.

All three modes should use similar methods for specifying the sentinal files.
ENH: Added missing __init__.py file for SEMTools module.

Reordered python modules to resolve ambiguities.
ENH: Update to include ITKv4 Mattes Performance fixes.
COMP: remove ITKV3_COMPATIBILITY entireley
ENH: Per requests of the slicer community, defaults changed.

Discussions with the Slicer registration community indicated that a
different set of defaults was requested.  These were created via
community input and the gui was re-organized to hide unnecessary values.
COMP: Removed deprecated V3 filters