BUG: Update save-state in BFit based on the last changes to ANTs
BUG: Update temporary tags for ITK and ANTs based on bia versions
ENH: ANTs testing with separate stages.
BUG: Fix a bug in BABC when intial atlasToSubjectTx is missing
ENH: Remove requirement for atlasToSubjectIntialTransform flag.
BUG: Avoid writing the inverse of the state file
ENH: Added cluster flags and remove debugging.
ENH: Convert savedState file to the restored forward and inverse composites

BRAINSTransformConvert reads the saved registration state file (in the
format of a composite transform. Then it restores SyN transform from its
internal state transforms and writes restored forward and inverse
composite transforms to the disk.

The usage:

~/BRAINSTransformConvert \
--inputTransform ./ANTsSavedState.h5 \
--outputTransformType Same \
--outputPrecisionType double \
--outputTransform outputPrefix

Then, it writes the forward and inverse composite transforms as
“outputPrefixComposite.h5” and “outputPrefixInverseComposite.h5” to the
disk.
ENH: Fixed segmentation phase of processing

The segmentation phase now uses an initialized SyN transform.
BUG: Fix BRAINSABC Failure for single modal images
BUG: Fixed some bugs in BRAINSTransformConvert and verified its outputs
BUG: Need to ensure range of threads are integer values.
ENH: Improved registration parameters for optimization.

the old ants parameters could now be time optimized by taking advantage
of new ants features.
STYLE: Remove aliasing that was confusing

In general unnecessary aliasing should be avoided.  The maintenance
of code with aliases has proven to be much more difficult than
simply using the fully qualified names.
ENH: Added debugging info.
BUG: Missing update on averaging filter

An update on the multipy stage of the averaging filter was missing
that caused an empty file to be generated.

Additional changes to remove unnecessary aliased variables were also
implemented to reduce confusion in the code.
STYLE:  ::Zero and ::One have been deprecated since 2012

Replace with ::ZeroValue() and ::OneValue() in order to
ensure forwards compatibility with ITK.
ENH: Syncronize with NAMICExternalProjects.