BUG: Fixed order of imports

PYTHONPATH was not initialized in time for importing
python modules.
ENH: Updated Workflow for ANTs state saving.
ENH: Add saveState and storeState to BFit and BABC
ENH: Added stub restoring ANTs registration

This provides stub files for integrating ANTs registrations with
BRAINSABC so that they can be updated in future steps without re-running.
ENH: Improved linkage of SyN to BRAINSABC.
ENH: InitializeTransformsPerStage is set on BFit
ENH: Testing new ANTs registration values.

Based on review of the ANTs/Scripts directory.
ENH: Provide consistent registration for ANTs.

This patch uses parameters that are closely
related to the proven parameters from
ANTs/Scripts/antsRegistrationSyN.sh

This increases the registration speed, and
also seems to work across a large quantity
of image qualities.
BUG: save-state transform should be cloned from the result transform in BFit
BUG: Update ITK tag and a temporary tag for ANTs so BTools can be compiled
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