BUG: Fixed final transform, updated the resampled output volume and other outputs accordingly
ENH: fixed all failing tests except acLowerBound, added translation of AC to origin as final step if atlas-registration mode is used.
STYLE: Code review of Ipek BCD changes

Removed dead code comments,  Removed debugging file writing,
Re-organized code to be more compact failure logic, fixed ITK style issues
Identified several places that need further investigation.
BUG: Removed aliased variables that were used inconsistently.
STYLE: Conform to ITK style.
ENH: When copying transforms, both FixedParameters and Parameters must be set.
ENH: Step 1 in decoupling outputs from transform estimation.
ENH: Remove duplicate functions, decouple outputs.

Some functions were duplicated in multiple compilation units.
Further work was done to decouple outputs from detectors.
ENH: Make function const correct

TransformResample does not modify the transform, so it should be
a const pointer.
ENH: Refactoring to modularize transform estimation

Put the complete transform estimations into the main class.
STYLE:  Removed deprecated LandmarkPaired.

The code for dealing with LandmarkPaird is now
isolated to it's own program.
PERF: Improved performance of BCD by minimizing work to be done.
BUG: Fix ACLowerBound test failure by passing proper image back to be written.
ENH: Update NIPYPE for new version of BCD.
ENH: Add New path for processing low res DWI
ENH: Updated to ITKv4.4.0 + MGHIO
STYLE: Useless ITK deprecated define removed.

The ITK_EXPORT define was set to nothing and had no
known remaining purpose.  It was removed to make the
over all code easier to understand.  There was,
understandably, a bit of confusion about the
need for this being pervasive in the code.

It is currently backwards compatible to have
this in code, but at some future point it will
be removed.
COMP: Suppress more superbuild warnings.
BUG: Landmark compare was unstable.

The LandmarkCompare program was comparing strings instead of landmarks.
That was very unstable and had no way to test for tolerance.  It also
used much custom code rather than the landmark readers/writers.

This was completely re-written to to reduce code, provide more complete
code coverage, and to add a tolerance level to allow small floating point
deviations in the landmark locations.
ENH: Update OpenCV to latest version.