ENH: Make Superbuild more like NAMIC Super project compliant.
ENH: Make ExternalBoost conformant with SuperBuild.
COMP: Fix type case of ANTs for name consistency.
COMP: Use latest UKF feature enhancements.
BUG: DTI-Reg is not a valid python identifier.
COMP: Automatic finding of python on Mac was not robust with the find_package command.
COMP: Minor c-style compilation error.
ENH: Update to include UKF nipype interface.
BUG: Stop returning error when all vectors are zero for Siemens
Merge pull request #51 from Chaircrusher/DWIConvert_Fix

BUG: Stop returning error when all vectors are zero for Siemens
ENH: add short flags for inputDicomDirectory & outputVolume
BUG: Handle abnormal case of Siemens missing gradients

If the input DICOM series is completely without gradients/b values,
zero gradient vectors were added twice, so there were twice as many
gradients in the headers as volumes in the file.
BUG: create usefull debug 2D branded image for BCD

When we use "writeBranded2DImage" flag in BCD, we want to have a 2D
debug image at the output that shows the midbrain base landmark centers
and the search area around them by a circle.

The current created 2D branded image just includes a fully colorfull
circle for the search area, but it does not show the fiducial center
point.

The current code is changed in a way so we can see usefull intended
information at the output 2D branded image.

Also, the related test baseline file is replaced based on new changes.
Merge pull request #52 from aghayoor/BCD2DBrandedImage

BUG: create usefull debug 2D branded image for BCD

Previous debug images did not have useful representation of
where the center of the fiducial was because it was filled in completely.
STYLE:  Remove unnecessary string conversion

Removed unnecessary string conversion to
character array that may cause problem for really long
paths.
ENH: Add 2D branded image writing for QC purposes.
BUG: BCD was applying the inital transform 2x

ENH: Modularize and re-use common code as functions.
ENH: First computational enhancement using std::inner_product
ENH: Make test suite more verbose in outputs for easier validation.
ENH:  Implement Atlas based final adjustment

BCD now has an option to finalize the alignment against
a template image.  with a shifting of the ACPOINT back
to zero.

This involved some major refactoring and renaming of
variables to make it easier to read, and better
describe the behaviors.