COMP: Add BRAINSDWICleanup too to remove bad gradients/volumes from NRRD files
DOC: Improved copyright notice statement.

The ITK copyright was copy-n-pasted everywhere.
This was now fixed to be compatible, but distinct
from ITK.
BUG: Compilation error introduced when updating license information.
ENH: Removed unused code.
ENH: Update BRAINSFit registration framework to ITKv4

BRAINSFit is tested and works successfully based on the ITKv4 registration
framework.

The updated BRAINSFit also uses the benefits of newly added Versor and
LBFGSB optimizers.

The new version can handle a multi stages registration process including
linear and non-linear (BSpline, SyN) transforms. A 3 level registration
process is run on each stage.

This version collapses all linear transforms to only one before
writing the final output transform to the disk. Just Notice that the
current version writes the collapsed "ScaleVersor3D" and "ScaleSkewVersor3D"
transforms as an affine transform.

We can enhance the current version by removing the collapsing step.
This can be done if we directly initialize the internal transform of the
registration filter rather than passing the initial transform as an
MovingInitialTransform to the registration framework.

This version should be built based on the ITK tag of the following gerrit
patch:
http://review.source.kitware.com/#/c/14682/
COMP: Made compileable with VTK6
ENH: Remove collapsing step in BRAINSFitv4

At each stage of the previous version of BRAINSFitv4, the initial
transform was passed to the registration framework as a
"MovingInitalTransform". Then at the end of each stage, the initial
transform was collapsed to the registration result.

In the current patch, we aim to optimize and update the parameters of
the initial transform directly.
For this method, the output transform is set as a pointer to the internal
transform of the registration filter. Then before registration
starts, parameters of the internal transform are updated based on the
input initial transform, and during the registration process, optimizer
works directly on this initialized internal transform.
It is an analogy to the method that was performed on ITKv3 registration
framework.

Finally, after registration, the result transform will replace the current
initial transform, and itself will be considered for the initializtion of
the next stage.

The advantage of the above method is that it can increase the
registration precision by removing the collapsing step and avoiding the
errors resulted from composing different types of transforms together.
COMP: Wrong library was linked.
COMP: Clean up library pathing

The path was wrong for where libs were installed.
COMP: remove CMakeFiles directories Ali mistakenly checked in
COMP: Removed long-obsolete code that won't work with VTK6
COMP: Changes for VTK6 forward compatibility
COMP: VTK5 and VTK6 compatibility issues

-#include "vtkVersionMacros.h"
+#include "vtkVersion.h"

The file vtkVersion.h exists in both vtk5 and vtk6
to subsequently include the correct version numbers
for vtk.  vtkVersionMacros.h only exists in vtk6 and
was causing compilation failures for vtk5.
BUG: VTK5 requires QVTK library to be linked.
COMP: fix BRAINSConstellationDetector VTK6 issues
COMP: change vtkVersionMacros.h to vtkVersion.h
COMP: Add itkTimeProbe.h to LLSBiasCorrector.hxx
ENH: BCut Test added for OpenCV updates

This set of changes allow for testing
different versions of OpenCV to ensure
that updates do not cause regressions
in the the results.
Merge pull request #81 from BRAINSia/BCutTest

BRAINSCut OpenCV Test
Merge pull request #79 from aghayoor/ENH_BFit_remove_collapse_step

ENH: Remove collapsing step in BRAINSFitv4