COMP: Fixed errors in CTestCustom.cmake.in
COMP: Added more ignore matches for SuperBuild cleaning.
ENH: Remove compiler warnings from BRAINSCut apps.
COMP:  Compiler warning in BRAINSCut indicated bug.

+::GetOneConnectedRegion( LabelImagePointerType& image, const unsigned char labelValue)

labelValue was not used, but then in that function the resultMask = ExtractLabel( multipleLabelVolume, 1 );
was hard coded to 1.  I think this was an incomplete refactoring where the labelValue is the desired
value to extract.

I also removed default paramters because they make the code difficult to read, and maintaining
backwards compatibility is not necessary.
ENH: Added script to help suppress warnings.

\author Hans J. Johnson
\date 2013-04-04
This script it to help identify regular epsression
patterns # for the CTEST_CUSTOM_WARNING_EXCEPTION
variable in a file like ${CMAKE_SOURCE_DIR}/CMake/CTestCustom.cmake.in
for the purpose of supressing irrelavant warnings.

It can be frustrating to find the correct regular
expressions that are needed to avoid a polluted
CDash submission

The intended usage paradigm is to do the following:
1. In a completely clean build directory, run cmake
   to your preferred settings
2. Run "make -j1 > CDASH_WARNING_LOGGER 2>&1" to make a
   static log of all the warning messages that
   you want to suppress
3. Modify the suppressions file used by this build system
   that is usually in ${CMAKE_SOURCE_DIR}/CMake/CTestCustom.cmake.in
4. python FindCTestMatchingWarnings.py CDASH_WARNING_LOGGER ${CMAKE_SOURCE_DIR}/CMake/CTestCustom.cmake.in
5. Review output from (4), if suppressable warnings
   identified, return to (3), else goto (6)
6. CELEBRATE AN UNSULLIED DASHBOARD!

USAGE BRAINSTools/Utilities/FindCTestMatchingWarnings.py <CDASH_WARNING_LOGGER> <$CMAKE_SOURCE_DIR/CMake/CTestCustom.cmake.in>
COMP: Set very large default test timeout.

Times are given in seconds.

Replace DART_TESTING_TIMEOUT with modern variable name CTEST_TEST_TIMEOUT.
COMP: Moved logic for building with FFTW before ITKv4 is built.
COMP: Comment out very long running test.
STYLE: Move to itk version of BSplineDeformableTransformInitializer.h

Now that we do not need to support both ITKv3 and ITKv4, use the common initializer
provided by ITKv4.
COMP: Syntax error in comment formatting.
ENH: Updated ITKv4 for syncronization with Slicer.
STYLE:  ITKv4 no longer needs transform registratoin

Removed ITKv3 work-arounds for specialized transform
registrations.
COMP: Remove summary warnings from SuperBuild.
STYLE: Assign more descriptive variable names.