ENH: BRAINSLandmarkInitializer works with multiple transformTypes

The BRAINSLandmarkInitializer has changed to support different transform
types after the recent changes to the itkLandmarkBasedTransformInitializer
class:
http://review.source.kitware.com/#/c/17847/

Based on new changes, an input flag is added to define the output
transform type:
--outputTransformType

This flag is defaulted to the AffineTransform (the only option that
existed before), and now can support VersorRigid3DTransform and
BSplineTransform too.

If BSplineTransform is chosen, we also need to use the following added
flags to define the parametric domain for the BSpline transform:
--inputReferenceImageFilename
--bsplineNumberOfControlPoints
BUG: MultiModal registration bug in BRAINSABC and BRAINSFit

Actually this patch includes fixing two bugs:
First, BRAINSABC was returning a failure when "restoreState" was not
defined in the command line.
The second bug was returning failure when we do not define neither
initial atlas to subject transform nor restoreState transform in
BRAINSABC, and this failure was related to a bug in BRAINSFit.
Both bugs are fixed and tested.
ENH: Conversion to composite files continued

After converting to composite files, it was necessary to add logic that
allows splitting the composite transforms apart for the purpose
of averaging.
BUG: Fix scaling of vectors by b-values
COMP: fix some gcc 4.9.2 warnings
COMP: gcc4.9.1 warnings for ANTs
Merge pull request #160 from BRAINSia/FSLToNrrdFix

BUG: Fix scaling of vectors by b-values
ENH: Provide skipping logic for template building phase.
ENH: Addition of an option in DWIConvert to read input BVector files that are transposed when converting FSL images to
NRRD images.
ENH: Add a GenerateCLP command line for GenerateAverageLmkFile

Usage:
$/GenerateAverageLmkFile \
--inputLandmarkFiles lmk1.fcsv,lmk2.fcsv,...,lmkn.fcsv \
--outputLandmarkFile outputAveLmk.fcsv
BUG: Fixed BCD Test failures on Dashboard

All BCD tests are passed successfully on Mac; however, 22 tests were
failed on the Linux system because MSP estimation generates slightly
different results on Mac and Linux. Despite of the difference between
landmark points locations, both results on Linux and Mac are valid.
Therefore, we need to have multiple baselines for the Mac and Linux
systems.
Fortunately, ITKTestDriver supports multiple baselines, and different
baseline names should have following pattern:
baselineFileName.nrrd
baselineFileName.1.nrrd

Also, it seems that the extension of the file name is important! For
example using multiple baselines does NOT work when files are named
as follows!
baselineFileName.nii.gz
baselineFileName.1.nii.gz

Therefore, I changed all the output files extensions to "nrrd" for the
BCD TestSuite.

Furthermore, 6 of the failures were related to the landmark fcsv files
comparison that is run by an internal program named "LandmarksCompare".
This program is modified in a way to support comparing with multiple
baseline files.
BUG: Fix BRAINSFitTest_ROIBSpline test failure
BUG: Replace the baselines of BCD tests based on CDash build
BUG: Fix a bug in BRAINSFit SyN registration
ENH: FIXING BUGS IN template use for phase 3.

The process of building the pipeline sould
be contained in one set of files, not distributed
across several files somewhat indeterminantly..

Removed unnecessary code.
Reorganize pipeline to be consistent
Fixed cross sectional bugs in refactoring.
More changes for BAW debugging.
ENH: Added GenerateAverageLmkFile interface.
ENH: Split required and optional items from datagrabber.

Fix data grabbers to grab correct information needed for longitudinal
processing.

Fixed Stage3 BRAINSCut inputs.
BUG: Incorrect syntax for custom pipeline arguments

Must specify the 'overwrite':True option to the dictionary.
ENH: Try to fix Brainstem segmentations.
BUG: Fixed a bug in GenericTransformImage