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
ENH: Addition of an option in DWIConvert to read input BVector files that are transposed when converting FSL images to
NRRD images.
COMP: Fixed compilation problems

IO modules were missing with previous suggested component
finding.
BUG: Fixed a bug in gtractResampleDWIInPlace

In image origin conversion, GetTranslation() is replaced by GetOffset().
ENH: Add a test for gtractResampleDWIInPlace

To create a test:
- I chose a sample DWI image and its corresponding T2 image.
- Extracted the b0 image of the DWI file using extractNrrdVectorIndex.
- Used BRAINSFit to a run a rigid registration between b0 image and T2
image.
- Ran gtractResampleDWIInPlace to align the input DWI image using the
rigid transform.

I did following to verify the ouput of the gtractResampleDWIInPlace
after
fixing its bug:
- I used ResampleInPlace as the interpolation option in BRAINSFit to
obtain warped b0 image.
- In Slicer, I compared the above warped b0 image by BRAINSFit with the
b0 component of the aligned DWI image by gtractResampleDWIInPlace to
make sure they completely overlaps.
BUG: Fixed a bug BRAINSHoughEyeDetector

In image origin conversion, GetTranslation() is replaced by GetOffset().
ENH: add reading from landmark file to BRAINSTalairach

A new flag called "inputLandmarksFile" is added to BRAINSTalairach.
Using this flag, all needed reference points (AC, PC, IRP and SLA) can
be passed to the program using an fcsv file.
Previously, the only option was passing the landmark coordinates directly
using their corresponding flags.
ENH: Improve quality of MALF outputs

Some mask based post processing is now done to improve mask qualities.
BUG: BRAINSCut DG move and template building fix
BRAINSCut probablity DataGrabber were placed into segmentation
section instead of default section.

template.py to check a proper brain label file
Merge pull request #162 from aghayoor/bTalairach

ENH: add reading from landmark file to BRAINSTalairach
Merge pull request #163 from BRAINSia/Fix_BAW_BCutCrashFiles

BUG: BRAINSCut DG move and template building fix
Merge pull request #161 from fbudin69500/master

ENH: Addition of an option in DWIConvert to read input BVector files tha...
Merge branch 'bsplineLmkInit' of https://github.com/aghayoor/BRAINSTools
ENH: Update ITKv4 to include performance fixes.
COMP: Incorrect function signature.

After adding transpose option to DWIConvert, the
ReadBVecs function signature was incorrect.
ENH: Lastest alpha ITK 4.7 release.
COMP: Consolidated duplicate code, fix include directory

The vtkITK conversion code was duplicated in the surface tree
in two spots.  Consolidated the duplicate code into a common library
used by multiple programs.

NOTE: The vtkITK library is a near exact copy from
the Slicer/Libs/vtkITK code base.