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: Fix warningsCOMP: get BRAINSSurfaceTools to build.
ENH: Add a regression test to BRAINSResample for ResampleInPlace

The new test shows two recently fixed bugs. These bugs would happen:
1- when a non-composite transform was used as the warp transform in
BRAINSResample.
2- when ResampleInPlace interpolation mode was used.

I did not need to add a new baseline, since this test should provide
exactly the same result as
BRAINSFitTest_RigidRotationNoMasksRiginInPlaceInterp.
COMP: Remove gcc 4.9 warnings
COMP: Remove more gcc 4.9 warnings
BUG: ReadTransformFromDisk can process a list of transforms now

When a list of transforms is passed as the input, this function adds all
the transforms in the list to a composite transform file, and returns
the result composite transform.
COMP: Improve Compilation for ITK modules

The COMPONENTS argument to find_package is convenient for simple projects, but complex projects that "find" ITK multiple times with different component requirements could just call find_package without the components list and then use itk_module_config from the ITKModuleAPI.cmake module (available after find_package(ITK) returns) to compute the requirements variables with a custom name:

find_package(ITK 4.5 REQUIRED)
itk_module_config(MyITK ${MyITK_COMPONENTS})
MyITK_INCLUDE_DIRS and MyITK_LIBRARIES
ENH: Adding MALF label fusion to autoworkup

The multi-atlas label fusion code initial testing is added to autoworkup
for initial data processing and testing.
COMP: Fix compilation linkage errors.
ENH: Initial code copied directly from BRAINS3/src/iplProg/GenusZero

Working Copy Root Path: /scratch/johnsonhj/src/BRAINS3
URL: https://www.nitrc.org/svn/brains/BRAINS/trunk
Relative URL: ^/BRAINS/trunk
Repository Root: https://www.nitrc.org/svn/brains
Repository UUID: 35260585-dc49-0410-9118-cf39a346c3ba
Revision: 13269
Node Kind: directory
Schedule: normal
Last Changed Author: wen
Last Changed Rev: 13269
Last Changed Date: 2012-06-18 14:39:29 -0500 (Mon, 18 Jun 2012)
STYLE: Clean code for easier maintenance.
ENH: Copy vtkITK from Slicer

Slicer source information:
origin git://github.com/Slicer/Slicer.git
commit 1813639d1a2578a0b74565c6a79257a13baecefd (HEAD, git-svn, master)
ENH: Migrate to Slicer version of vtkITK, and update to VTK version 6

This patch set also conforms to newer build models.
COMP: Remove compilation warning of returning without value.
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.