COMP: fix core dump due to premature object destruction
BUG: fix BRAINSFitTest_ROIBSpline test failure
Merge pull request #150 from aghayoor/fixROIBSpline

BUG: fix BRAINSFitTest_ROIBSpline test failure
BUG: increase the tolerance for BRAINSFitTest_ROIBSpline
ENH: Added --dry-run feature

It can be convenient to determine which jobs would have run for
diagnostic purposes.  The --dry-run feature does not submit the work
but computes all the other diagnostics and prints useful messages to
to the screen.
COMP: Replace Rigod{2,3}Transform with derived classes

The problem was that in ITK3, Rigid3Dtransform could
be used directly, but in ITK4, it is a base class
that should never be instantiated. I replaced
Rigid3DTransform with VersorTransform, and
Rigid2DTransform with CenteredRigid2DTransform.
COMP: Initialize m_AtlasToSubjectInitialTransform
BUG: Symmetric bounding box in training and detection phases of BCD
ENH: perform the local search of BCD in Freq domain

The "FindCandidatePoints" method is reimplemented to do the local search
in freqency domain.
First, based on the search bounding box, an ROI image is created from
the input MSP volume. Also, the landmark template intensities are
arranged inside an moving template image.
Then, for both fixed and moving images, corresponding maskes are
created, and the "MaskedFFTNormalizedCorrelationImageFilter" is used to
the final optimum match.

BCD is run faster now:
The average of previous run time: 3m40
The average of current run time: 1m40

That shows more than 2x speed increase.
ENH: Add version number to input template and LLS model files
ENH: add the new template files to ReferenceAtlas/20140916_BCD directory

The current LLS model file (LLSModel_50Lmks.h5) and template model file
(T1_50Lmks.mdl) are updated.
New model files have version ID (v1.0) embeded in them.
ENH: Update the current address of BCD model files to the new one
ENH: Remove irrelevent parameters from BRAINSFit

The following parameters are cleaned from the code and xml file:

useCachingOfBSplineWeightsMode
metricSeed
forceMINumberOfThreads
permitParameterVariation
useExplicitPDFDerivativesMode
WIP: Needs more work on SEM tools. DO NOT SUBMIT THIS.
COMP: ITK Components needed for build.
WIP: Removed BRAINSSurface building.
ENH: Updated SEMTools to new command line usage.
BUG: Filenames needed to change from hdf5 to h5 extension in autoworkup.
BUG: Eliminate unnecessary handling of version

Started to refactor and elminiate the unnecessary complex
handling of versions.  Previously the code required users
of BCD to ensure that the versions matched before model generation
and during all subsequent calls to the various landmark programs.

This hard codes the consistent versions in a single location so
that if future changes are necessary, only one string needs to be changed
to indicate a consistent set of files.
ENH: add the new template files to ReferenceAtlas/20141004_BCD directory

The current LLS model file (LLSModel_50Lmks.h5) and template model
file (T1_50Lmks.mdl) are updated.
New model files have version ID (version=2.0) embeded in them.