ENH: Scripts to run freesurfer longitudinal analysis

These scripts allow running freesurfer longitudinal
analsysis from raw data.
ENH: SEMTOOLS updated with lastest command line parsing.
COMP: normalize gradient vectors before writing to FSL files
ENH: Provide better error checking for using ID transform.
ENH:  Add BRAINSLabelStats

Vincent Magnotta wrote this little program to make measurements for various
projects. This has many uses for a stand-alone program that will take output
these measurements and label the output based on a file defining the label
names. This implements the ability to read fsl xml files and the ants label
definitions.

A couple of additional features are you can add an arbitrary number of columns
and values to the CSV based results. This can be used to define the subject and
scan ID or add a name for the type of measurements (e.g. FA, MD, etc). I have
also added calculation of the median and allow the user to determine how to
compute the median values based on the histogram.

It would be trivial to add a CSV format.
STYLE: Cleanup code style.
COMP: Remove compiler warnigns.
WIP: BRAINSFit is built and run

BFit is tested and works for:
- linear transforms (rigid/ScaleVersor/ScaleSkewVersor/Affine)
- metric types (MMI, MSE, NC, JointHist)
- having several levels (e.g. rigid,ScaleVersor,Affine)
- input initial transform
- auto initial transform
- input fixed and moving masks
- auto masks mode

However, This branch should not be merged because BRAINSFit is not
stable for versor transforms and BSpline.
BFit should be hold on at the curret step till LBFGSOptimizer and
Versor optimizers are moved to ITKv4.
WIP: Conflicts are fixed and LBFGSOptimizer is added to ITK

At this patch I made changes to several files to make the different
parts of BRAINSTools compatible with new version of BRAINSFitv4.

Also, several configuration issues are solved, and now BRIANSTools
is built succesfully based on the last version of ITK that includs
the LBFGSOptimizer.
WIP: update itk and Ants tags
WIP: add LBFGS optimizer to BSpline registration
WIP: fix the initial transform issue
WIP: complete refactoring of BSpline Reg in BFHT hxx file
WIP: update ITK tag
ENH: update based on upstream master
WIP: changes to templatehelper file for bspline
WIP: Update ITK tag
WIP: new changes to Bspline, compiled,run,bad
WIP: add versor optimizer
WIP: add versor optimizer, approved