ENH: Integration of ANTs Multimodal Registration into BRAINSFitHelper

While doing SyN registration, you can use SetFixedVolume2() and
SetMovingVolume2() in BRAINSFitHelper to run a multi modal image
registration.
In BRAINSFit, SyN registration had been hard coded to run one stage of
registration using ANTs.
Now this stage can have one or two metrics (for multi-modality
registration). All the parameters of the second metric is the same as
the first metric except for the fixed and moving volumes.
ENH: BRAINSABC multimodal functionality

Adding capabilities for the SyN stage of multi-modal registration in
BABC.  If there are more than 1 modality specified, then use
both modalities for the metric.
WIP: BRAINSABC multimodal functionality
WIP: working version with the local option

Conflicts:
	AutoWorkup/Template.config
	AutoWorkup/utilities/configFileParser.py
WIP: SyN Registration parameter tunning
BUG: Fix the bug introduced by merging
ENH: Add multi-modal capsbilities to BRAINSFit

I incorporated multi-metric registration for all stages of BRAINSFit
and added command line options to BRAINSFit.xml to take in the secondary
images.
ENH: Change the classifier in BRAINSABC

Add a KNN based tissue classification component to BRAINSABC.

After each EM estimation phase, a set of clean plugs (i.e.
areas where there is greater than 66% chance being that structure)

Are chosen and a Fuzzy KNN is used to re-estimate probabilities of each region.

ComputeEMPosteriors and ComputeKNNPosteriors are set in one function
called ComputePosteriors, that means KNN is run at each iteration of EM
loop.
Also, the dirtyThresholdedLabels image is the one that is used in
ComputeKNNPosteriors, since it has all labels (not only foreground regions).