Merge pull request #54 from aghayoor/master

BUG: Three test failures are fixed after recent changes to BCD
ENH: Update ReferenceAtlas information.
ENH: Update SimpleITK to ITKv4 latest compatible version for double/single precision.
ENH: Add all tools to SEMTools required for AutoWorkup to run.
ENH: Improvements to the autoworkup scripts for BCD

Recent atlas based fixes for BCD have been incorporated into autoworkup.
ENH: Update for new POSTERIORS definitions.
ENH: Add capabilities to write out csv log file in a report

It is nice to be able to write out the metric value in a CSV file for
knowing the quality of registration results for various metrics.

This feature fits nicely with BRAINSFit tools.

The new command line option is
--logFileReport

A file to write out final information report in CSV file:
FixedImageName,FixedMaskName,MovingImageName,MovingMaskName,MetricName,MetricValue
ENH: Add "logFileReport" to BRAINSFit

A file to write out final information report in CSV file:
MetricName,MetricValue,FixedImageName,FixedMaskName,MovingImageName,MovingMaskName
BUG: Python pathing was incorrect.
BUG: fix crash in BRAINSABC
ENH: Added the UnbiasedNonLocalMeans filter to BRAINSTools.
ENH: Added the SlicerJointRicianAnisotropicLMMSEFilter.
ENH: Using python multiprocess.Pool() for multiple subjects

By using the python multiprocess.Pool() we can more easily dispatch
many subjects workflows in parallel very easily.
BUG: Fixed Second stage BRAINSABC custom xml generation.
DOC: Add more documentation
BUG: fixed regression from dicomtonrrdconverter

Now can read non-dwi DICOM series again.
BUG: Fixed cleanup posteriors for new file names

The new atlas has a different set of prior names.  Also verified
that each file named has an explicit action, and no default fall though
actions are allowed.
BUG: Fixed for new atlas file names.
BUG: Fixed bug in nipype for ants regisration.
BUG: missing increment of channel index for diagnostic printing.