BUG: Update BRAINSTools to BRAINSFit fix for centerOfROI initializer

Created by: jcfr

Tested-by: Hans Johnson hans-johnson@uiowa.edu

$ git shortlog e257e62...29d203c --no-merges
Alexander Leinoff (5):
      COMP: BCD should only request VTK when building GUI
      COMP: CompareImageFilter should only use VTK when building GUI
      BUG: Replaces all baselines for BCDTests
      BUG: Fixes typo in previous commit
      BUG: Fixes version check in top level CMAKELists.txt

Ali Ghayoor (13):
      ENH: Upgrade vnl_powell to itkPowellOptimizerv4 in BCD
      ENH: Write the debug image based on requested debug level
      ENH: BCD can process input images with different dynamic range
      ENH: Change tolerance and step size for Powell optimizer
      BUG: Fixed a bug in BABC when a low debugLevel requested
      ENH: New parameters for multimodal segmentation in BABC
      ENH: Updated purePlugsThreshold value for AutoWorkup
      BUG: fixed a bug in BABC denoise filtering
      ENH: Initialize a matrix variable
      ENH: remove an intermediate variable to avoid extra memory usage
      BUG: defined an orderedmap class for BABC
      STYLE: Cleanup unnecessary if statement
      ENH: Prevent holes in created brain mask by ROIAutoFilter

Andrey Fedorov (2):
      BUG: fix centerOfROI initializer
      ENH: adjust restriction on the required registration phases

Hans J. Johnson (40):
      ENH: Update ITK, ANTS, and teem
      STYLE: Remove MinSizeRel option
      COMP: Resolve clang static analysis warnings
      BUG:  Compilation error fixed due to typo.
      ENH: Update external tools support.
      COMP: Improve coverage by using removeIntensityOutliers flag.
      COMP: Force C++11 compliance testing
      COMP: Added compatibility testing with apple and CXX11
      BUG: Nipype now reqires invert_initial_moving_transform to be set
      ENH: Selection of denoising filter improved.
      ENH: Changed options to reflect current processing
      ENH: Updated ANTs for improved DenoiseImage
      BUG: The Rician noise model fails for DenoiseImage
      ENH: Added key files for new denoised gaussian images.
      ENH: Use denoised images for atlas reference
      ENH: Add atlas images to reference atlas.
      ENH: Fine-tune denoising options in BAW.
      BUG: Need to work around nipype bug
      ENH: Use denoised t1 from atlas for registration
      ENH: Return to using Rician de-noising from ANTs
      BUG: Error in respecting the NSLOTS variable
      PERF:  Constrain memory usage for KNN phase
      PERF: Update ABC workflow to reflect memory with KNN
      BUG: Serialize printing from threaded sections
      STYLE: Print table consistently
      BUG: Need to pass all denoised images into BRAINSABC
      STYLE: Make usage of variable names consistent
      STYLE: Cleanup unsuded ComputeLabels references
      BUG: Internal ordering for dictionary missed first element
      BUG: This is an unsatisfactory solution
      BUG: Fix to allow all allocated slots to be used
      ENH: Consolidate and syncronize different ANTs run parameters
      BUG: Fix running of ANTs consistently
      ENH: Add N4 bias correction after denoising
      BUG: Missing ',' in python list.
      ENH: Improve error reporting for improper input
      STYLE: Uniformly describe registration parameters.
      PERF: New AntsJointFusion is well multithreaded
      ENH: Add automatic image unwrapping
      BUG: Fix mismatched function parameter calls.

Jean-Christophe Fillion-Robin (1):
      COMP: Force CMAKE_CONFIGURATION_TYPES only when using multi-config generator

Regina Kim (7):
      BUG: Fix Landmark Workflow
      ENH: Update antsDenoise IO specification
      ENH: Rewording to JointFusion from MALF
      ENH: Linear Regression Rescaling
      ENH: JointFusion Update for T2
      ENH: Add JointFusion masking option
      ENH: 1.5 Tesla T2-w excluded from JointFusion