COMP: Update BRAINSTools - Remove ITKv3 compatibility / Tweak BRAINSFit.xml

See #3829

$ git shortlog slicer-2014-08-27-6b15c2b..slicer-2014-09-15-411dee9
David Welch (2):
      ENH: Modified atlas xml name
      ENH: Added print statement to diagnose missing sentinal file

Hans Johnson (6):
      BUG: Uniformly apply modify_qsub_args for configuring qsub_args.
      BUG: Fixed logic for set notation.
      PERF: Fixed job submission logic to speed job start.
      BUG: Add consistent use-sentinal file.
      ENH: Added missing __init__.py file for SEMTools module.
      ENH: Per requests of the slicer community, defaults changed.

Jean-Christophe Fillion-Robin (2):
      Revert "COMP: fine-tune VTK dependencies"
      Revert "COMP: move find_package(VTK) down to individual project directories"

Kent Williams (3):
      COMP: Allow BRAINSTransformConvert without output transform file
      COMP: Remove global declarations from GenericTransformImage.h
      COMP: remove ITKV3_COMPATIBILITY entireley

Regina Kim (3):
      ENH: Allow template building to only do new files
      ENH: Add code for identifying the brain stem
      BUG: ATLAS_DIRECTORY to ATLAS_INSTALLING_DIRECTORY

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23678 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Update BRAINStools to include fixes for shadowed declarations.

$ git shortlog 868c290d..6f9986
Jean-Christophe Fillion-Robin (2):
      Revert "COMP: Fix unused variable warning in BRAINSFitHelperTemplate"
      Revert "COMP: Fix shadowed declaration warning"

Kent Williams (2):
      COMP: Removed deprecated V3 filters
      COMP: Remove shadow declaration warnings

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23679 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: #3846 fixes crash when trying to use label map seeding

With the change to VTKv6 some member variables can be null, probably
due to the tensor pipeline not being correctly initialized.

This avoids the crash, but issue #3846 is not fixed (tractography
does not work).

From: Steve Pieper <pieper@bwh.harvard.edu>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23680 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Fixed ExtensionWizard immediate scripted module loading

Problem was that settingsList returned a tuple, which is not mutable and therefore rawSearchPaths.append failed.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23681 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Remove unused dependency to ITKDeprecated from ResampleDTIVolume

The dependency was probably added by "mistake" when the module
"Utilities/Maintenance/WhatModulesITK.py" was used to create the list of
dependent modules (r23413). Since the header "itkSemaphore.h" was
specified in the code but was commented, "WhatModulesITK" reported its
associated module ITKDeprecated as required.

This commit removes the commented code and updates the CMakeLists.txt

Thanks to "Gib Bogle <g.bogle@auckland.ac.nz>" for reporting the problem.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23682 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Update EMSegment to fix EMSeg_SlicerCommonInterfaceTestGeneral test

This commit ensures the ITK IO factory associated with
executable vtkSlicerCommonInterfaceTest are registered.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23683 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Fix OtsuThresholdImageFilterTest on Windows

This commit ensures that "SEM_LAUNCH_COMMAND" variable will be defined
for both CLIs and remote modules.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23684 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Update ModelToLabelMap and remove unused dependency to ITKDeprecated

In r23660, the dependency to AnalyzeImageIO headers has been removed.
This commit also removes the now unneeded dependency to "ITKDeprecated".

Thanks to "Gib Bogle <g.bogle@auckland.ac.nz>" for reporting the problem.

Co-authored-by: Bradley Lowekamp <blowekamp@mail.nih.gov>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23685 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Fix qMRMLVolumePropertyNodeWidgetTest1

This commit fixes the failing test by ensuring the vtkRenderingContextOpenGL
module is initialized.

The following error was occurring on all three platforms:

// ----------
Generic Warning: In /path/to/VTKv6/Rendering/Context2D/vtkContextDevice2D.cxx, line 27
Error: no override found for 'vtkContextDevice2D'.
// ----------

For more details, see:
  http://www.vtk.org/Wiki/VTK/Build_System_Migration#How_Implementation_Modules_Are_Initialized
  http://www.vtk.org/Wiki/VTK/VTK_6_Migration/Factories_now_require_defines


Finally, let's also note that the test executable was compiled with:

-DvtkRenderingContext2D_AUTOINIT="1(vtkRenderingContextOpenGL)"
-DvtkRenderingCore_AUTOINIT="4(vtkInteractionStyle,vtkRenderingFreeType,vtkRenderingFreeTypeOpenGL,vtkRenderingOpenGL)"
-DvtkRenderingFreeType_AUTOINIT="1(vtkRenderingFreeTypeFontConfig)"
-DvtkRenderingVolume_AUTOINIT="1(vtkRenderingVolumeOpenGL)"

and was linked against vtkRenderingContextOpenGL.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23686 3bd1e089-480b-0410-8dfb-8563597acbee