Merge pull request #567 from mehrtash/update-TCIABrowser

Update TCIABrowser
ENH: Adding SPHARM-PDM extension to the SlicerExtension index

Shape analysis has become of increasing interest to the medical community due to its potential to precisely locate morphological changes between healthy and pathological structures. SPHARM-PDM is a tool that computes point-based models using a parametric boundary description for the computing of Shape analysis.
The point-based models computed with the SPHARM-PDM tool can be used in combination with the also UNC designed statistical tool shapeAnalysisMANCOVA to perform quantitative morphological assessment of structural changes at speciﬁc locations.

Authors Beatriz Paniagua (UNC), Francois Budin (UNC), Martin Styner (UNC)
Merge pull request #568 from fbudin69500/add-SPHARM-PDM

ENH: Adding SPHARM-PDM extension to the SlicerExtension index
Fixed build error in linux and mac
Merge pull request #569 from xiaofengliu/update-mabmis

Fixed build error in linux and mac
Update TCIABrowser

* correct the revision number, as the old one was invalid after repository
   transfer
* new revision includes the icon

Compare link is not available since the repository has changed, and the
old revision number refers to a non-existent repository.
Merge pull request #573 from fedorov/update-TCIABrowser

Update TCIABrowser
ENH: SlicerRT 0.13.2: Fixed contour conversion issues; Added mask option for gamma dose comparison. See more info at https://www.assembla.com/code/slicerrt/subversion/changesets/compare/1439...1468
ENH: GelDosimetry 0.1.2: Added option to manually remove points from calibration plot before polynomial fitting; Added option to use mask contour for dose comparison; Minor improvements, bugfixes. See more info at https://www.assembla.com/code/slicerrt/subversion/changesets/compare/1325...1469
Merge pull request #575 from SlicerRt/update-GelDosimetry

ENH: GelDosimetry 0.1.2: Added option to manually remove points from cal...
Merge pull request #574 from SlicerRt/update-SlicerRT

ENH: SlicerRT 0.13.2: Fixed contour conversion issues; Added mask option...
ENH: Addition of find_package(Subversion) to build correctly the extension on the Windows factory, and moved find_package(git) to Common.cmake
Merge pull request #576 from fbudin69500/update-SPHARM-PDM

ENH: Addition of find_package(Subversion) to build correctly the extensi...
ENH: Update dtiprocess version from r187 to r213

ENH: Enable storing of DTI properties as separate scalar point data
BUG: To perform ExperimentalUpload, EXTENSION_SUPERBUILD_BINARY_DIR needs to be defined. It was not defined anymore since we had removed include(Slicer_USE_FILE)
ENH: Updated the Superbuild system to add find_package(Subversion) and find_package(git) as well as remove the inclusion of
BUG: property 'svn:externals' deleted from 'IowaChanges20100105'
BUG: Branch dwiAtlas_Debug_Wendy was removed
ENH: Branch ITKv4 was removed because it couldn't download
'https://www.nitrc.org/svn/brains/BRAINSExecutionModel/trunk
and because it was not used anymore
ENH: remove DWIPrivateLibrary that was empty and improvement of packaging as a Slicer extension
ENH: By default, compilation of all the tools statically
BUG: dtiestimDTI_WLS_Test was not passing. We updated the test and the baseline image
COMP: Make building more robust.
When building against external ITK with DCMTK (as in slicer)
the DCMTK find package was not very robust in the default cmake
utilitities.  Thsi makes a more robust version that allows
superbuild to be more robust.
BUG: Fix Cmake warning
DTIProcess/CMake/SlicerExtensionsConfigureMacros.cmake:144:28
Argument not separated from preceding token by whitespace.
DTIProcess/CMake/SlicerExtensionsConfigureMacros.cmake:174:50
Argument not separated from preceding token by whitespace.
COMP: got rid of need for itkV3Compatibility
ENH: Modification of dtiestim version to 1.1.2 after last modification ( mask filter precision )
ENH: Addition of a larger tolerance for direction and origin difference when applying a mask filter. New tolerance set to 0.001 instead of default tolerance (1e-06).
ENH: Let the choice to change INSTALL_* directories
BUG: removed a warning form fibertrack
ENH&BUG: Install paths were not given from Superbuild project and static compila
tion had problems. Addition of a possibility to Superbuild the project independe
ntly from being an extension
BUG: this->ProcessObject::GetOutput(1) must be a valid output or program segmentation faults.
ENH: Remove old command line parser commented out code.
ENH: Verification of the version of ITK chosen. Warning message if wrong version chosen. This verification was done only if ITK was not found, which was a bug
STYLE: Remove debugging statements in configure step.
COMP: TransformWriter is more strict in ITKv4.5 about type matching
STYLE: Remove unnecessary file.
COMP: Fixed compilation with new SlicerExecutionModel
ENH: allow mask to be different in origin and spacing
ENH: ctest when stand-alone and executable-only build option
Merge pull request #580 from fbudin69500/update-DTIProcess

ENH: Update dtiprocess version from r187 to r213
ENH: Update FiberViewerLight from r65 to r68

BUG: To perform ExperimentalUpload, EXTENSION_SUPERBUILD_BINARY_DIR needs to be defined. It was not defined anymore since we had removed include()
http://www.nitrc.org/plugins/scmsvn/viewcvs.php?view=rev&root=fvlight&revision=68
ENH: Reorganization of CMake to add find_package(git) and find_package(Subversion) in Common.cmake
ENH: Reorganization of FiberViewerLight.cmake to look for SlicerExecutionModel before ITK
http://www.nitrc.org/plugins/scmsvn/viewcvs.php?view=rev&root=fvlight&revision=67
BUG: FiberViewerLight was including  when compiled as an extension. Doing this was including some Slicer CMake files. This used to work because those Slicer CMake files were the same as the CMake files contained in FiberViewerLight. In the latest version of Slicer, those files have changed and this was creating an incompatibility.  is not included anymore to avoid those conflicts
http://www.nitrc.org/plugins/scmsvn/viewcvs.php?view=rev&root=fvlight&revision=66
ENH: Update DTIAtlasFiberAnalyzer from r114 to r128

BUG: To perform ExperimentalUpload, EXTENSION_SUPERBUILD_BINARY_DIR needs to be defined. It was not defined anymore since we had removed include(Slicer_USE_FILE)
http://www.nitrc.org/plugins/scmsvn/viewcvs.php?view=rev&root=dti_tract_stat&revision=128
ENH: Updated dtiprocess version compiled to latest version (r211)
ENH: Update ITK version compiled by SuperBuild
BUG: Removed include(${Slicer_USE_FILE}) which was not necessary and was creating issues by including Superbuild files from Slicer when package was build as an extension instead of using the files included in the current package
BUG: Superbuild was not working because of missing RUNTIME_INSTALL setting for DTIAtlasFiberAnalyzer when not built as an extension
ENH: Addition of find_package(Subversion) and find_package(git) in case those are not in the PATH of the system
http://www.nitrc.org/plugins/scmsvn/viewcvs.php?view=rev&root=dti_tract_stat&revision=127
BUG: FiberViewerLight was including  when compiled as an extension. Doing this was including some Slicer CMake files. This used to work because those Slicer CMake files were the same as the CMake files contained in FiberViewerLight. In the latest version of Slicer, those files have changed and this was creating an incompatibility.  is not included anymore to avoid those conflicts
http://www.nitrc.org/plugins/scmsvn/viewcvs.php?view=rev&root=dti_tract_stat&revision=126
BUG: std::isnan doesn't exist on Windows. Builds DTIAtlasFiberAnalyzerLauncher even on Linux
http://www.nitrc.org/plugins/scmsvn/viewcvs.php?view=rev&root=dti_tract_stat&revision=125
ENH: Updated DTIProcess version and better packaging for Slicer extension
http://www.nitrc.org/plugins/scmsvn/viewcvs.php?view=rev&root=dti_tract_stat&revision=124
BUG: Updated Superbuild issues. Extension_DIR was set when using Superbuild even if FiberViewerLight was not build as an extension
http://www.nitrc.org/plugins/scmsvn/viewcvs.php?view=rev&root=dti_tract_stat&revision=123
BUG: Tests were not performed if DTIAtlasFiberAnalyzer was built as an extension
http://www.nitrc.org/plugins/scmsvn/viewcvs.php?view=rev&root=dti_tract_stat&revision=122
STYLE: Since there was already a tag "dti_tract_stat_1.4" on NITRC, the version number of DTIAtlasFiberAnalyzer in its xml description file was changed to 1.4.1
http://www.nitrc.org/plugins/scmsvn/viewcvs.php?view=rev&root=dti_tract_stat&revision=121
COMP: Add required parameters to SEMMacroBuildCLI for FiberCompare
http://www.nitrc.org/plugins/scmsvn/viewcvs.php?view=rev&root=dti_tract_stat&revision=120
BUG: inverse_rescale_p_value was not declared in void Processing::WritingDataInVTK
http://www.nitrc.org/plugins/scmsvn/viewcvs.php?view=rev&root=dti_tract_stat&revision=119
MergeStatWith Fiber
ENH: Allows to inverse the p-value mapping
ENH: Maps Arclength using the closest fiber point
dtitractstat
ENH: rewrote sorting functions using std::sort
ENH: Addition of a function to save the original fibers with the arclength as a scalar field
BUG: Rewrote arclength computation function
BUG: If "ad" is given as a command line argument, it is modified internally to be interpreted as "l1"
ENH: Computation of statistics stops before last fiber point instead of after last final point
DTIAtlasFiberAnalyzer:
ENH: Saves original fibers with new arclength field instead of resampled fibers
http://www.nitrc.org/plugins/scmsvn/viewcvs.php?view=rev&root=dti_tract_stat&revision=118
ENH: SuperBuild passes Subversion_SVN_EXECUTABLE to its subprojects
BUG: DTIAtlasFiberAnalyser_BINARY_DIR & DTIAtlasFiberAnalyser_SOURCE_DIR had been removed from DTIAtlasFiberAnalyzer's CMakeLists.txt
http://www.nitrc.org/plugins/scmsvn/viewcvs.php?view=rev&root=dti_tract_stat&revision=117
BUG: Launcher.cxx had not been added
http://www.nitrc.org/plugins/scmsvn/viewcvs.php?view=rev&root=dti_tract_stat&revision=116
COMP: trouble building within NamicExternalProjects
Error message from SEMMacroBuildCLI that INSTALL_RUNTIME_DESTINATION
is not defined. Not sure if this will bother Slicer.
http://www.nitrc.org/plugins/scmsvn/viewcvs.php?view=rev&root=dti_tract_stat&revision=115
Merge pull request #584 from fbudin69500/update-DTIAtlasFiberAnalyzer

ENH: Update DTIAtlasFiberAnalyzer from r114 to r128
Merge pull request #582 from fbudin69500/update-FiberViewerLight

ENH: Update FiberViewerLight from r65 to r68
BUG: Updating DTIProcess from r213 to r214

BUG: Searching for SVN and passing its path in the Superbuild process to compile as a Slicer extension. The value of this variable seems to be required:
http://slicer.cdash.org/viewBuildError.php?buildid=192440

http://www.nitrc.org/plugins/scmsvn/viewcvs.php?view=rev&root=dtiprocess&revision=214