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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.

Home Page: http://www.nitrc.org/projects/spharm-pdm

License: Apache License 2.0

CMake 7.78% C++ 80.61% C 3.79% Python 7.82%

3d-slicer-extension spherical-harmonics 3d-models decomposition

spharm-pdm's Introduction

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.

SPHARM-PDM is now available as a 3D Slicer extension (http://www.slicer.org) and as a SlicerSALT module (https://salt.slicer.org/)

Prerequisites

On 3D Slicer and SlicerSALT, Shape Analysis Module uses:

Shape Population Viewer extension which displays the outputs generated by Shape Analysis Module.
- To install Shape Population Viewer on 3D Slicer, follow these instructions:
  1. Download Shape Population Viewer executable on NITRC
  2. In 3D Slicer, add the folder where Shape Population Viewer executable is stored at Edit/Application Settings/Modules/Add (https://www.slicer.org/wiki/File:ModulesSettings.png)
  3. Restart 3D Slicer
Mesh To Label Map, which will be downloaded automatically with Shape Analysis Module (https://www.slicer.org/wiki/Documentation/Nightly/Extensions/MeshToLabelMap)

License

See License.txt

More information

Find the tool on NITRC

spharm-pdm's People

Contributors

Stargazers

Watchers

spharm-pdm's Issues

Case 0: s01_hippolabels_hres_L_MNI - step 0: ParaToSPHARMMesh completed with errors

Hi!

When I used the SPHARM, Shape Analysis Module to analyze my volume data, an error occurred in the Step3, Parameters to SPHARM Mesh:

Case 0: s01_hippolabels_hres_L_MNI - step 0: ParaToSPHARMMesh completed with errors

ParaToSPHARMMesh terminated with an unknown exception.

The debug info showed that:

Found CommandLine Module, target is C:/Users/11276/AppData/Roaming/NA-MIC/Extensions-28257/SPHARM-PDM/lib/Slicer-4.10/cli-modules/ParaToSPHARMMeshCLP.exe
ModuleType: CommandLineModule
ParaToSPHARMMesh command line:

C:/Users/11276/AppData/Roaming/NA-MIC/Extensions-28257/SPHARM-PDM/lib/Slicer-4.10/cli-modules/ParaToSPHARMMeshCLP.exe --subdivLevel 10 --spharmDegree 15 --thetaIteration 100 --phiIteration 100 --paraOut --medialMesh --FinalFlip 0 C:/Users/11276/AppData/Local/Temp/Slicer/BJCCE_vtkMRMLModelNodeE.vtp C:/Users/11276/AppData/Local/Temp/Slicer/BJCCE_vtkMRMLModelNodeF.vtp C:/Users/11276/Desktop/SPHARM-Tutorial/Output_hippo_sub/Step3_ParaToSPHARMMesh/s01_hippolabels_hres_L_MNI_pp_surf

Can you give me some advice about that? Thank you for your kind assistance!

Zeng

Extension icon is invalid

Please specify a valid extension icon in the CMake files. Due to how the extension appears in the Extensions Manager, users may think that it is broken:

Fix build error when building against VTK9

See https://slicer.cdash.org/index.php?project=SlicerPreview&date=2021-03-10&filtercount=1&showfilters=1&field1=buildname&compare1=63&value1=SPHARM-PDM

Modules/CLI/MetaMeshTools/vtkPolyDataToitkMesh.cxx:82:26: error: no matching member function for call to 'GetNextCell'

Modules/CLI/MetaMeshTools/STL2Meta.cxx:93:70: error: invalid initialization of non-const reference of type ‘const vtkIdType*& {aka const long long int*&}’ from an rvalue of type ‘const vtkIdType* {aka const long long int*}’

Order of coefficients in the file `SPHARM.coef`

Hi.

I was wondering in which order the coefficients are saved in the xx_SPHARM.coef files. Sorry, I couldn't find it anywhere.

Thanks,

Windows build does not work with newer CMake on Windows

If #55 is worked-around by setting the Fortran compiler environment variable in SPHARM-PDM's CMakeLists, this error occurs when building using CMake 3.15.1:

-- Detecting Fortran/C Interface
  CMake Error in C:/cmake-3.15.1/share/cmake-3.15/Modules/FortranCInterface/CMakeLists.txt:
    MSVC_RUNTIME_LIBRARY value 'MultiThreadedDLL' not known for this Fortran
    compiler.
  
  
  CMake Error at C:/cmake-3.15.1/share/cmake-3.15/Modules/FortranCInterface/Detect.cmake:31 (try_compile):
    Failed to generate test project build system.
  Call Stack (most recent call first):
    C:/cmake-3.15.1/share/cmake-3.15/Modules/FortranCInterface.cmake:224 (include)
    LAPACKE/CMakeLists.txt:7 (include)
  
  
  -- Configuring incomplete, errors occurred!

This does not occur in the SlicerSALT factory build, which uses CMake 3.13.4

Fix -Wtautological-undefined-compare in MeshMath

/Volumes/Dashboards/Stable/SSALT-0-build/SPHARM-PDM/Modules/CLI/MetaMeshTools/MeshMath.cxx:3744:48: warning: reference cannot be bound to dereferenced null pointer in
      well-defined C++ code; comparison may be assumed to always evaluate to true [-Wtautological-undefined-compare]
      if( inputMesh->GetPoint( i, point1 ) && &Xval[i] != NULL )
                                               ^~~~~~~    ~~~~

Need to improve Fortran compiler finding for Windows/Mac Slicer extension build

The current method used on the Slicer factory machine to find the Fortran compiler needs some work.

This line:
https://github.com/Slicer/DashboardScripts/blob/af76712f7afd0e82f489f3f29ff64fd8569afb3f/overload-vs2015-slicerextensions_preview_nightly.cmake#L55

should set the environment variable, but this doesn't seem to be picked up by the extension build

Create Github project for shapeworks

Would be great if you could create a GitHub repo for this project.

That would allow us to remove SVN requirements for SPHARM-PDM

See

SPHARM-PDM/Modules/CLI/CMakeLists.txt

Lines 133 to 150 in d2f5762

 option(COMPILE_shapeworks "Compile shapeworks." OFF) 

 if(COMPILE_shapeworks) 

 set(shapeworks_REPOSITORY https://www.nitrc.org/svn/shapeworks/code CACHE STRING "" FORCE) 

 ExternalProject_Add(shapeworks 

 SVN_REPOSITORY ${shapeworks_REPOSITORY} 

 SVN_REVISION -r 78 

 SVN_USERNAME slicerbot 

 SVN_PASSWORD slicer 

 UPDATE_COMMAND "" 

 SOURCE_DIR shapeworks 

 BINARY_DIR shapeworks-build 

 CMAKE_GENERATOR ${gen} 

 CMAKE_ARGS 

 -DITK_DIR:PATH=${ITK_DIR} 

 ${external_projects_vars} 

 INSTALL_COMMAND "" 

 ) 

 endif(COMPILE_shapeworks)

If you grant me admin push access, I can take care of converting the history to Git.

cc: @juanprietob

Spatial Object code needs to be updated for ITK 5.1

See errors here:
http://slicer.cdash.org/viewBuildError.php?buildid=1891245

Windows factory builds failing

Nightly overload builds are failing, both for Slicer4 and SlicerPreview:

The error indicates to me that WIN32 is somehow not defined, causing the wrong #include directive to be used.

SegPostProcess parameters to be shown in the GUI

The Shape Analysis Module xml should be modifed such we allow the user the option to interact with the following options in the GUI in Slicer: --noCCL --noClosing --noLS
They should display in the Advanced PostProcess Segmentation tab.

Build fails on Ubuntu with Ninja generator

Environment:

Ubuntu 20.04
CMake 3.18.6
Ninja 1.10.0

Abbreviated log:

$ cmake -B build -G 'Ninja' -D Slicer_DIR=$SLICER_NIGHTLY_DIR .
[ no errors ]
$ ninja -C build
[ ... ]
[14/17] Performing install step for 'SPHARM-PDM'
/bin/sh: 1: : Permission denied
[14/17] Forcing configure step for 'SPHARM-PDM'
FAILED: SPHARM-PDM-prefix/src/SPHARM-PDM-stamp/SPHARM-PDM-install 
cd /home/allem/src/SPHARM-PDM/build/SPHARM-PDM-build && "" "" && /snap/cmake/787/bin/cmake -E touch /home/allem/src/SPHARM-PDM/build/SPHARM-PDM-prefix/src/SPHARM-PDM-stamp/SPHARM-PDM-install
[16/17] Forcing configure step for 'SPHARM-PDM'
ninja: build stopped: subcommand failed.

You can see the problematic command: ... && "" "" && .... Obviously "" "" is not a valid command, so that line fails with permission denied (executable "" does not exist).

Somehow the SPHARM-PDM install step is producing this bad command and causing failures.

This occurs using Slicer Stable (4.11.20210226) and Nightly (b4c6004ef 2021-09-15). The build succeeds if using the 'Unix Makefiles' generator, so I use that as a workaround.

$ cmake -B build -G 'Unix Makefiles' -D Slicer_DIR=$SLICER_NIGHTLY_DIR .
[ no errors ]
$ make -C build -j
[ ... ]
[ 94%] Performing install step for 'SPHARM-PDM'
[100%] Completed 'SPHARM-PDM'
make[2]: Leaving directory '/home/allem/src/SPHARM-PDM/build'
[100%] Built target SPHARM-PDM
make[1]: Leaving directory '/home/allem/src/SPHARM-PDM/build'
make: Leaving directory '/home/allem/src/SPHARM-PDM/build'

Clean up unused variables to reduce warnings

CMAKE build failed using windows visual studio as generator

I am not quite familiar with C++ as well as CMAKE (3.26.0) and I would like to get SPHARM-PDM working for my research project. I was trying to build SPHARM-PDM using CMakeList.txt in the project root directory on my windows system that has installed Visual Studio 17 2022.

Error message:
fatal: detected dubious ownership in repository at 'E:/LX/Research/SPHARM-PDM/Build/GROUPS'
'E:/LX/Research/SPHARM-PDM/Build/GROUPS' is on a file system that doesnot record ownership
To add an exception for this directory, call:
git config --global --add safe.directory E:/LX/Research/SPHARM-PDM/Build/GROUPS
CMake Error at groups-subbuild/groups-populate-prefix/tmp/groups-populate-gitclone.cmake:49 (message):
Failed to checkout tag: '2f20e1728f06db8af4949e727c9b2adb5d232f27'

C:\Program Files\Microsoft Visual Studio\2022\Community\MSBuild\Microsoft\VC\v170\Microsoft.CppCommon.targets(249,5): error MSB8066: Custom build for 'E:\LX\Research\SPHARM-PDM\Build\groups-subbuild\CMakeFiles\c54297943f6cbc9cf03b2ac48e7052d6\groups-populate-download.rule;E:\LX\Research\SPHARM-PDM\Build\groups-subbuild\CMakeFiles\c54297943f6cbc9cf03b2ac48e7052d6\groups-populate-update.rule;E:\LX\Research\SPHARM-PDM\Build\groups-subbuild\CMakeFiles\c54297943f6cbc9cf03b2ac48e7052d6\groups-populate-patch.rule;E:\LX\Research\SPHARM-PDM\Build\groups-subbuild\CMakeFiles\c54297943f6cbc9cf03b2ac48e7052d6\groups-populate-configure.rule;E:\LX\Research\SPHARM-PDM\Build\groups-subbuild\CMakeFiles\c54297943f6cbc9cf03b2ac48e7052d6\groups-populate-build.rule;E:\LX\Research\SPHARM-PDM\Build\groups-subbuild\CMakeFiles\c54297943f6cbc9cf03b2ac48e7052d6\groups-populate-install.rule;E:\LX\Research\SPHARM-PDM\Build\groups-subbuild\CMakeFiles\c54297943f6cbc9cf03b2ac48e7052d6\groups-populate-test.rule;E:\LX\Research\SPHARM-PDM\Build\groups-subbuild\CMakeFiles\d396c4e67dc45ccccc5b3f8ba7632a55\groups-populate-complete.rule;E:\LX\Research\SPHARM-PDM\Build\groups-subbuild\CMakeFiles\612a54e623e26e37e5b59cb9366b51d3\groups-populate.rule' exited with code 1. [E:\LX\Research\SPHARM-PDM\Build\groups-subbuild\groups-populate.vcxproj]

CMake Error at C:/Program Files/CMake/share/cmake-3.26/Modules/FetchContent.cmake:1622 (message):
Build step for groups failed: 1
Call Stack (most recent call first):
C:/Program Files/CMake/share/cmake-3.26/Modules/FetchContent.cmake:1646 (__FetchContent_directPopulate)
SuperBuild.cmake:30 (FetchContent_Populate)
CMakeLists.txt:55 (include)

Configuring incomplete, errors occurred!

In fact, I don't really want to compile the project as a slicer plugin but to compile each module as independent command line tools that has a python binding interface, and I wonder how should I rewrite the CMakeLists.txt in the CommandLineTool folder? Thanks in advance!

SpharmTools SegFaulting

Hi everyone, I am playing with your command line tools, getting acquainted with SPHARMs and realized that SpharmTools got segfaulting on me. Without gotting deeply involved into the theory, I found that setting for( int i = 1; i < LENGTH; i++ ) to for( int i = 1; i < LENGTH-1; i++ ) in line 1302 of Libraries/Shape/Numerics/SphericalHarmonicPolynomial.txx resolved the issue (see diff below). I do not know if this is a sensible solution, but it gives me sensible results (curves).

--- a/Libraries/Shape/Numerics/SphericalHarmonicPolynomial.txx
+++ b/Libraries/Shape/Numerics/SphericalHarmonicPolynomial.txx
@@ -1299,7 +1299,7 @@ void SphericalHarmonicPolynomial<TDimension>::GetOneRidgePoint(unsigned int from
     std::ofstream out;
     out.open("test.txt" );
     out << "NUMBER_OF_POINTS=9999" << std::endl << "DIMENSION=3" << std::endl << "TYPE=Curve" << std::endl;
-    for( int i = 1; i < LENGTH; i++ )
+    for( int i = 1; i < LENGTH-1; i++ )
       {
       prev = current;
       current = next;

Best Stefan

SegPostProcess fails for some labelmaps

Reported by @lassoan, in Kitware/SlicerSALT#123

This can be also reproduced by using only SegPostProcess module. Set this image as input, create a new image for output, check Advanced / Enforced spacing in x, y, and z direction, click Apply. => result is a black image - ERROR!

The problem is that region for the output image is not computed correctly - the output image is in a different place. This becomes clear when showing regions of the input and output volumes in 3D:

GenParaMesh completed with errors

Hi!

I used the SPHARM-PDM to analyze the segmented hippocampal subregion ( SlicerSALT 2.2.1 on ubuntu 18.04), I encountered an error in the Step2, GenParaMesh.
It provides a warning:
Euler equation not satisfied. Euler number: 16762-16762=0

When I check the .nrrd file in the SegPostProcess folder using itksnap, I find a hole in the 3D view of the subregion. Is there any method to fill holes? Thank you very much!

Associate 3d-slicer-extension topic with the repository

Could you associate the 3d-slicer-extension GitHub topic so that it is listed here: https://github.com/topics/3d-slicer-extension

To learn more about topic, read https://help.github.com/en/articles/about-topics

MacOS dashboard broken

Computron has been missing Fortran compilers for a while

-- Looking up any Fortran compiler -- Looking up any Fortran compiler - Fortran_COMPILER-NOTFOUND CMake Error at /Users/svc-dashboard/D/Support/CMake-3.17.2.app/Contents/share/cmake-3.17/Modules/FindPackageHandleStandardArgs.cmake:164 (message): Could NOT find Fortran (missing: Fortran_COMPILER_ID) Call Stack (most recent call first): /Users/svc-dashboard/D/Support/CMake-3.17.2.app/Contents/share/cmake-3.17/Modules/FindPackageHandleStandardArgs.cmake:445 (_FPHSA_FAILURE_MESSAGE) /Users/svc-dashboard/D/P/S-0-E-b/SPHARM-PDM-build/CMake/FindFortran.cmake:625 (find_package_handle_standard_args) SuperBuild/External_LAPACK.cmake:147 (find_package) /D/P/S-0/CMake/ExternalProjectDependency.cmake:842 (include) /D/P/S-0/CMake/ExternalProjectDependency.cmake:916 (ExternalProject_Include_Dependencies) SuperBuild.cmake:53 (ExternalProject_Include_Dependencies) CMakeLists.txt:55 (include)

Increase Flip Option table height for better usability

The table in the Advanced Parameters to SPHARM mesh under Flip Options is too small, it only allows to see one subject at a time. It would be easier to use if more subject were visible

paraOut option in ParaToSPHARMMesh does not work

Setting the paraOut parameter to True isn't writing the colormap in the VTK files

Add Phi and Theta parameter files to procrustes aligned meshes

After running shape analysis module with the proc-aligned option enabled, the vtk output files do not have the paraphi and paratheta colormaps in them. They should have them.

How to install SPHARM-PDM on ubuntu:

Thanks a lot for your sharing!
But I'm still confused with the installation and usage of SPHARM-PDM on Ubuntu. Can you show me more detail or instruction links on this problem?
Thank you!

Step 0- Mesh to label map is cropping condyles

@allemangD @bpaniagua @jcfr
Hi David and Bea
Please note in the powerpoint below that the Step 0 in Spharm both in the slcierCMf and Salt implementations are cropping the TMJ condyles.
Can you please prioritize this issue? Thank you!
SPHARM_demo.pptx

Option `COMPILE_shapeworks` is broken

FWIW, trying to build shapeworks currently fail with the following:

In file included from /home/jcfr/Projects/SPHARM-PDM-build-standalone/ITKv4-install/include/ITK-4.11/itkLightObject.h:21:0,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/ITKv4-install/include/ITK-4.11/itkObject.h:31,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/ITKv4-install/include/ITK-4.11/itkDataObject.h:31,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleProcrustesRegistration.h:18,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleProcrustesRegistration.cxx:15:
/home/jcfr/Projects/SPHARM-PDM-build-standalone/ITKv4-install/include/ITK-4.11/itkMacro.h:587:27: error: token ""error ITK_TEMPLATE_TXX is no longer a supported identifier, you should replace with ITK_MANUAL_INSTANTIATION as a replacement"" is not valid in preprocessor expressions
 #define ITK_TEMPLATE_TXX  "error ITK_TEMPLATE_TXX is no longer a supported identifier, you should replace with ITK_MANUAL_INSTANTIATION as a replacement"
                           ^
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleEvents.h:121:5: note: in expansion of macro ‘ITK_TEMPLATE_TXX’
 #if ITK_TEMPLATE_TXX
     ^
/home/jcfr/Projects/SPHARM-PDM-build-standalone/ITKv4-install/include/ITK-4.11/itkMacro.h:587:27: error: token ""error ITK_TEMPLATE_TXX is no longer a supported identifier, you should replace with ITK_MANUAL_INSTANTIATION as a replacement"" is not valid in preprocessor expressions
 #define ITK_TEMPLATE_TXX  "error ITK_TEMPLATE_TXX is no longer a supported identifier, you should replace with ITK_MANUAL_INSTANTIATION as a replacement"
                           ^
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleDomain.h:109:5: note: in expansion of macro ‘ITK_TEMPLATE_TXX’
 #if ITK_TEMPLATE_TXX
     ^
/home/jcfr/Projects/SPHARM-PDM-build-standalone/ITKv4-install/include/ITK-4.11/itkMacro.h:587:27: error: token ""error ITK_TEMPLATE_TXX is no longer a supported identifier, you should replace with ITK_MANUAL_INSTANTIATION as a replacement"" is not valid in preprocessor expressions
 #define ITK_TEMPLATE_TXX  "error ITK_TEMPLATE_TXX is no longer a supported identifier, you should replace with ITK_MANUAL_INSTANTIATION as a replacement"
                           ^
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleNeighborhood.h:132:5: note: in expansion of macro ‘ITK_TEMPLATE_TXX’
 #if ITK_TEMPLATE_TXX
     ^
/home/jcfr/Projects/SPHARM-PDM-build-standalone/ITKv4-install/include/ITK-4.11/itkMacro.h:587:27: error: token ""error ITK_TEMPLATE_TXX is no longer a supported identifier, you should replace with ITK_MANUAL_INSTANTIATION as a replacement"" is not valid in preprocessor expressions
 #define ITK_TEMPLATE_TXX  "error ITK_TEMPLATE_TXX is no longer a supported identifier, you should replace with ITK_MANUAL_INSTANTIATION as a replacement"
                           ^
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleSystem.h:498:5: note: in expansion of macro ‘ITK_TEMPLATE_TXX’
 #if ITK_TEMPLATE_TXX
     ^
In file included from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleAttribute.h:22:0,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleSystem.h:22,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleProcrustesRegistration.h:21,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleProcrustesRegistration.cxx:15:
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleEvents.h: In copy constructor ‘itk::ParticleEventWithIndex::ParticleEventWithIndex(const itk::ParticleEventWithIndex&)’:
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleEvents.h:75:3: warning: base class ‘class itk::ParticleEvent’ should be explicitly initialized in the copy constructor [-Wextra]
   ParticleEventWithIndex(const ParticleEventWithIndex &v)
   ^
[2/7] Building CXX object ITKParticleSystem/CMakeFiles/ITKParticleSystem.dir/itkParticleSystem.cxx.o
FAILED: ITKParticleSystem/CMakeFiles/ITKParticleSystem.dir/itkParticleSystem.cxx.o 
/usr/bin/c++  -DITK_IO_FACTORY_REGISTER_MANAGER -IITKIOFactoryRegistration -I/home/jcfr/Projects/SPHARM-PDM-build-standalone/ITKv4-install/include/ITK-4.11 -I/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/Utilities -I/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem -I/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/tinyxml -Wall -Wcast-align -Wdisabled-optimization -Wextra -Wformat=2 -Winvalid-pch -Wno-format-nonliteral -Wpointer-arith -Wshadow -Wunused -Wwrite-strings -funit-at-a-time -Wno-strict-overflow -Wno-deprecated -Wno-invalid-offsetof -Woverloaded-virtual -Wstrict-null-sentinel  -Wall -Wcast-align -Wdisabled-optimization -Wextra -Wformat=2 -Winvalid-pch -Wno-format-nonliteral -Wpointer-arith -Wshadow -Wunused -Wwrite-strings -funit-at-a-time -Wno-strict-overflow -Wno-deprecated -Wno-invalid-offsetof -Woverloaded-virtual -Wstrict-null-sentinel   -msse2  -msse2 -O2 -g -DNDEBUG -MD -MT ITKParticleSystem/CMakeFiles/ITKParticleSystem.dir/itkParticleSystem.cxx.o -MF ITKParticleSystem/CMakeFiles/ITKParticleSystem.dir/itkParticleSystem.cxx.o.d -o ITKParticleSystem/CMakeFiles/ITKParticleSystem.dir/itkParticleSystem.cxx.o -c /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleSystem.cxx
In file included from /home/jcfr/Projects/SPHARM-PDM-build-standalone/ITKv4-install/include/ITK-4.11/itkLightObject.h:21:0,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/ITKv4-install/include/ITK-4.11/itkObject.h:31,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/ITKv4-install/include/ITK-4.11/itkDataObject.h:31,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleSystem.h:18,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleSystem.cxx:15:
/home/jcfr/Projects/SPHARM-PDM-build-standalone/ITKv4-install/include/ITK-4.11/itkMacro.h:587:27: error: token ""error ITK_TEMPLATE_TXX is no longer a supported identifier, you should replace with ITK_MANUAL_INSTANTIATION as a replacement"" is not valid in preprocessor expressions
 #define ITK_TEMPLATE_TXX  "error ITK_TEMPLATE_TXX is no longer a supported identifier, you should replace with ITK_MANUAL_INSTANTIATION as a replacement"
                           ^
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleEvents.h:121:5: note: in expansion of macro ‘ITK_TEMPLATE_TXX’
 #if ITK_TEMPLATE_TXX
     ^
/home/jcfr/Projects/SPHARM-PDM-build-standalone/ITKv4-install/include/ITK-4.11/itkMacro.h:587:27: error: token ""error ITK_TEMPLATE_TXX is no longer a supported identifier, you should replace with ITK_MANUAL_INSTANTIATION as a replacement"" is not valid in preprocessor expressions
 #define ITK_TEMPLATE_TXX  "error ITK_TEMPLATE_TXX is no longer a supported identifier, you should replace with ITK_MANUAL_INSTANTIATION as a replacement"
                           ^
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleDomain.h:109:5: note: in expansion of macro ‘ITK_TEMPLATE_TXX’
 #if ITK_TEMPLATE_TXX
     ^
/home/jcfr/Projects/SPHARM-PDM-build-standalone/ITKv4-install/include/ITK-4.11/itkMacro.h:587:27: error: token ""error ITK_TEMPLATE_TXX is no longer a supported identifier, you should replace with ITK_MANUAL_INSTANTIATION as a replacement"" is not valid in preprocessor expressions
 #define ITK_TEMPLATE_TXX  "error ITK_TEMPLATE_TXX is no longer a supported identifier, you should replace with ITK_MANUAL_INSTANTIATION as a replacement"
                           ^
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleNeighborhood.h:132:5: note: in expansion of macro ‘ITK_TEMPLATE_TXX’
 #if ITK_TEMPLATE_TXX
     ^
/home/jcfr/Projects/SPHARM-PDM-build-standalone/ITKv4-install/include/ITK-4.11/itkMacro.h:587:27: error: token ""error ITK_TEMPLATE_TXX is no longer a supported identifier, you should replace with ITK_MANUAL_INSTANTIATION as a replacement"" is not valid in preprocessor expressions
 #define ITK_TEMPLATE_TXX  "error ITK_TEMPLATE_TXX is no longer a supported identifier, you should replace with ITK_MANUAL_INSTANTIATION as a replacement"
                           ^
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleSystem.h:498:5: note: in expansion of macro ‘ITK_TEMPLATE_TXX’
 #if ITK_TEMPLATE_TXX
     ^
In file included from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleAttribute.h:22:0,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleSystem.h:22,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleSystem.cxx:15:
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleEvents.h: In copy constructor ‘itk::ParticleEventWithIndex::ParticleEventWithIndex(const itk::ParticleEventWithIndex&)’:
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleEvents.h:75:3: warning: base class ‘class itk::ParticleEvent’ should be explicitly initialized in the copy constructor [-Wextra]
   ParticleEventWithIndex(const ParticleEventWithIndex &v)
   ^
[3/7] Building CXX object ShapeWorksRun/CMakeFiles/ShapeWorksRun.dir/ShapeWorksRun.cxx.o
FAILED: ShapeWorksRun/CMakeFiles/ShapeWorksRun.dir/ShapeWorksRun.cxx.o 
/usr/bin/c++  -DITK_IO_FACTORY_REGISTER_MANAGER -IITKIOFactoryRegistration -I/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/Utilities -I/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem -I/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/tinyxml -isystem /home/jcfr/Projects/SPHARM-PDM-build-standalone/ITKv4-install/include/ITK-4.11 -isystem /home/jcfr/Projects/SPHARM-PDM-build-standalone/ITKv4-install/include -Wall -Wcast-align -Wdisabled-optimization -Wextra -Wformat=2 -Winvalid-pch -Wno-format-nonliteral -Wpointer-arith -Wshadow -Wunused -Wwrite-strings -funit-at-a-time -Wno-strict-overflow -Wno-deprecated -Wno-invalid-offsetof -Woverloaded-virtual -Wstrict-null-sentinel  -Wall -Wcast-align -Wdisabled-optimization -Wextra -Wformat=2 -Winvalid-pch -Wno-format-nonliteral -Wpointer-arith -Wshadow -Wunused -Wwrite-strings -funit-at-a-time -Wno-strict-overflow -Wno-deprecated -Wno-invalid-offsetof -Woverloaded-virtual -Wstrict-null-sentinel   -msse2  -msse2 -O2 -g -DNDEBUG -MD -MT ShapeWorksRun/CMakeFiles/ShapeWorksRun.dir/ShapeWorksRun.cxx.o -MF ShapeWorksRun/CMakeFiles/ShapeWorksRun.dir/ShapeWorksRun.cxx.o.d -o ShapeWorksRun/CMakeFiles/ShapeWorksRun.dir/ShapeWorksRun.cxx.o -c /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksRun/ShapeWorksRun.cxx
In file included from /home/jcfr/Projects/SPHARM-PDM-build-standalone/ITKv4-install/include/ITK-4.11/itkLightObject.h:21:0,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/ITKv4-install/include/ITK-4.11/itkObject.h:31,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/ITKv4-install/include/ITK-4.11/itkDataObject.h:31,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleSystem.h:18,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksRun/ShapeWorksRunApp.h:22,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksRun/ShapeWorksRun.cxx:16:
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleEvents.h:121:5: error: token ""error ITK_TEMPLATE_TXX is no longer a supported identifier, you should replace with ITK_MANUAL_INSTANTIATION as a replacement"" is not valid in preprocessor expressions
 #if ITK_TEMPLATE_TXX
     ^
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleDomain.h:109:5: error: token ""error ITK_TEMPLATE_TXX is no longer a supported identifier, you should replace with ITK_MANUAL_INSTANTIATION as a replacement"" is not valid in preprocessor expressions
 #if ITK_TEMPLATE_TXX
     ^
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleNeighborhood.h:132:5: error: token ""error ITK_TEMPLATE_TXX is no longer a supported identifier, you should replace with ITK_MANUAL_INSTANTIATION as a replacement"" is not valid in preprocessor expressions
 #if ITK_TEMPLATE_TXX
     ^
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleSystem.h:498:5: error: token ""error ITK_TEMPLATE_TXX is no longer a supported identifier, you should replace with ITK_MANUAL_INSTANTIATION as a replacement"" is not valid in preprocessor expressions
 #if ITK_TEMPLATE_TXX
     ^
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleVectorFunction.h:115:5: error: token ""error ITK_TEMPLATE_TXX is no longer a supported identifier, you should replace with ITK_MANUAL_INSTANTIATION as a replacement"" is not valid in preprocessor expressions
 #if ITK_TEMPLATE_TXX
     ^
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleRegionDomain.h:128:5: error: token ""error ITK_TEMPLATE_TXX is no longer a supported identifier, you should replace with ITK_MANUAL_INSTANTIATION as a replacement"" is not valid in preprocessor expressions
 #if ITK_TEMPLATE_TXX
     ^
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleClipRegionDomain.h:94:5: error: token ""error ITK_TEMPLATE_TXX is no longer a supported identifier, you should replace with ITK_MANUAL_INSTANTIATION as a replacement"" is not valid in preprocessor expressions
 #if ITK_TEMPLATE_TXX
     ^
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleImageDomain.h:147:5: error: token ""error ITK_TEMPLATE_TXX is no longer a supported identifier, you should replace with ITK_MANUAL_INSTANTIATION as a replacement"" is not valid in preprocessor expressions
 #if ITK_TEMPLATE_TXX
     ^
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleImageDomainWithGradients.h:159:5: error: token ""error ITK_TEMPLATE_TXX is no longer a supported identifier, you should replace with ITK_MANUAL_INSTANTIATION as a replacement"" is not valid in preprocessor expressions
 #if ITK_TEMPLATE_TXX
     ^
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleGradientDescentPositionOptimizer.h:154:5: error: token ""error ITK_TEMPLATE_TXX is no longer a supported identifier, you should replace with ITK_MANUAL_INSTANTIATION as a replacement"" is not valid in preprocessor expressions
 #if ITK_TEMPLATE_TXX
     ^
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleEntropyGradientFunction.h:212:5: error: token ""error ITK_TEMPLATE_TXX is no longer a supported identifier, you should replace with ITK_MANUAL_INSTANTIATION as a replacement"" is not valid in preprocessor expressions
 #if ITK_TEMPLATE_TXX
     ^
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleQualifierEntropyGradientFunction.h:164:5: error: token ""error ITK_TEMPLATE_TXX is no longer a supported identifier, you should replace with ITK_MANUAL_INSTANTIATION as a replacement"" is not valid in preprocessor expressions
 #if ITK_TEMPLATE_TXX
     ^
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleImageDomainWithHessians.h:205:5: error: token ""error ITK_TEMPLATE_TXX is no longer a supported identifier, you should replace with ITK_MANUAL_INSTANTIATION as a replacement"" is not valid in preprocessor expressions
 #if ITK_TEMPLATE_TXX
     ^
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleImageDomainWithCurvature.h:192:5: error: token ""error ITK_TEMPLATE_TXX is no longer a supported identifier, you should replace with ITK_MANUAL_INSTANTIATION as a replacement"" is not valid in preprocessor expressions
 #if ITK_TEMPLATE_TXX
     ^
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleImplicitSurfaceDomain.h:179:5: error: token ""error ITK_TEMPLATE_TXX is no longer a supported identifier, you should replace with ITK_MANUAL_INSTANTIATION as a replacement"" is not valid in preprocessor expressions
 #if ITK_TEMPLATE_TXX
     ^
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleMeanCurvatureAttribute.h:128:5: error: token ""error ITK_TEMPLATE_TXX is no longer a supported identifier, you should replace with ITK_MANUAL_INSTANTIATION as a replacement"" is not valid in preprocessor expressions
 #if ITK_TEMPLATE_TXX
     ^
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleCurvatureEntropyGradientFunction.h:191:5: error: token ""error ITK_TEMPLATE_TXX is no longer a supported identifier, you should replace with ITK_MANUAL_INSTANTIATION as a replacement"" is not valid in preprocessor expressions
 #if ITK_TEMPLATE_TXX
     ^
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkPowerOfTwoPointTree.h:298:5: error: token ""error ITK_TEMPLATE_TXX is no longer a supported identifier, you should replace with ITK_MANUAL_INSTANTIATION as a replacement"" is not valid in preprocessor expressions
 #if ITK_TEMPLATE_TXX
     ^
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleRegionNeighborhood.h:148:5: error: token ""error ITK_TEMPLATE_TXX is no longer a supported identifier, you should replace with ITK_MANUAL_INSTANTIATION as a replacement"" is not valid in preprocessor expressions
 #if ITK_TEMPLATE_TXX
     ^
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleSurfaceNeighborhood.h:92:5: error: token ""error ITK_TEMPLATE_TXX is no longer a supported identifier, you should replace with ITK_MANUAL_INSTANTIATION as a replacement"" is not valid in preprocessor expressions
 #if ITK_TEMPLATE_TXX
     ^
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleOmegaGradientFunction.h:204:5: error: token ""error ITK_TEMPLATE_TXX is no longer a supported identifier, you should replace with ITK_MANUAL_INSTANTIATION as a replacement"" is not valid in preprocessor expressions
 #if ITK_TEMPLATE_TXX
     ^
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkMaximumEntropySurfaceSampler.h:333:5: error: token ""error ITK_TEMPLATE_TXX is no longer a supported identifier, you should replace with ITK_MANUAL_INSTANTIATION as a replacement"" is not valid in preprocessor expressions
 #if ITK_TEMPLATE_TXX
     ^
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleDualVectorFunction.h:498:5: error: token ""error ITK_TEMPLATE_TXX is no longer a supported identifier, you should replace with ITK_MANUAL_INSTANTIATION as a replacement"" is not valid in preprocessor expressions
 #if ITK_TEMPLATE_TXX
     ^
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleEnsembleNormalPenaltyFunction.h:130:5: error: token ""error ITK_TEMPLATE_TXX is no longer a supported identifier, you should replace with ITK_MANUAL_INSTANTIATION as a replacement"" is not valid in preprocessor expressions
 #if ITK_TEMPLATE_TXX
     ^
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleEnsembleMeanFunction.h:98:5: error: token ""error ITK_TEMPLATE_TXX is no longer a supported identifier, you should replace with ITK_MANUAL_INSTANTIATION as a replacement"" is not valid in preprocessor expressions
 #if ITK_TEMPLATE_TXX
     ^
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleEnsembleEntropyFunction.h:184:5: error: token ""error ITK_TEMPLATE_TXX is no longer a supported identifier, you should replace with ITK_MANUAL_INSTANTIATION as a replacement"" is not valid in preprocessor expressions
 #if ITK_TEMPLATE_TXX
     ^
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleGeneralEntropyGradientFunction.h:187:5: error: token ""error ITK_TEMPLATE_TXX is no longer a supported identifier, you should replace with ITK_MANUAL_INSTANTIATION as a replacement"" is not valid in preprocessor expressions
 #if ITK_TEMPLATE_TXX
     ^
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkMaximumEntropyCorrespondenceSampler.h:263:5: error: token ""error ITK_TEMPLATE_TXX is no longer a supported identifier, you should replace with ITK_MANUAL_INSTANTIATION as a replacement"" is not valid in preprocessor expressions
 #if ITK_TEMPLATE_TXX
     ^
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksRun/ShapeWorksRunApp.h:170:5: error: token ""error ITK_TEMPLATE_TXX is no longer a supported identifier, you should replace with ITK_MANUAL_INSTANTIATION as a replacement"" is not valid in preprocessor expressions
 #if ITK_TEMPLATE_TXX
     ^
In file included from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleAttribute.h:22:0,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleSystem.h:22,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksRun/ShapeWorksRunApp.h:22,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksRun/ShapeWorksRun.cxx:16:
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleEvents.h: In copy constructor ‘itk::ParticleEventWithIndex::ParticleEventWithIndex(const itk::ParticleEventWithIndex&)’:
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleEvents.h:75:3: warning: base class ‘class itk::ParticleEvent’ should be explicitly initialized in the copy constructor [-Wextra]
   ParticleEventWithIndex(const ParticleEventWithIndex &v)
   ^
In file included from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkMaximumEntropySurfaceSampler.h:20:0,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkMaximumEntropyCorrespondenceSampler.h:18,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksRun/ShapeWorksRunApp.h:25,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksRun/ShapeWorksRun.cxx:16:
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleCurvatureEntropyGradientFunction.h: In instantiation of ‘class itk::ParticleCurvatureEntropyGradientFunction<float, 3u>’:
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkMaximumEntropySurfaceSampler.h:294:13:   required from ‘class itk::MaximumEntropySurfaceSampler<itk::Image<float, 3u> >’
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkMaximumEntropyCorrespondenceSampler.h:36:18:   required from ‘class itk::MaximumEntropyCorrespondenceSampler<itk::Image<float, 3u> >’
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksRun/ShapeWorksRunApp.h:118:63:   required from here
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleEntropyGradientFunction.h:134:18: warning: ‘double itk::ParticleEntropyGradientFunction<TGradientNumericType, VDimension>::EstimateSigma(unsigned int, const typename itk::ParticleEntropyGradientFunction<TGradientNumericType, VDimension>::Superclass::ParticleSystemType::PointVectorType&, const std::vector<double>&, const PointType&, double, double, int&) const [with TGradientNumericType = float; unsigned int VDimension = 3u; typename itk::ParticleEntropyGradientFunction<TGradientNumericType, VDimension>::Superclass::ParticleSystemType::PointVectorType = std::vector<itk::ParticlePointIndexPair<3u>, std::allocator<itk::ParticlePointIndexPair<3u> > >; itk::ParticleEntropyGradientFunction<TGradientNumericType, VDimension>::PointType = itk::Point<double, 3u>]’ was hidden [-Woverloaded-virtual]
   virtual double EstimateSigma(unsigned int, const typename ParticleSystemType::PointVectorType &,
                  ^
In file included from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkMaximumEntropySurfaceSampler.h:25:0,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkMaximumEntropyCorrespondenceSampler.h:18,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksRun/ShapeWorksRunApp.h:25,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksRun/ShapeWorksRun.cxx:16:
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleCurvatureEntropyGradientFunction.h:122:18: warning:   by ‘double itk::ParticleCurvatureEntropyGradientFunction<TGradientNumericType, VDimension>::EstimateSigma(unsigned int, unsigned int, const typename itk::ParticleCurvatureEntropyGradientFunction<TGradientNumericType, VDimension>::Superclass::ParticleSystemType::PointVectorType&, const std::vector<double>&, const PointType&, double, double, int&, double&) const [with TGradientNumericType = float; unsigned int VDimension = 3u; typename itk::ParticleCurvatureEntropyGradientFunction<TGradientNumericType, VDimension>::Superclass::ParticleSystemType::PointVectorType = std::vector<itk::ParticlePointIndexPair<3u>, std::allocator<itk::ParticlePointIndexPair<3u> > >; itk::ParticleCurvatureEntropyGradientFunction<TGradientNumericType, VDimension>::PointType = itk::Point<double, 3u>]’ [-Woverloaded-virtual]
   virtual double EstimateSigma( unsigned int, unsigned int, const typename ParticleSystemType::PointVectorType &,
                  ^
In file included from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkMaximumEntropySurfaceSampler.h:20:0,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkMaximumEntropyCorrespondenceSampler.h:18,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksRun/ShapeWorksRunApp.h:25,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksRun/ShapeWorksRun.cxx:16:
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleOmegaGradientFunction.h: In instantiation of ‘class itk::ParticleOmegaGradientFunction<float, 3u>’:
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkMaximumEntropySurfaceSampler.h:297:13:   required from ‘class itk::MaximumEntropySurfaceSampler<itk::Image<float, 3u> >’
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkMaximumEntropyCorrespondenceSampler.h:36:18:   required from ‘class itk::MaximumEntropyCorrespondenceSampler<itk::Image<float, 3u> >’
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksRun/ShapeWorksRunApp.h:118:63:   required from here
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleEntropyGradientFunction.h:134:18: warning: ‘double itk::ParticleEntropyGradientFunction<TGradientNumericType, VDimension>::EstimateSigma(unsigned int, const typename itk::ParticleEntropyGradientFunction<TGradientNumericType, VDimension>::Superclass::ParticleSystemType::PointVectorType&, const std::vector<double>&, const PointType&, double, double, int&) const [with TGradientNumericType = float; unsigned int VDimension = 3u; typename itk::ParticleEntropyGradientFunction<TGradientNumericType, VDimension>::Superclass::ParticleSystemType::PointVectorType = std::vector<itk::ParticlePointIndexPair<3u>, std::allocator<itk::ParticlePointIndexPair<3u> > >; itk::ParticleEntropyGradientFunction<TGradientNumericType, VDimension>::PointType = itk::Point<double, 3u>]’ was hidden [-Woverloaded-virtual]
   virtual double EstimateSigma(unsigned int, const typename ParticleSystemType::PointVectorType &,
                  ^
In file included from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkMaximumEntropySurfaceSampler.h:28:0,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkMaximumEntropyCorrespondenceSampler.h:18,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksRun/ShapeWorksRunApp.h:25,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksRun/ShapeWorksRun.cxx:16:
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleOmegaGradientFunction.h:135:18: warning:   by ‘double itk::ParticleOmegaGradientFunction<TGradientNumericType, VDimension>::EstimateSigma(unsigned int, unsigned int, const typename itk::ParticleOmegaGradientFunction<TGradientNumericType, VDimension>::Superclass::ParticleSystemType::PointVectorType&, const std::vector<double>&, const PointType&, double, double, int&, double&, unsigned int) const [with TGradientNumericType = float; unsigned int VDimension = 3u; typename itk::ParticleOmegaGradientFunction<TGradientNumericType, VDimension>::Superclass::ParticleSystemType::PointVectorType = std::vector<itk::ParticlePointIndexPair<3u>, std::allocator<itk::ParticlePointIndexPair<3u> > >; itk::ParticleOmegaGradientFunction<TGradientNumericType, VDimension>::PointType = itk::Point<double, 3u>]’ [-Woverloaded-virtual]
   virtual double EstimateSigma( unsigned int, unsigned int,
                  ^
In file included from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleSystem.h:30:0,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksRun/ShapeWorksRunApp.h:22,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksRun/ShapeWorksRun.cxx:16:
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleRegionNeighborhood.h: In instantiation of ‘class itk::ParticleRegionNeighborhood<3u>’:
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleSurfaceNeighborhood.h:33:18:   required from ‘class itk::ParticleSurfaceNeighborhood<itk::Image<float, 3u> >’
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkMaximumEntropySurfaceSampler.h:311:75:   required from ‘class itk::MaximumEntropySurfaceSampler<itk::Image<float, 3u> >’
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkMaximumEntropyCorrespondenceSampler.h:36:18:   required from ‘class itk::MaximumEntropyCorrespondenceSampler<itk::Image<float, 3u> >’
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksRun/ShapeWorksRunApp.h:118:63:   required from here
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleNeighborhood.h:89:25: warning: ‘unsigned int itk::ParticleNeighborhood<VDimension>::FindNeighborhoodPoints(const PointType&, double, itk::ParticleNeighborhood<VDimension>::PointVectorType&) const [with unsigned int VDimension = 3u; itk::ParticleNeighborhood<VDimension>::PointType = itk::Point<double, 3u>; itk::ParticleNeighborhood<VDimension>::PointVectorType = std::vector<itk::ParticlePointIndexPair<3u>, std::allocator<itk::ParticlePointIndexPair<3u> > >]’ was hidden [-Woverloaded-virtual]
   virtual unsigned int  FindNeighborhoodPoints(const PointType &, double, PointVectorType &) const
                         ^
In file included from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleSurfaceNeighborhood.h:18:0,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkMaximumEntropySurfaceSampler.h:27,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkMaximumEntropyCorrespondenceSampler.h:18,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksRun/ShapeWorksRunApp.h:25,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksRun/ShapeWorksRun.cxx:16:
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleRegionNeighborhood.h:63:27: warning:   by ‘itk::ParticleRegionNeighborhood<VDimension>::PointVectorType itk::ParticleRegionNeighborhood<VDimension>::FindNeighborhoodPoints(const PointType&, double) const [with unsigned int VDimension = 3u; itk::ParticleRegionNeighborhood<VDimension>::PointVectorType = std::vector<itk::ParticlePointIndexPair<3u>, std::allocator<itk::ParticlePointIndexPair<3u> > >; itk::ParticleRegionNeighborhood<VDimension>::PointType = itk::Point<double, 3u>]’ [-Woverloaded-virtual]
   virtual PointVectorType FindNeighborhoodPoints(const PointType &, double) const;
                           ^
In file included from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleSystem.h:30:0,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksRun/ShapeWorksRunApp.h:22,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksRun/ShapeWorksRun.cxx:16:
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleNeighborhood.h:84:27: warning: ‘itk::ParticleNeighborhood<VDimension>::PointVectorType itk::ParticleNeighborhood<VDimension>::FindNeighborhoodPoints(const PointType&, std::vector<double>&, double) const [with unsigned int VDimension = 3u; itk::ParticleNeighborhood<VDimension>::PointVectorType = std::vector<itk::ParticlePointIndexPair<3u>, std::allocator<itk::ParticlePointIndexPair<3u> > >; itk::ParticleNeighborhood<VDimension>::PointType = itk::Point<double, 3u>]’ was hidden [-Woverloaded-virtual]
   virtual PointVectorType FindNeighborhoodPoints(const PointType &, std::vector<double> &,
                           ^
In file included from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleSurfaceNeighborhood.h:18:0,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkMaximumEntropySurfaceSampler.h:27,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkMaximumEntropyCorrespondenceSampler.h:18,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksRun/ShapeWorksRunApp.h:25,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksRun/ShapeWorksRun.cxx:16:
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleRegionNeighborhood.h:63:27: warning:   by ‘itk::ParticleRegionNeighborhood<VDimension>::PointVectorType itk::ParticleRegionNeighborhood<VDimension>::FindNeighborhoodPoints(const PointType&, double) const [with unsigned int VDimension = 3u; itk::ParticleRegionNeighborhood<VDimension>::PointVectorType = std::vector<itk::ParticlePointIndexPair<3u>, std::allocator<itk::ParticlePointIndexPair<3u> > >; itk::ParticleRegionNeighborhood<VDimension>::PointType = itk::Point<double, 3u>]’ [-Woverloaded-virtual]
   virtual PointVectorType FindNeighborhoodPoints(const PointType &, double) const;
                           ^
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleSurfaceNeighborhood.h: In instantiation of ‘class itk::ParticleSurfaceNeighborhood<itk::Image<float, 3u> >’:
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkMaximumEntropySurfaceSampler.h:311:75:   required from ‘class itk::MaximumEntropySurfaceSampler<itk::Image<float, 3u> >’
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkMaximumEntropyCorrespondenceSampler.h:36:18:   required from ‘class itk::MaximumEntropyCorrespondenceSampler<itk::Image<float, 3u> >’
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksRun/ShapeWorksRunApp.h:118:63:   required from here
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleRegionNeighborhood.h:63:27: warning: ‘itk::ParticleRegionNeighborhood<VDimension>::PointVectorType itk::ParticleRegionNeighborhood<VDimension>::FindNeighborhoodPoints(const PointType&, double) const [with unsigned int VDimension = 3u; itk::ParticleRegionNeighborhood<VDimension>::PointVectorType = std::vector<itk::ParticlePointIndexPair<3u>, std::allocator<itk::ParticlePointIndexPair<3u> > >; itk::ParticleRegionNeighborhood<VDimension>::PointType = itk::Point<double, 3u>]’ was hidden [-Woverloaded-virtual]
In file included from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkMaximumEntropySurfaceSampler.h:27:0,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkMaximumEntropyCorrespondenceSampler.h:18,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksRun/ShapeWorksRunApp.h:25,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksRun/ShapeWorksRun.cxx:16:
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleSurfaceNeighborhood.h:66:27: warning:   by ‘itk::ParticleSurfaceNeighborhood<TImage>::PointVectorType itk::ParticleSurfaceNeighborhood<TImage>::FindNeighborhoodPoints(const PointType&, std::vector<double>&, double) const [with TImage = itk::Image<float, 3u>; itk::ParticleSurfaceNeighborhood<TImage>::PointVectorType = std::vector<itk::ParticlePointIndexPair<3u>, std::allocator<itk::ParticlePointIndexPair<3u> > >; itk::ParticleSurfaceNeighborhood<TImage>::PointType = itk::Point<double, 3u>]’ [-Woverloaded-virtual]
   virtual PointVectorType FindNeighborhoodPoints(const PointType &, std::vector<double> &, double) const;
                           ^
In file included from /home/jcfr/Projects/SPHARM-PDM-build-standalone/ITKv4-install/include/ITK-4.11/itkImageBase.hxx:34:0,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/ITKv4-install/include/ITK-4.11/itkImageBase.h:787,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/ITKv4-install/include/ITK-4.11/itkNeighborhoodAccessorFunctor.h:22,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/ITKv4-install/include/ITK-4.11/itkImage.h:28,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksRun/ShapeWorksRunApp.h:24,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksRun/ShapeWorksRun.cxx:16:
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkMaximumEntropySurfaceSampler.h: In instantiation of ‘class itk::MaximumEntropySurfaceSampler<itk::Image<float, 3u> >’:
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkMaximumEntropyCorrespondenceSampler.h:36:18:   required from ‘class itk::MaximumEntropyCorrespondenceSampler<itk::Image<float, 3u> >’
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksRun/ShapeWorksRunApp.h:118:63:   required from here
/home/jcfr/Projects/SPHARM-PDM-build-standalone/ITKv4-install/include/ITK-4.11/itkProcessObject.h:521:16: warning: ‘virtual void itk::ProcessObject::SetInput(const DataObjectIdentifierType&, itk::DataObject*)’ was hidden [-Woverloaded-virtual]
   virtual void SetInput(const DataObjectIdentifierType & key, DataObject *input);
                ^
In file included from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkMaximumEntropyCorrespondenceSampler.h:18:0,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksRun/ShapeWorksRunApp.h:25,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksRun/ShapeWorksRun.cxx:16:
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkMaximumEntropySurfaceSampler.h:94:8: warning:   by ‘itk::MaximumEntropySurfaceSampler<itk::Image<float, 3u> >::SetInput’ [-Woverloaded-virtual]
   void SetInput( unsigned int index, const TImage * image ) 
        ^
[4/7] Building CXX object ShapeWorksGroom/CMakeFiles/ShapeWorksGroom.dir/ShapeWorksGroom.cxx.o
FAILED: ShapeWorksGroom/CMakeFiles/ShapeWorksGroom.dir/ShapeWorksGroom.cxx.o 
/usr/bin/c++  -DITK_IO_FACTORY_REGISTER_MANAGER -IITKIOFactoryRegistration -I/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/Utilities -I/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem -I/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/tinyxml -isystem /home/jcfr/Projects/SPHARM-PDM-build-standalone/ITKv4-install/include/ITK-4.11 -isystem /home/jcfr/Projects/SPHARM-PDM-build-standalone/ITKv4-install/include -Wall -Wcast-align -Wdisabled-optimization -Wextra -Wformat=2 -Winvalid-pch -Wno-format-nonliteral -Wpointer-arith -Wshadow -Wunused -Wwrite-strings -funit-at-a-time -Wno-strict-overflow -Wno-deprecated -Wno-invalid-offsetof -Woverloaded-virtual -Wstrict-null-sentinel  -Wall -Wcast-align -Wdisabled-optimization -Wextra -Wformat=2 -Winvalid-pch -Wno-format-nonliteral -Wpointer-arith -Wshadow -Wunused -Wwrite-strings -funit-at-a-time -Wno-strict-overflow -Wno-deprecated -Wno-invalid-offsetof -Woverloaded-virtual -Wstrict-null-sentinel   -msse2  -msse2 -O2 -g -DNDEBUG -MD -MT ShapeWorksGroom/CMakeFiles/ShapeWorksGroom.dir/ShapeWorksGroom.cxx.o -MF ShapeWorksGroom/CMakeFiles/ShapeWorksGroom.dir/ShapeWorksGroom.cxx.o.d -o ShapeWorksGroom/CMakeFiles/ShapeWorksGroom.dir/ShapeWorksGroom.cxx.o -c /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksGroom/ShapeWorksGroom.cxx
In file included from /home/jcfr/Projects/SPHARM-PDM-build-standalone/ITKv4-install/include/ITK-4.11/itkLightObject.h:21:0,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/ITKv4-install/include/ITK-4.11/itkObject.h:31,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/ITKv4-install/include/ITK-4.11/itkRegion.h:31,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/ITKv4-install/include/ITK-4.11/itkImageRegion.h:31,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/ITKv4-install/include/ITK-4.11/itkImage.h:21,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksGroom/isolate.h:18,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksGroom/ShapeWorksGroom.cxx:20:
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleEvents.h:121:5: error: token ""error ITK_TEMPLATE_TXX is no longer a supported identifier, you should replace with ITK_MANUAL_INSTANTIATION as a replacement"" is not valid in preprocessor expressions
 #if ITK_TEMPLATE_TXX
     ^
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleDomain.h:109:5: error: token ""error ITK_TEMPLATE_TXX is no longer a supported identifier, you should replace with ITK_MANUAL_INSTANTIATION as a replacement"" is not valid in preprocessor expressions
 #if ITK_TEMPLATE_TXX
     ^
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleNeighborhood.h:132:5: error: token ""error ITK_TEMPLATE_TXX is no longer a supported identifier, you should replace with ITK_MANUAL_INSTANTIATION as a replacement"" is not valid in preprocessor expressions
 #if ITK_TEMPLATE_TXX
     ^
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleSystem.h:498:5: error: token ""error ITK_TEMPLATE_TXX is no longer a supported identifier, you should replace with ITK_MANUAL_INSTANTIATION as a replacement"" is not valid in preprocessor expressions
 #if ITK_TEMPLATE_TXX
     ^
In file included from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleAttribute.h:22:0,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleSystem.h:22,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksGroom/transform_tool.h:18,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksGroom/center.h:22,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksGroom/ShapeWorksGroom.cxx:21:
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleEvents.h: In copy constructor ‘itk::ParticleEventWithIndex::ParticleEventWithIndex(const itk::ParticleEventWithIndex&)’:
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ITKParticleSystem/itkParticleEvents.h:75:3: warning: base class ‘class itk::ParticleEvent’ should be explicitly initialized in the copy constructor [-Wextra]
   ParticleEventWithIndex(const ParticleEventWithIndex &v)
   ^
In file included from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksGroom/blur.h:60:0,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksGroom/ShapeWorksGroom.cxx:27:
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksGroom/blur.txx: In member function ‘virtual void shapetools::blur<T, D>::operator()(typename shapetools::blur<T, D>::image_type::Pointer)’:
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksGroom/blur.txx:47:78: warning: declaration of ‘blur’ shadows a member of ‘shapetools::blur<T, D>’ [-Wshadow]
   typename itk::DiscreteGaussianImageFilter<image_type, image_type>::Pointer blur
                                                                              ^
In file included from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksGroom/ShapeWorksGroom.cxx:27:0:
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksGroom/blur.h:33:1: note: shadowed declaration is here
 {
 ^
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksGroom/ShapeWorksGroom.cxx: In function ‘int main(int, char**)’:
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksGroom/ShapeWorksGroom.cxx:298:16: warning: unused variable ‘oka’ [-Wunused-variable]
           bool oka = true;
                ^
In file included from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksGroom/blur.h:60:0,
                 from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksGroom/ShapeWorksGroom.cxx:27:
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksGroom/blur.txx: In instantiation of ‘void shapetools::blur<T, D>::operator()(typename shapetools::blur<T, D>::image_type::Pointer) [with T = float; unsigned int D = 3u; typename shapetools::blur<T, D>::image_type::Pointer = itk::SmartPointer<itk::Image<float, 3u> >]’:
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksGroom/ShapeWorksGroom.cxx:437:1:   required from here
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksGroom/blur.txx:48:69: warning: declaration of ‘blur’ shadows a member of ‘shapetools::blur<float, 3u>’ [-Wshadow]
     = itk::DiscreteGaussianImageFilter<image_type, image_type>::New();
                                                                     ^
In file included from /home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksGroom/ShapeWorksGroom.cxx:27:0:
/home/jcfr/Projects/SPHARM-PDM-build-standalone/SPHARM-PDM-build/Modules/CLI/shapeworks/ShapeWorksGroom/blur.h:33:1: note: shadowed declaration is here
 {
 ^

Support tab separated input data

Generalized procrustes alignment missing

The current SlicerSALT shape analysis module does not provide an option to perform also Generalized rigid-body procrustes alignment as in the original SPHARM-PDM pipeline. Such a alignment is the norm for most shape analysis pipeline and should be added to the module. This is only necessary if there is (a) no prior registration template and (b) if so requested by the user (I think it should be "on" by default).
This would involve:

computing a mean shape from all the ellipse aligned data in the current output folder
rerunning ParatoSPHARM with (1) as the rigid registration template
recomputing the mean shape using the procrustes aligned data
rerunning ParatoSPHARM with (3) as the rigid registration template, and return to step (3) as long as the mean shape changes in a major way (e.g. a Hausdorff surface change of more than 1 voxel size)

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	option(COMPILE_shapeworks "Compile shapeworks." OFF)
	if(COMPILE_shapeworks)
	set(shapeworks_REPOSITORY https://www.nitrc.org/svn/shapeworks/code CACHE STRING "" FORCE)
	ExternalProject_Add(shapeworks
	SVN_REPOSITORY ${shapeworks_REPOSITORY}
	SVN_REVISION -r 78
	SVN_USERNAME slicerbot
	SVN_PASSWORD slicer
	UPDATE_COMMAND ""
	SOURCE_DIR shapeworks
	BINARY_DIR shapeworks-build
	CMAKE_GENERATOR ${gen}
	CMAKE_ARGS
	-DITK_DIR:PATH=${ITK_DIR}
	${external_projects_vars}
	INSTALL_COMMAND ""
	)
	endif(COMPILE_shapeworks)