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Apr 4, 2016  02:04 AM | shahrokh nasseri
Problem with SPHARM_Tutorial_Data_July2015
Hello  Spharm experts;

I can run SPHARM_Tutorial_Data_July2015.zip using the manual of SPHARM-PDM_Tutorial_July2015.pdf, but unfortunately I can not get completey the outputs of this tutorial when I compare my output files with output files included in the zip file of SPHARM_Tutorial_Data_July2015.zip.
The specfications of my operating system, Slicer and exetnsions installed are the following lines:
[sn@localhost Slicer-4.4.0-2015-10-30-linux-amd64]$ uname --all
Linux localhost.localdomain 3.11.10-301.fc20.x86_64 #1 SMP Thu Dec 5 14:01:17 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
[sn@localhost Slicer-4.4.0-2015-10-30-linux-amd64]$ ./Slicer
Session start time .......: 2016-04-04 12:33:02
Slicer version ...........: 4.4.0-2015-10-30 (revision 24684) linux-amd64 - installed
Operating system .........: Linux / 3.11.10-301.fc20.x86_64 / #1 SMP Thu Dec 5 14:01:17 UTC 2013 - 64-bit
Memory ...................: 3954 MB physical, 5999 MB virtual
CPU ......................: GenuineIntel 1.603 MHz, 1 cores
Developer mode enabled ...: no
Prefer executable CLI ....: no
Additional module paths ..: /home/sn/.config/NA-MIC/Extensions-24684/SlicerRT/lib/Slicer-4.4/cli-modules, /home/sn/.config/NA-MIC/Extensions-24684/SlicerRT/lib/Slicer-4.4/qt-loadable-modules, /home/sn/.config/NA-MIC/Extensions-24684/SlicerRT/lib/Slicer-4.4/qt-scripted-modules, /home/sn/.config/NA-MIC/Extensions-24684/SPHARM-PDM/lib/Slicer-4.4/cli-modules, /home/sn/.config/NA-MIC/Extensions-24684/ChangeTracker/lib/Slicer-4.4/cli-modules, /home/sn/.config/NA-MIC/Extensions-24684/ChangeTracker/lib/Slicer-4.4/qt-scripted-modules, /home/sn/.config/NA-MIC/Extensions-24684/ModelToModelDistance/lib/Slicer-4.4/cli-modules, /home/sn/.config/NA-MIC/Extensions-24684/ShapePopulationViewer/lib/Slicer-4.4/cli-modules, /home/sn/.config/NA-MIC/Extensions-24684/MeshToLabelMap/lib/Slicer-4.4/cli-modules
Number of registered modules: 175
Number of instantiated modules: 175
Number of loaded modules: 175
Switch to module:  "Welcome"
Switch to module:  "ShapeAnalysis"
Found CommandLine Module, target is  /home/sn/.config/NA-MIC/Extensions-24684/SPHARM-PDM/lib/Slicer-4.4/cli-modules/ShapeAnalysisModule
ModuleType: CommandLineModule
Shape Analysis Module command line:
/home/sn/.config/NA-MIC/Extensions-24684/SPHARM-PDM/lib/Slicer-4.4/cli-modules/ShapeAnalysisModule --verb --RescaleSegPostProcess --sx 0.5 --sy 0.5 --sz 0.5 --label 1 --NumberofIterations 1000 --SubdivLevelValue 10 --SPHARMDegreeValue 15 --thetaIterationValue 100 --phiIterationValue 100 --columVolumeFile 0 --varX 10 --varY 10 --varZ 10 --regTemplate None --flipTemplate None --paraOutTemplate --noFlip --HorizontalGridPara 5 --VerticalGridPara 5 --UseProcalign --startRegularization 10 --endRegularization 0.01 --optimizationIt 200 --RelativeWeight 1 /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/small_sample.csv /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1
Shape Analysis Module standard output:
------ Shape Analysis Module start -----
Computing ShapeAnalysisModule...
/home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/
/home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/ShapeAnalysisModule.bms
Number of Datas: 4
Executing BatchMake...
Case:0    /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/origData/groupA_01_hippo.gipl.gz    none
Doing Post Processing
Status: Start SegPostProcessCLP 0    /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/origData/groupA_01_hippo.gipl.gz    none /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/PostProcess/groupA_01_hippo_pp.gipl.gz --rescale --space 0.5,0.5,0.5
run: 'SegPostProcessCLP' '''0    /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/origData/groupA_01_hippo.gipl.gz    none' '/home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/PostProcess/groupA_01_hippo_pp.gipl.gz' --rescale --space '0.5,0.5,0.5'''
Status: Finish: Execution time 300ms
Doing GenParaMesh
Status: Start GenParaMeshCLP --EulerFile --outEulerName /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/EulerFiles/groupA_01_hippo_euler.txt --iter 1000 --label 1 /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/PostProcess/groupA_01_hippo_pp.gipl.gz /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupA_01_hippo_pp_para.vtk /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupA_01_hippo_pp_surf.vtk
run: 'GenParaMeshCLP' ''--EulerFile --outEulerName '/home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/EulerFiles/groupA_01_hippo_euler.txt' --iter '1000' --label '1' '/home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/PostProcess/groupA_01_hippo_pp.gipl.gz' '/home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupA_01_hippo_pp_para.vtk' '/home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupA_01_hippo_pp_surf.vtk'''
Status: Finish: Execution time 300ms
GenParaMesh Error:terminate called after throwing an instance of itk::ImageFileReaderException
what():  /home/kitware/Dashboards/Nightly/S-0-E-b/SPHARM-PDM-build/ITKv4-install/include/ITK-4.7/itkImageFileReader.hxx:143:
Could not create IO object for reading file /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/PostProcess/groupA_01_hippo_pp.gipl.gz
The file doesnt exist.
Filename =
Doing ParaToSPHARMMesh
Creating Template
Status: Start ParaToSPHARMMeshCLP /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupA_01_hippo_pp_para.vtk /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupA_01_hippo_pp_surf.vtk /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Template/groupA_01_hippo_pp_surf --subdivLevel 10 --spharmDegree 15 --FinalFlip 0 --paraOut --phiIteration 100 --thetaIteration 100 --medialMesh
run: 'ParaToSPHARMMeshCLP' '''/home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupA_01_hippo_pp_para.vtk' '/home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupA_01_hippo_pp_surf.vtk' '/home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Template/groupA_01_hippo_pp_surf' --subdivLevel '10' --spharmDegree '15' --FinalFlip '0' --paraOut --phiIteration '100' --thetaIteration '100' --medialMesh''
Status: Finish: Execution time 3001ms
ParaToSPHARMMesh: ERROR: In /home/kitware/Dashboards/Nightly/S-0-E-b/SPHARM-PDM-build/VTK/IO/Legacy/vtkDataReader.cxx, line 466
vtkPolyDataReader (0x2702100): Unable to open file: /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupA_01_hippo_pp_surf.vtk
ERROR: In /home/kitware/Dashboards/Nightly/S-0-E-b/SPHARM-PDM-build/VTK/IO/Legacy/vtkDataReader.cxx, line 466
vtkPolyDataReader (0x2702100): Unable to open file: /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupA_01_hippo_pp_para.vtk
regTemplate: groupA_01_hippo_pp_surfSPHARM.vtk
flipTemplate: groupA_01_hippo_pp_surfSPHARM.coef
Status: Start ParaToSPHARMMeshCLP /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupA_01_hippo_pp_para.vtk /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupA_01_hippo_pp_surf.vtk /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupA_01_hippo_pp_surf --regTemplateFileOn --regTemplate /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Template/groupA_01_hippo_pp_surfSPHARM.vtk --flipTemplateOn --flipTemplate /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Template/groupA_01_hippo_pp_surfSPHARM.coef --subdivLevel 10 --spharmDegree 15 --FinalFlip 0 --paraOut --phiIteration 100 --thetaIteration 100 --medialMesh
run: 'ParaToSPHARMMeshCLP' '''/home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupA_01_hippo_pp_para.vtk' '/home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupA_01_hippo_pp_surf.vtk' '/home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupA_01_hippo_pp_surf' --regTemplateFileOn --regTemplate '/home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Template/groupA_01_hippo_pp_surfSPHARM.vtk' --flipTemplateOn --flipTemplate '/home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Template/groupA_01_hippo_pp_surfSPHARM.coef' --subdivLevel '10' --spharmDegree '15' --FinalFlip '0' --paraOut --phiIteration '100' --thetaIteration '100' --medialMesh''
Status: Finish: Execution time 3902ms
ParaToSPHARMMesh: ERROR: In /home/kitware/Dashboards/Nightly/S-0-E-b/SPHARM-PDM-build/VTK/IO/Legacy/vtkDataReader.cxx, line 466
vtkPolyDataReader (0x17b8b80): Unable to open file: /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupA_01_hippo_pp_surf.vtk
ERROR: In /home/kitware/Dashboards/Nightly/S-0-E-b/SPHARM-PDM-build/VTK/IO/Legacy/vtkDataReader.cxx, line 466
vtkPolyDataReader (0x17b8b80): Unable to open file: /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupA_01_hippo_pp_para.vtk
Generic Warning: In /home/kitware/Dashboards/Nightly/S-0-E-b/SPHARM-PDM-build/VTK/IO/Legacy/vtkDataReader.cxx, line 1388
Error reading ascii data. Possible mismatch of datasize with declaration.
/home/kitware/Dashboards/Nightly/S-0-E-b/SPHARM-PDM-build/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_svd.txx: suspicious return value (3) from SVDC
/home/kitware/Dashboards/Nightly/S-0-E-b/SPHARM-PDM-build/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_svd.txx: M is 3x3
M = [ ...
-nan             -nan             -nan
-nan             -nan             -nan
-nan             -nan             -nan  ]
/home/kitware/Dashboards/Nightly/S-0-E-b/SPHARM-PDM-build/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_svd.txx: suspicious return value (3) from SVDC
/home/kitware/Dashboards/Nightly/S-0-E-b/SPHARM-PDM-build/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_svd.txx: M is 3x3
M = [ ...
-nan             -nan             -nan
-nan             -nan             -nan
-nan             -nan             -nan  ]
/home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupA_01_hippo_pp_surf_paraPhiHalf.txt
Case:0    /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/origData/groupA_02_hippo.gipl.gz    none
Doing Post Processing
Status: Start SegPostProcessCLP 0    /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/origData/groupA_02_hippo.gipl.gz    none /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/PostProcess/groupA_02_hippo_pp.gipl.gz --rescale --space 0.5,0.5,0.5
run: 'SegPostProcessCLP' '''0    /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/origData/groupA_02_hippo.gipl.gz    none' '/home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/PostProcess/groupA_02_hippo_pp.gipl.gz' --rescale --space '0.5,0.5,0.5'''
Status: Finish: Execution time 301ms
Doing GenParaMesh
Status: Start GenParaMeshCLP --EulerFile --outEulerName /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/EulerFiles/groupA_02_hippo_euler.txt --iter 1000 --label 1 /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/PostProcess/groupA_02_hippo_pp.gipl.gz /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupA_02_hippo_pp_para.vtk /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupA_02_hippo_pp_surf.vtk
run: 'GenParaMeshCLP' ''--EulerFile --outEulerName '/home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/EulerFiles/groupA_02_hippo_euler.txt' --iter '1000' --label '1' '/home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/PostProcess/groupA_02_hippo_pp.gipl.gz' '/home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupA_02_hippo_pp_para.vtk' '/home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupA_02_hippo_pp_surf.vtk'''
Status: Finish: Execution time 301ms
GenParaMesh Error:terminate called after throwing an instance of itk::ImageFileReaderException
what():  /home/kitware/Dashboards/Nightly/S-0-E-b/SPHARM-PDM-build/ITKv4-install/include/ITK-4.7/itkImageFileReader.hxx:143:
Could not create IO object for reading file /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/PostProcess/groupA_02_hippo_pp.gipl.gz
The file doesnt exist.
Filename = /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/PostProcess/groupA_02_hippo_pp.gipl.gz
Doing ParaToSPHARMMesh
regTemplate: groupA_01_hippo_pp_surfSPHARM.vtk
flipTemplate: groupA_01_hippo_pp_surfSPHARM.coef
Status: Start ParaToSPHARMMeshCLP /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupA_02_hippo_pp_para.vtk /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupA_02_hippo_pp_surf.vtk /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupA_02_hippo_pp_surf --regTemplateFileOn --regTemplate /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Template/groupA_01_hippo_pp_surfSPHARM.vtk --flipTemplateOn --flipTemplate /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Template/groupA_01_hippo_pp_surfSPHARM.coef --subdivLevel 10 --spharmDegree 15 --FinalFlip 0 --paraOut --phiIteration 100 --thetaIteration 100 --medialMesh
run: 'ParaToSPHARMMeshCLP' '''/home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupA_02_hippo_pp_para.vtk' '/home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupA_02_hippo_pp_surf.vtk' '/home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupA_02_hippo_pp_surf' --regTemplateFileOn --regTemplate '/home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Template/groupA_01_hippo_pp_surfSPHARM.vtk' --flipTemplateOn --flipTemplate '/home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Template/groupA_01_hippo_pp_surfSPHARM.coef' --subdivLevel '10' --spharmDegree '15' --FinalFlip '0' --paraOut --phiIteration '100' --thetaIteration '100' --medialMesh''
Status: Finish: Execution time 3901ms
ParaToSPHARMMesh: ERROR: In /home/kitware/Dashboards/Nightly/S-0-E-b/SPHARM-PDM-build/VTK/IO/Legacy/vtkDataReader.cxx, line 466
vtkPolyDataReader (0x1c3cb80): Unable to open file: /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupA_02_hippo_pp_surf.vtk
ERROR: In /home/kitware/Dashboards/Nightly/S-0-E-b/SPHARM-PDM-build/VTK/IO/Legacy/vtkDataReader.cxx, line 466
vtkPolyDataReader (0x1c3cb80): Unable to open file: /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupA_02_hippo_pp_para.vtk
Generic Warning: In /home/kitware/Dashboards/Nightly/S-0-E-b/SPHARM-PDM-build/VTK/IO/Legacy/vtkDataReader.cxx, line 1388
Error reading ascii data. Possible mismatch of datasize with declaration.
/home/kitware/Dashboards/Nightly/S-0-E-b/SPHARM-PDM-build/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_svd.txx: suspicious return value (3) from SVDC
/home/kitware/Dashboards/Nightly/S-0-E-b/SPHARM-PDM-build/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_svd.txx: M is 3x3
M = [ ...
-nan             -nan             -nan
-nan             -nan             -nan
-nan             -nan             -nan  ]
/home/kitware/Dashboards/Nightly/S-0-E-b/SPHARM-PDM-build/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_svd.txx: suspicious return value (3) from SVDC
/home/kitware/Dashboards/Nightly/S-0-E-b/SPHARM-PDM-build/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_svd.txx: M is 3x3
M = [ ...
-nan             -nan             -nan
-nan             -nan             -nan
-nan             -nan             -nan  ]
/home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupA_02_hippo_pp_surf_paraPhiHalf.txt
Case:1    /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/origData/groupB_01_hippo.gipl.gz    none
Doing Post Processing
Status: Start SegPostProcessCLP 1    /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/origData/groupB_01_hippo.gipl.gz    none /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/PostProcess/groupB_01_hippo_pp.gipl.gz --rescale --space 0.5,0.5,0.5
run: 'SegPostProcessCLP' '''1    /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/origData/groupB_01_hippo.gipl.gz    none' '/home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/PostProcess/groupB_01_hippo_pp.gipl.gz' --rescale --space '0.5,0.5,0.5'''
Status: Finish: Execution time 300ms
Doing GenParaMesh
Status: Start GenParaMeshCLP --EulerFile --outEulerName /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/EulerFiles/groupB_01_hippo_euler.txt --iter 1000 --label 1 /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/PostProcess/groupB_01_hippo_pp.gipl.gz /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupB_01_hippo_pp_para.vtk /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupB_01_hippo_pp_surf.vtk
run: 'GenParaMeshCLP' ''--EulerFile --outEulerName '/home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/EulerFiles/groupB_01_hippo_euler.txt' --iter '1000' --label '1' '/home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/PostProcess/groupB_01_hippo_pp.gipl.gz' '/home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupB_01_hippo_pp_para.vtk' '/home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupB_01_hippo_pp_surf.vtk'''
Status: Finish: Execution time 300ms
GenParaMesh Error:terminate called after throwing an instance of itk::ImageFileReaderException
what():  /home/kitware/Dashboards/Nightly/S-0-E-b/SPHARM-PDM-build/ITKv4-install/include/ITK-4.7/itkImageFileReader.hxx:143:
Could not create IO object for reading file /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/PostProcess/groupB_01_hippo_pp.gipl.gz
The file doesnt exist.
Filename = /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/PostProcess/groupB_01_hippo_pp.gipl.gz
Doing ParaToSPHARMMesh
regTemplate: groupA_01_hippo_pp_surfSPHARM.vtk
flipTemplate: groupA_01_hippo_pp_surfSPHARM.coef
Status: Start ParaToSPHARMMeshCLP /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupB_01_hippo_pp_para.vtk /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupB_01_hippo_pp_surf.vtk /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupB_01_hippo_pp_surf --regTemplateFileOn --regTemplate /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Template/groupA_01_hippo_pp_surfSPHARM.vtk --flipTemplateOn --flipTemplate /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Template/groupA_01_hippo_pp_surfSPHARM.coef --subdivLevel 10 --spharmDegree 15 --FinalFlip 0 --paraOut --phiIteration 100 --thetaIteration 100 --medialMesh
run: 'ParaToSPHARMMeshCLP' '''/home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupB_01_hippo_pp_para.vtk' '/home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupB_01_hippo_pp_surf.vtk' '/home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupB_01_hippo_pp_surf' --regTemplateFileOn --regTemplate '/home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Template/groupA_01_hippo_pp_surfSPHARM.vtk' --flipTemplateOn --flipTemplate '/home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Template/groupA_01_hippo_pp_surfSPHARM.coef' --subdivLevel '10' --spharmDegree '15' --FinalFlip '0' --paraOut --phiIteration '100' --thetaIteration '100' --medialMesh''
Status: Finish: Execution time 3901ms
ParaToSPHARMMesh: ERROR: In /home/kitware/Dashboards/Nightly/S-0-E-b/SPHARM-PDM-build/VTK/IO/Legacy/vtkDataReader.cxx, line 466
vtkPolyDataReader (0x2c4cb80): Unable to open file: /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupB_01_hippo_pp_surf.vtk
ERROR: In /home/kitware/Dashboards/Nightly/S-0-E-b/SPHARM-PDM-build/VTK/IO/Legacy/vtkDataReader.cxx, line 466
vtkPolyDataReader (0x2c4cb80): Unable to open file: /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupB_01_hippo_pp_para.vtk
Generic Warning: In /home/kitware/Dashboards/Nightly/S-0-E-b/SPHARM-PDM-build/VTK/IO/Legacy/vtkDataReader.cxx, line 1388
Error reading ascii data. Possible mismatch of datasize with declaration.
/home/kitware/Dashboards/Nightly/S-0-E-b/SPHARM-PDM-build/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_svd.txx: suspicious return value (3) from SVDC
/home/kitware/Dashboards/Nightly/S-0-E-b/SPHARM-PDM-build/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_svd.txx: M is 3x3
M = [ ...
-nan             -nan             -nan
-nan             -nan             -nan
-nan             -nan             -nan  ]
/home/kitware/Dashboards/Nightly/S-0-E-b/SPHARM-PDM-build/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_svd.txx: suspicious return value (3) from SVDC
/home/kitware/Dashboards/Nightly/S-0-E-b/SPHARM-PDM-build/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_svd.txx: M is 3x3
M = [ ...
-nan             -nan             -nan
-nan             -nan             -nan
-nan             -nan             -nan  ]
/home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupB_01_hippo_pp_surf_paraPhiHalf.txt
Case:1    /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/origData/groupB_02_hippo.gipl.gz    none
Doing Post Processing
Status: Start SegPostProcessCLP 1    /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/origData/groupB_02_hippo.gipl.gz    none /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/PostProcess/groupB_02_hippo_pp.gipl.gz --rescale --space 0.5,0.5,0.5
run: 'SegPostProcessCLP' '''1    /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/origData/groupB_02_hippo.gipl.gz    none' '/home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/PostProcess/groupB_02_hippo_pp.gipl.gz' --rescale --space '0.5,0.5,0.5'''
Status: Finish: Execution time 300ms
Doing GenParaMesh
Status: Start GenParaMeshCLP --EulerFile --outEulerName /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/EulerFiles/groupB_02_hippo_euler.txt --iter 1000 --label 1 /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/PostProcess/groupB_02_hippo_pp.gipl.gz /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupB_02_hippo_pp_para.vtk /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupB_02_hippo_pp_surf.vtk
run: 'GenParaMeshCLP' ''--EulerFile --outEulerName '/home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/EulerFiles/groupB_02_hippo_euler.txt' --iter '1000' --label '1' '/home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/PostProcess/groupB_02_hippo_pp.gipl.gz' '/home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupB_02_hippo_pp_para.vtk' '/home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupB_02_hippo_pp_surf.vtk'''
Status: Finish: Execution time 300ms
GenParaMesh Error:terminate called after throwing an instance of itk::ImageFileReaderException
what():  /home/kitware/Dashboards/Nightly/S-0-E-b/SPHARM-PDM-build/ITKv4-install/include/ITK-4.7/itkImageFileReader.hxx:143:
Could not create IO object for reading file /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/PostProcess/groupB_02_hippo_pp.gipl.gz
The file doesnt exist.
Filename =
Doing ParaToSPHARMMesh
regTemplate: groupA_01_hippo_pp_surfSPHARM.vtk
flipTemplate: groupA_01_hippo_pp_surfSPHARM.coef
Status: Start ParaToSPHARMMeshCLP /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupB_02_hippo_pp_para.vtk /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupB_02_hippo_pp_surf.vtk /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupB_02_hippo_pp_surf --regTemplateFileOn --regTemplate /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Template/groupA_01_hippo_pp_surfSPHARM.vtk --flipTemplateOn --flipTemplate /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Template/groupA_01_hippo_pp_surfSPHARM.coef --subdivLevel 10 --spharmDegree 15 --FinalFlip 0 --paraOut --phiIteration 100 --thetaIteration 100 --medialMesh
run: 'ParaToSPHARMMeshCLP' '''/home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupB_02_hippo_pp_para.vtk' '/home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupB_02_hippo_pp_surf.vtk' '/home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupB_02_hippo_pp_surf' --regTemplateFileOn --regTemplate '/home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Template/groupA_01_hippo_pp_surfSPHARM.vtk' --flipTemplateOn --flipTemplate '/home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Template/groupA_01_hippo_pp_surfSPHARM.coef' --subdivLevel '10' --spharmDegree '15' --FinalFlip '0' --paraOut --phiIteration '100' --thetaIteration '100' --medialMesh''
Status: Finish: Execution time 3901ms
ParaToSPHARMMesh: ERROR: In /home/kitware/Dashboards/Nightly/S-0-E-b/SPHARM-PDM-build/VTK/IO/Legacy/vtkDataReader.cxx, line 466
vtkPolyDataReader (0x3752b80): Unable to open file: /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupB_02_hippo_pp_surf.vtk
ERROR: In /home/kitware/Dashboards/Nightly/S-0-E-b/SPHARM-PDM-build/VTK/IO/Legacy/vtkDataReader.cxx, line 466
vtkPolyDataReader (0x3752b80): Unable to open file: /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupB_02_hippo_pp_para.vtk
Generic Warning: In /home/kitware/Dashboards/Nightly/S-0-E-b/SPHARM-PDM-build/VTK/IO/Legacy/vtkDataReader.cxx, line 1388
Error reading ascii data. Possible mismatch of datasize with declaration.
/home/kitware/Dashboards/Nightly/S-0-E-b/SPHARM-PDM-build/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_svd.txx: suspicious return value (3) from SVDC
/home/kitware/Dashboards/Nightly/S-0-E-b/SPHARM-PDM-build/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_svd.txx: M is 3x3
M = [ ...
-nan             -nan             -nan
-nan             -nan             -nan
-nan             -nan             -nan  ]
/home/kitware/Dashboards/Nightly/S-0-E-b/SPHARM-PDM-build/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_svd.txx: suspicious return value (3) from SVDC
/home/kitware/Dashboards/Nightly/S-0-E-b/SPHARM-PDM-build/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_svd.txx: M is 3x3
M = [ ...
-nan             -nan             -nan
-nan             -nan             -nan
-nan             -nan             -nan  ]
/home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupB_02_hippo_pp_surf_paraPhiHalf.txt
Executing BatchMake: Done!
Execute Meshmath...
Mapping parameters in SPHARM template meshes using MeshMath
Path for MeshMathTemplate: /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Template/
DONE COMPUTING SPHARM
Unable to open file: /home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/SPHARM/groupB_02_hippo_pp_para.vtk
Error: Generic Warning: In /home/kitware/Dashboards/Nightly/S-0-E-b/SPHARM-PDM-build/VTK/IO/Legacy/vtkDataReader.cxx, line 1388
Error: Error reading ascii data. Possible mismatch of datasize with declaration.
Error: /home/kitware/Dashboards/Nightly/S-0-E-b/SPHARM-PDM-build/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_svd.txx: suspicious return value (3) from SVDC
Error: /home/kitware/Dashboards/Nightly/S-0-E-b/SPHARM-PDM-build/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_svd.txx: M is 3x3
Error: M = [ ...
Error:             -nan             -nan             -nan
Error:             -nan             -nan             -nan
Error:             -nan             -nan             -nan  ]
Error: /home/kitware/Dashboards/Nightly/S-0-E-b/SPHARM-PDM-build/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_svd.txx: suspicious return value (3) from SVDC
Error: /home/kitware/Dashboards/Nightly/S-0-E-b/SPHARM-PDM-build/ITKv4/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_svd.txx: M is 3x3
Error: M = [ ...
Error:             -nan             -nan             -nan
Error:             -nan             -nan             -nan
Error:             -nan             -nan             -nan  ]
Executing BatchMake: Error!
Shape Analysis Module completed without errors
When I see into the Tutorial_Output1 folder, the folders of Tutorial_Output1/EulerFiles and /Tutorial_Output1/Mesh/PostProcess are empty. Why?!
[sn@localhost Tutorial_Output1]$ ls -LR
.:
BatchMake_Scripts  EulerFiles  Mesh  OutputGroupFile  ShapeAnalysisModule.bms  Template
./BatchMake_Scripts:
./EulerFiles:
./Mesh:
PostProcess  SPHARM
./Mesh/PostProcess:
./Mesh/SPHARM:
groupA_01_hippo_pp_surfMedialAxisScalars.csv         groupA_02_hippo_pp_surf_paraPhi.txt                  groupB_01_hippo_pp_surfSPHARM_ellalign.vtk
groupA_01_hippo_pp_surf_medialMeshArea.txt           groupA_02_hippo_pp_surf_paraTheta.txt                groupB_01_hippo_pp_surfSPHARMMedialAxis.vtk
groupA_01_hippo_pp_surf_medialMeshPartialArea.txt    groupA_02_hippo_pp_surf_para.vtk                     groupB_01_hippo_pp_surfSPHARMMedialMesh.vtk
groupA_01_hippo_pp_surf_medialMeshPartialRadius.txt  groupA_02_hippo_pp_surfSPHARM.coef                   groupB_01_hippo_pp_surfSPHARM_procalign.vtk
groupA_01_hippo_pp_surf_medialMeshRadius.txt         groupA_02_hippo_pp_surfSPHARM_ellalign.coef          groupB_01_hippo_pp_surfSPHARM.vtk
groupA_01_hippo_pp_surf_paraPhi.txt                  groupA_02_hippo_pp_surfSPHARM_ellalign.vtk           groupB_02_hippo_pp_surfMedialAxisScalars.csv
groupA_01_hippo_pp_surf_paraTheta.txt                groupA_02_hippo_pp_surfSPHARMMedialAxis.vtk          groupB_02_hippo_pp_surf_medialMeshArea.txt
groupA_01_hippo_pp_surf_para.vtk                     groupA_02_hippo_pp_surfSPHARMMedialMesh.vtk          groupB_02_hippo_pp_surf_medialMeshPartialArea.txt
groupA_01_hippo_pp_surfSPHARM.coef                   groupA_02_hippo_pp_surfSPHARM_procalign.vtk          groupB_02_hippo_pp_surf_medialMeshPartialRadius.txt
groupA_01_hippo_pp_surfSPHARM_ellalign.coef          groupA_02_hippo_pp_surfSPHARM.vtk                    groupB_02_hippo_pp_surf_medialMeshRadius.txt
groupA_01_hippo_pp_surfSPHARM_ellalign.vtk           groupB_01_hippo_pp_surfMedialAxisScalars.csv         groupB_02_hippo_pp_surf_paraPhi.txt
groupA_01_hippo_pp_surfSPHARMMedialAxis.vtk          groupB_01_hippo_pp_surf_medialMeshArea.txt           groupB_02_hippo_pp_surf_paraTheta.txt
groupA_01_hippo_pp_surfSPHARMMedialMesh.vtk          groupB_01_hippo_pp_surf_medialMeshPartialArea.txt    groupB_02_hippo_pp_surf_para.vtk
groupA_01_hippo_pp_surfSPHARM_procalign.vtk          groupB_01_hippo_pp_surf_medialMeshPartialRadius.txt  groupB_02_hippo_pp_surfSPHARM.coef
groupA_01_hippo_pp_surfSPHARM.vtk                    groupB_01_hippo_pp_surf_medialMeshRadius.txt         groupB_02_hippo_pp_surfSPHARM_ellalign.coef
groupA_02_hippo_pp_surfMedialAxisScalars.csv         groupB_01_hippo_pp_surf_paraPhi.txt                  groupB_02_hippo_pp_surfSPHARM_ellalign.vtk
groupA_02_hippo_pp_surf_medialMeshArea.txt           groupB_01_hippo_pp_surf_paraTheta.txt                groupB_02_hippo_pp_surfSPHARMMedialAxis.vtk
groupA_02_hippo_pp_surf_medialMeshPartialArea.txt    groupB_01_hippo_pp_surf_para.vtk                     groupB_02_hippo_pp_surfSPHARMMedialMesh.vtk
groupA_02_hippo_pp_surf_medialMeshPartialRadius.txt  groupB_01_hippo_pp_surfSPHARM.coef                   groupB_02_hippo_pp_surfSPHARM_procalign.vtk
groupA_02_hippo_pp_surf_medialMeshRadius.txt         groupB_01_hippo_pp_surfSPHARM_ellalign.coef          groupB_02_hippo_pp_surfSPHARM.vtk
./OutputGroupFile:
ShapeAnalysisModule_OutputFile.csv
./Template:
groupA_01_hippo_pp_surfMedialAxisScalars.csv         groupA_01_hippo_pp_surf_paraPhi.txt          groupA_01_hippo_pp_surfSPHARM_ellalign.vtk
groupA_01_hippo_pp_surf_medialMeshArea.txt           groupA_01_hippo_pp_surf_paraTheta.txt        groupA_01_hippo_pp_surfSPHARMMedialAxis.vtk
groupA_01_hippo_pp_surf_medialMeshPartialArea.txt    groupA_01_hippo_pp_surf_para.vtk             groupA_01_hippo_pp_surfSPHARMMedialMesh.vtk
groupA_01_hippo_pp_surf_medialMeshPartialRadius.txt  groupA_01_hippo_pp_surfSPHARM.coef           groupA_01_hippo_pp_surfSPHARM.vtk
groupA_01_hippo_pp_surf_medialMeshRadius.txt         groupA_01_hippo_pp_surfSPHARM_ellalign.coef
[sn@localhost Tutorial_Output1]$

The folders of Tutorial_Output1/EulerFiles and Tutorial_Output1/Mesh/PostProcess are empty and the files of *_pp_para.vtk and *_pp_surf.vtk are not produced.
Why can not I get output of this tutorial completey?
Please help me.
Your sincerely
Shahrokh
Apr 10, 2016  03:04 AM | Beatriz Paniagua
RE: Problem with SPHARM_Tutorial_Data_July2015
Hello Shahrokh,


Sorry it has taken so long. Thank you for including such a detailed log of the errors you are encountering.
I think we should go step by step and try to diagnose the problems in order:

First, you should install the last Slicer stable release: Slicer 4.5. is the most current version. In your log file I see 4.4.0. 

Then, the first error that I can read in your post is related with not being able to read the post process image, which is the result of SegPostProcess. A number of different things could be happening: 1) your output folder has not been created due to permission problems. Please, make sure your output folder is created, as well as Mesh folder inside it and that the postprocess folder inside Mesh is also created. Do you see the/home/sn/SPHARM/SPHARM_Tutorial_Data_July2015/Tutorial_Output1/Mesh/PostProcess/groupA_01_hippo_pp.gipl.gz file inside?

Could you please check those two things and get back to us letting us know how it went? We can go from there.
Sorry you are experiencing problems, we will try to help as much as possible.


Thank you,
Beatriz
Apr 27, 2016  06:04 AM | shahrokh nasseri
RE: Problem with SPHARM_Tutorial_Data_July2015
Hi Dear Beatriz,

I sucess to do SPHARM-PDM tutorial (July 2015) using Fedora core 22 (64 bit) without output in "Particle Correspondence", The folder of ParticleCorrespondence is empty. I get the following error:

Shape Analysis Module standard error:
Error: Could not run ParticleModule:
No such file or directory
Is it (Particle Correspondence) necessary to do statistical analysis?

In finally, I want to analysis with Hotelling T-squared test according to your article entitled "3D Osteoarthritic Changes in TMJ Condylar Morphology Correlates with Specific Systemic and Local Biomarkers of Disease".
I guess to do it, I must execute shapeAnalysisMANCOVA_Wizard program in spharm-pdm_v1.11_linux64.zip in bash command (not in Slicer). Is it true?
Anyway, when I execute it and want to set parameters it, according to your pdf file tutorial (shapeAnalysisMANCOVA_Wizard, NA-MIC Tutorial Contest: Summer 2011). I do not know how to set parameters. I send you the csv output file of spharm-pdm module in slicer (ShapeAnalysisModule_OutputFile.csv). Please guide me for solving it.
Thanks a lot,
Shahrokh
Apr 27, 2016  07:04 AM | Beatriz Paniagua
RE: Problem with SPHARM_Tutorial_Data_July2015
Hi Shahrokh,


I am glad to hear that you got spharm-pdm to provide results for you. Before performing any statistical analysis, please remember that quality control is specially important for TMJs. Wrt your questions:

1. ParticleCorrespondence is a module that is no longer supported, and it will be removed in the next spharm-pdm distribution. It was initially designed to do a fine tuning of the coordinates of the PDM, so you do not need it to produce results.

2. You are right that if you want to run shapeAnalysisMANCOVA (which also a discontinued product of the spharm package past v.1.11) you have to run the package from that version you mention. I dont understand what you mean about setting your parameters. There are several follow up questions in order I can help you setting parameters:

- What is the input data for the analysis? The attached csv shows all data associated with the spharm-pdm processing. The type of analysis do you want depends on the study design. Do you do a pre-registration of your samples? If so use the *surfSPHARM.vtk column as inputs. If you want a best surface fit you have to use the procrustes aligned or ellipsoid aligned models.

- What is the measurement you want to compute? Shape differences between two groups? Correlation of shape differences and independent variables? - In the paper you mentioned we were doing several of these experiments, for the group differences we ran a grouptest and Hotelling t-square as our metric, with a significance level of 0.05. 


Please, provide a little more information and I will try my best to help.

Beatriz
May 1, 2016  02:05 AM | shahrokh nasseri
RE: Problem with SPHARM_Tutorial_Data_July2015
Hi Dear Beatriz,

This study includes CBCT data acquired from 20 patients with TMJ OA and 40 healthy controls. Left and right condyles were cropped and segmented with MATLAB, itksnap and Slicer for generating 3D-binary images (mat files) and then convert to gipl format by SPHARM in MATLAB. In the first phase of it, I want to study shape differences and morphological changes between two groups. For determination these differences, I get the following models and volumes in spharm module in Slicer:

Post Processed Segmentation(none), Parameterization of Original Surface(*_pp_para.vtk), SPHARM Surface in Original Space(*_pp_surfSPHARM.vtk), SPHARM Coefficient in Original Space(*_pp_surfSPHARM.coef), SPHARM Surface in Ellipsoid Aligned Space(*_pp_surfSPHARM_ellalign.vtk), SPHARM Coefficient in Ellipsoid Aligned Space(*_pp_surfSPHARM_ellalign.coef), SPHARM Surface in Procaligned Space(*_pp_surfSPHARM_procalign.vtk), Euler Number(2), Spherical topology(1)

I do all steps mentioned in SPHARM-MAT Documentation (Release 1.0.0). According with chapter 5 in this documentation (SURFACE ALIGNMENT), I think that SPHARM-PDM do the registration automatically for example with first order ellipsoid for alignment. Is it true? If so, why do you point out to do pre-registration in your last reply and also you mentioned in your paper (Osteoarthritis and Cartilage 22 (2014))? If it is wrong and I must do pre-registration, is there an automatic way for the registration?

Please we suppose that my data (you mentioned *surfSHARM.vtk) are registered. I want to do the steps mentioned in the pdf manual file of shapeAnalysisMANCOVA_Wizard (NA-MIC Tutorial Contest: Summer 2011, ShapeAnalysisMANCOVA_Wizard-Tutorial.pdf). I do following steps precisely:
Step 1: Run shapeAnalysisMANCOVA_Wizard in bash terminal
Step 2: In first tab (CSV File), I click on "Load File" and load csv output file of Slicer (ShapeAnalysisModule_OutputFile.csv, attached in my last message)
Step 3: According with the manual of ShapeAnalysisMANCOVA_Wizard-Tutorial.pdf, I got to the second tab (Test Parameters), I check the box "Group test". At this moment, unfortunately, I can not see the list of headers of the group test columns to chose the desired parameters, for example SPHARM Surface in Original Space!? Why? Where I'm wrong?

Please guide me,
Thanks a lot,
Shahrokh
May 2, 2016  07:05 AM | Beatriz Paniagua
RE: Problem with SPHARM_Tutorial_Data_July2015
Hi Shahrokh,


Thank you for providing more details on your study design.
I think that SPHARM-PDM do the registration automatically for example with first order ellipsoid for alignment. Is it true? If so, why do you point out to do pre-registration in your last reply and also you mentioned in your paper (Osteoarthritis and Cartilage 22 (2014))? If it is wrong and I must do pre-registration, is there an automatic way for the registration?

What SPHARM-PDM uses the first ellipsoid is for 1) a pose correction that is performed over the parameterization only (before even a pdm is generated) and 2) it is true that after that step there is a pdm ellipsoide-aligned. The three PDM families SPHARM-PDM provides are *surfSPHARM.vtk, *surfSPOHARM_ellalign.vtk and *surfSPHARM_procalign.vtk. All of those PDM collections have a pose corrected parameterization that uses the 1st order ellipsoid, but we do not call that a registration. 

In our OO 2014 paper, we choose to perform an initial registration to our binary images based in a semi automatic method based in anatomical landmarks of the TMJ neck (as many of the TMJ OA samples have huge dismorphologies in the condylar heads). Since we do not want our SPHARM generated PDM's  to override this expert registration, we use the *surfSPHARM.vtk files. The fact these files have a pose corrected parameterization has nothing do do with registration.
Step 3: According with the manual of ShapeAnalysisMANCOVA_Wizard-Tutorial.pdf, I got to the second tab (Test Parameters), I check the box "Group test". At this moment, unfortunately, I can not see the list of headers of the group test columns to chose the desired parameters, for example SPHARM Surface in Original Space!? Why? Where I'm wrong?

Have you selected the group column in the CSV file paramter tab? You will have to click in the text box that reads select input file column and then double click in a cell of the column named "SPHARM Surface in Original Space(*_pp_surfSPHARM.vtk)". A number should appear into your text box, before you go onto Test Parameters and group test column title in the "test column" foldable menu. Does this make sense?


I hope that helps,
Beatriz
May 10, 2016  06:05 AM | shahrokh nasseri
RE: Problem with SPHARM_Tutorial_Data_July2015
Hi Dear Beatriz,
 
Thanks a lot for getting back to me, your comprehensive reply and valuable tips and also very grateful for your explanation about registration.
 
At this point, I want to have a quick and integrated overview of the steps in the shape analysis with SPHARM.
As you mentioned in the last answer, I am doing the following steps in two ways.
First way:
1- After loading csv file in "csv File" tab (ShapeAnalysisModule_OutputFile.csv file), I check checkbox of "select groups".
2- Double click in a cell of the column named "SPHARM Surface in Original Space". A number (in my case, 5) is appeared into the text box of "select groups".
3- In "Test parameters" tab, I check checkbox of "group Test". At this time, the name of header (SPHARM Surface in Original Space) is appeared.
4- I do not change the defaults of statistic type (Hotteling), FDR discovery level (0.05), cutoff of p-value (0.05) and number of permutations (10000).
5- I click on the "Run" button.
6- A window is opened that contains a message: "Do you want to open Slicer with the Mrml scene already loaded?" I click on Yes button. I must mention that I installed Slicer3 (Slicer3-3.6.3-2011-03-04-linux-x86_64) in addition to the Slicer4 (Slicer-4.5.0.1-linux-amd64) in my computer.  At this time, Slicer3 is opened and I get the message of "Slicer had trouble loading the scene file. Scene may contain empty datasets." and nothing happened?! How can I create Mrml scene? In other words, what outputs (for example *_pp_para.vtk, *_pp_surfSPHARM.vtk, *_pp_surfSPHARM.coef, *_pp_surfSPHARM_ellalign.vtk, *_pp_surfSPHARM_ellalign.coef and   *_pp_surfSPHARM_procalign.vtk) should I use to create Mrml scene? and how?
 
Second way:
1- After loading csv file in "csv File" tab (ShapeAnalysisModule_OutputFile.csv file), I check checkbox of "select input file column".
2- Double click in a cell of the column named "SPHARM Surface in Original Space". A number (in my case, 5) is appeared into the text box of "select input file column".
3- In "Test parameters" tab, I check checkbox of "group Test". At this time, the name of header (SPHARM Surface in Original Space) is NOT appeared!!
4- Anyway, I do not change the defaults of statistic type (Hotteling), FDR discovery level (0.05), cutoff of p-value (0.05) and number of permutations (10000).
5- I click on the "Run" button.
6- After a few moments, the following files and folder are created in the folder that contains csv file (ShapeAnalysisModule_OutputFile.csv file):
ShapeAnalysisModule_OutputFile.csv
ShapeAnalysisModule_OutputFile.csv_commandline.txt
ShapeAnalysisModule_OutputFile.csv_DiffMagnitude.txt
ShapeAnalysisModule_OutputFile.csv_diffMesh.txt
ShapeAnalysisModule_OutputFile.csv_GLM_correctedMean.meta
ShapeAnalysisModule_OutputFile.csv_mancovaBonferroniP.txt
ShapeAnalysisModule_OutputFile.csv_mancovaFDRP.txt
ShapeAnalysisModule_OutputFile.csv_mancovaRawP.txt
ShapeAnalysisModule_OutputFile.csv_meanAll_uncorrected.meta
ShapeAnalysisModule_OutputFile.csv_meanAll_uncorrected.vtk
ShapeAnalysisModule_OutputFile.csv_meanA.meta
ShapeAnalysisModule_OutputFile.csv_meanB.meta
ShapeAnalysisModule_OutputFile.csv_normProjections.txt
transformFiles (empty folder)
 
7- At this time, Slicer3 is opened and nothing happened!! Why? What is the application of the outputs mentioned above?
 
Please guide me.
Best regards,
Shahrokh
May 10, 2016  06:05 AM | shahrokh nasseri
RE: Problem with SPHARM_Tutorial_Data_July2015
Hi Dear Beatriz,
Thanks a lot for getting back to me, your comprehensive reply and valuable tips and also very grateful for your explanation about registration.
At this point, I want to have a quick and integrated overview of the steps in the shape analysis with SPHARM.
As you mentioned in the last answer, I am doing the following steps in two ways.
 
First way:
1- After loading csv file in "csv File" tab (ShapeAnalysisModule_OutputFile.csv file), I check checkbox of "select groups".
2- Double click in a cell of the column named "SPHARM Surface in Original Space". A number (in my case, 5) is appeared into the text box of "select groups".
3- In "Test parameters" tab, I check checkbox of "group Test". At this time, the name of header (SPHARM Surface in Original Space) is appeared.
4- I do not change the defaults of statistic type (Hotteling), FDR discovery level (0.05), cutoff of p-value (0.05) and number of permutations (10000).
5- I click on the "Run" button.
6- A window is opened that contains a message: "Do you want to open Slicer with the Mrml scene already loaded?" I click on Yes button. I must mention that I installed Slicer3 (Slicer3-3.6.3-2011-03-04-linux-x86_64) in addition to the Slicer4 (Slicer-4.5.0.1-linux-amd64) in my computer.  At this time, Slicer3 is opened and I get the message of "Slicer had trouble loading the scene file. Scene may contain empty datasets." and nothing happened?! How can I create Mrml scene? In other words, what outputs (for example *_pp_para.vtk, *_pp_surfSPHARM.vtk, *_pp_surfSPHARM.coef, *_pp_surfSPHARM_ellalign.vtk, *_pp_surfSPHARM_ellalign.coef and   *_pp_surfSPHARM_procalign.vtk) should I use to create Mrml scene? and how?
 
Second way:
1- After loading csv file in "csv File" tab (ShapeAnalysisModule_OutputFile.csv file), I check checkbox of "select input file column".
2- Double click in a cell of the column named "SPHARM Surface in Original Space". A number (in my case, 5) is appeared into the text box of "select input file column".
3- In "Test parameters" tab, I check checkbox of "group Test". At this time, the name of header (SPHARM Surface in Original Space) is NOT appeared!!
4- Anyway, I do not change the defaults of statistic type (Hotteling), FDR discovery level (0.05), cutoff of p-value (0.05) and number of permutations (10000).
5- I click on the "Run" button.
6- After a few moments, the following files and folder are created in the folder that contains csv file (ShapeAnalysisModule_OutputFile.csv file):
ShapeAnalysisModule_OutputFile.csv
ShapeAnalysisModule_OutputFile.csv_commandline.txt
ShapeAnalysisModule_OutputFile.csv_DiffMagnitude.txt
ShapeAnalysisModule_OutputFile.csv_diffMesh.txt
ShapeAnalysisModule_OutputFile.csv_GLM_correctedMean.meta
ShapeAnalysisModule_OutputFile.csv_mancovaBonferroniP.txt
ShapeAnalysisModule_OutputFile.csv_mancovaFDRP.txt
ShapeAnalysisModule_OutputFile.csv_mancovaRawP.txt
ShapeAnalysisModule_OutputFile.csv_meanAll_uncorrected.meta
ShapeAnalysisModule_OutputFile.csv_meanAll_uncorrected.vtk
ShapeAnalysisModule_OutputFile.csv_meanA.meta
ShapeAnalysisModule_OutputFile.csv_meanB.meta
ShapeAnalysisModule_OutputFile.csv_normProjections.txt
transformFiles (empty folder)
 
7- At this time, Slicer3 is opened and nothing happened!! Why? What is the application of the outputs mentioned above?
 
Please guide me.
Best regards,
Shahrokh
May 10, 2016  06:05 AM | Beatriz Paniagua
RE: Problem with SPHARM_Tutorial_Data_July2015
Hi Shahrokh,

I am happy to hear things are moving forward.

The steps that you mention are all good ways to run statistical analysis to test for group differences in Spharm. The error you mention in the First way is a legacy error. Before, spharm used to create mrml scene files to load in Slicer, but that is no longer supported. The files resulting from the Second way are the right results files.

At this point you will have to run some analysis steps manually on your own to visualize the results. Could you please let me know how did you run the spharm pdm pipeline? Via command line or Slicer extension? Also what OS: MacOS, Linux or Windows?


I am happy to guide you through the necessary steps once you provide that information.
Thank you,


Beatriz
May 11, 2016  04:05 AM | shahrokh nasseri
RE: Problem with SPHARM_Tutorial_Data_July2015
Hi Dear Beatriz,

At first when I started working with SPHARM in 2012, I run SPHARM on MATLAB Version 7.6.0.324 (R2008a) in Fedora core 13 (Linux 2.6.33.3-85.fc13.i686.PAE). I did exactly all the steps that mentioned in SPHARM-MAT Documentation (Release 1.0.0, June 18, 2010; ShenLab@IUSM) about running SPHARM-MAT and SPHARM-PDM.

Recently, I noticed that it is very simple to work with SPHARM in 3D Slicer. So I installed Slicer 4.5.0-1 (r24735) and also MeshToLabelMap, ModelToModelDistance, ShapePopulationViewer and SPHARM-PDM extensions on Fedora core 22 (64 bit).

In response to your question how I run SPHARM-PDM pipeline, I should mention that I do exactly the steps outlined in your SPHARM-PDM user tutorial (the University of North Carolina of Chapel Hill, July 2015).

Please guide me to run analysis steps to visualize the results.
Thank you for your patience and cooperation.

Shahrokh
May 15, 2016  08:05 PM | shahrokh nasseri
RE: Problem with SPHARM_Tutorial_Data_July2015
Hi Dear Beatriz,

Excuse me to send twice this message.

At this point you will have to run some analysis steps manually on your own to visualize the results. Could you please let me know how did you run the spharm pdm pipeline? Via command line or Slicer extension? Also what OS: MacOS, Linux or Windows?

At first when I started working with SPHARM in 2012, I run SPHARM on MATLAB Version 7.6.0.324 (R2008a) in Fedora core 13 (Linux 2.6.33.3-85.fc13.i686.PAE). I did exactly all the steps that mentioned in SPHARM-MAT Documentation (Release 1.0.0, June 18, 2010; ShenLab@IUSM) about running SPHARM-MAT and SPHARM-PDM.

Recently, I noticed that it is very simple to work with SPHARM in 3D Slicer. So I installed Slicer 4.5.0-1 (r24735) and also MeshToLabelMap, ModelToModelDistance, ShapePopulationViewer and SPHARM-PDM extensions on Fedora core 22 (64 bit).

In response to your question how I run SPHARM-PDM pipeline, I should mention that I do exactly the steps outlined in your SPHARM-PDM user tutorial (the University of North Carolina of Chapel Hill, July 2015).

Please guide me to run analysis steps to visualize the results.
Thank you for your patience and cooperation.
Shahrokh
May 16, 2016  09:05 AM | Beatriz Paniagua
RE: Problem with SPHARM_Tutorial_Data_July2015
Hi Shahrokh,


Great! Thank you for the information.


In order to visualize the results of shapeanalysismancova, you will have to use Meta2VTK and MeshMath that are executables that are distributed with SPHARM-PDM. If you are working in Linux, you can find them in /pathtoyourhomefolder/.config/NA-MIC/Extensions-yourslicerversionhere/SPHARM-PDM/lib/Slicer-4.5/ExternalBin. You can find your Slicer version by the Help menu>>About 3D Slicer. Your version number will be in the second line of that dialog, preceded by a letter "r".

You will have to run Meta2VTK to convert all meta files into VTK:
Meta2VTK inputmeta outputvtk

Then, you will have to load the scalar maps into the VTK you just created. You can use the average all uncorrected, as the display mesh is only for anatomical reference. You can do that with MeshMath, using the KWMtoPolyData flag.

MeshMath input.vtk outputwithScalars.vtk -KWMtoPolyData statisticalfiles.txt name_of_scalar_field_your_choice

You can use shapepopulationviewer (SPV) to visualize the vtk with the statistical color maps (p-values, etc). SPV is a slicer extension, more documentation and resources here:

https://www.nitrc.org/projects/shapepopv...
https://www.nitrc.org/docman/view.php/75...
https://www.slicer.org/slicerWiki/index....



I hope that helps.
Best,

Beatriz
Jun 8, 2016  02:06 AM | shahrokh nasseri
RE: Problem with SPHARM_Tutorial_Data_July2015

Dear Beatriz

 

Thank you so much for all of your help and guidance what you have done so far. Fortunately, at now I can do all the steps in spharm. I have some
questions
about of analysis and statistical interpretation that I hope you will help me. In other words, I hope you tell me how to analyze and interpret the results of statistical analysis in spharm?


First question:

Is the significance relationship between signed distance map and p-value map (e.g., mancovaRawP)?

I expected that there would be a direct relationship between signed distance and p-value color-coded maps. In other words, is it expected that p-values in the specific region, relation with other regions, reduces as signed magnitudes of the distance in this specific region (between mean surface of normal group and mean surface of OA group) is larger than other regions?
OR

I expected that if the mean condylar surface in normal group is shrinking below the mean condylar surface in OA group in the the same area
specified, there is also a decrease in the amount of p-value.
With this message, I attached a tar.gz file with the name of  PvalueMapAndDistanceMap.tar.gz included two images with the names of SignedDistanceMap_Anterior.png and PvalueMap_anterior.png.

Can you analyze these images? Also, can you make relevant these images together in terms of color?

 

Second question:

The outputs of shapeAnalysisMANCOVA_Wizard are meta files with the extensions as *_meanA.meta and *_meanB.meta. How can created these
surfaces? Is this mean surface can be representative of its group? 


Third question:
The contents of files as *_mancovaBonferroniP.txt or *_mancovaFDRP.txt is 1 exactly! Why? Similar as following lines:

 NUMBER_OF_POINTS = 1002

DIMENSION = 1

TYPE = Scalar

1

1

1

1

...


What I did was wrong?

 


Please guide me.


Best regards,

Shahrokh

Jun 14, 2016  03:06 PM | Beatriz Paniagua
RE: Problem with SPHARM_Tutorial_Data_July2015
Hi Shahrokh,


Sorry for the delay in responding this question.

Is there a relationship between signed distance map and p-value map (e.g., mancovaRawP)?
Not necessarily. The p-value maps illustrate significantly different local shape changes between the two populations introduced in mancova. This is not related to the magnitude of the measurement.

I expected that there would be a direct relationship between signed distance and p-value color-coded maps. In other words, is it expected that p-values in the specific region, relation with other regions, reduces as signed magnitudes of the distance in this specific region (between mean surface of normal group and mean surface of OA group) is larger than other regions?
Again, not necessarily. See response above.
Can you analyze these images? Also, can you make relevant these images together in terms of color?
Thanks for sharing your images. Large magnitudes of change between the two means do not have to result in more significant changes. A lot of things are in play for example variability of the measurement in the region.
The outputs of shapeAnalysisMANCOVA_Wizard are meta files with the extensions as *_meanA.meta and *_meanB.meta. How can created these
surfaces? Is this mean surface can be representative of its group?
These means are the results of averaging the coordinate points of each one of the populations. The mean is just a way to describe your group, but of course it mean a data reduction. If your group includes a lot of shape variability it will be all averaged in the end, and it wont be able to represent the group well. Just curious, what is the n of each one of your groups?
The contents of files as *_mancovaBonferroniP.txt or *_mancovaFDRP.txt is 1 exactly!
That means that your p-values do not survive correction for false positives in the threshold you specified in the shapenalysismancova_wizard program.




I hope that helps.
Please, let me know if you have any further questions.



Best,

Beatriz
Jun 15, 2016  08:06 PM | shahrokh nasseri
RE: Problem with SPHARM_Tutorial_Data_July2015
Hi;
Dear Beatriz

Thank you very much for your comments and tips. I should think carefully what you said.
The number of left normal condyle and left OA condyle groups were 25 and 20. Also the number of right normal condyle and right OA condyle groups were 15 and 20.

Again, thank you very much.

Best regards,
Shahrokh