Hello SPHARM experts, 

I have successfully completed the tutorial (SPHARM-PDM_Tutorial_July2015.pdf), and obtained the exact same results.

However, doing the same procedure on my own data (.nii format) gives me some errors. (I'm using the latest version of Slicer (4.5.0-1), and I'm on Ubuntu 14.04).

The error says it is unable to open pp_surf.vtk and pp_para.vtk, however, both files exist and can be opened. The data inside looks normal. I really appreciate it if you could tell me what is wrong here. Thanks.

Following is my log:

Shape Analysis Module standard output:

------ Shape Analysis Module start -----
Computing ShapeAnalysisModule...
/home/nm/SPHARM_data/Tutorial_Output1/
/home/nm/SPHARM_data/Tutorial_Output1/ShapeAnalysisModule.bms
Number of Datas: 4
Executing BatchMake...
Case:/home/nm/SPHARM_data/origData/95330358_090112/my_data.nii
Doing Post Processing
Status: Start SegPostProcessCLP /home/nm/SPHARM_data/origData/95330358_090112/my_data.nii /home/nm/SPHARM_data/Tutorial_Output1/Mesh/PostProcess/my_data_pp.gipl.gz --rescale --space 0.5,0.5,0.5
run: 'SegPostProcessCLP' '''/home/nm/SPHARM_data/origData/95330358_090112/my_data.nii' '/home/nm/SPHARM_data/Tutorial_Output1/Mesh/PostProcess/my_data_pp.gipl.gz' --rescale --space '0.5,0.5,0.5'''
Status: Finish: Execution time 3001ms
Doing GenParaMesh
Status: Start GenParaMeshCLP --EulerFile --outEulerName /home/nm/SPHARM_data/Tutorial_Output1/EulerFiles/my_data_euler.txt --iter 126 --label 1 /home/nm/SPHARM_data/Tutorial_Output1/Mesh/PostProcess/my_data_pp.gipl.gz /home/nm/SPHARM_data/Tutorial_Output1/Mesh/SPHARM/my_data_pp_para.vtk /home/nm/SPHARM_data/Tutorial_Output1/Mesh/SPHARM/my_data_pp_surf.vtk
run: 'GenParaMeshCLP' ''--EulerFile --outEulerName '/home/nm/SPHARM_data/Tutorial_Output1/EulerFiles/my_data_euler.txt' --iter '126' --label '1' '/home/nm/SPHARM_data/Tutorial_Output1/Mesh/PostProcess/my_data_pp.gipl.gz' '/home/nm/SPHARM_data/Tutorial_Output1/Mesh/SPHARM/my_data_pp_para.vtk' '/home/nm/SPHARM_data/Tutorial_Output1/Mesh/SPHARM/my_data_pp_surf.vtk'''
Status: Finish: Execution time 301ms
Doing ParaToSPHARMMesh
Creating Template
Status: Start ParaToSPHARMMeshCLP /home/nm/SPHARM_data/Tutorial_Output1/Mesh/SPHARM/my_data_pp_para.vtk /home/nm/SPHARM_data/Tutorial_Output1/Mesh/SPHARM/my_data_pp_surf.vtk /home/nm/SPHARM_data/Tutorial_Output1/Template/my_data_pp_surf --subdivLevel 10 --spharmDegree 15 --FinalFlip 0 --paraOut --phiIteration 100 --thetaIteration 100 --medialMesh
run: 'ParaToSPHARMMeshCLP' '''/home/nm/SPHARM_data/Tutorial_Output1/Mesh/SPHARM/my_data_pp_para.vtk' '/home/nm/SPHARM_data/Tutorial_Output1/Mesh/SPHARM/my_data_pp_surf.vtk' '/home/nm/SPHARM_data/Tutorial_Output1/Template/my_data_pp_surf' --subdivLevel '10' --spharmDegree '15' --FinalFlip '0' --paraOut --phiIteration '100' --thetaIteration '100' --medialMesh''
Status: Finish: Execution time 1500ms
ParaToSPHARMMesh: ERROR: In /home/kitware/Dashboards/Nightly/S-450-E-b/SPHARM-PDM-build/VTK/IO/Legacy/vtkDataReader.cxx, line 466
vtkPolyDataReader (0x1f210f0): Unable to open file: /home/nm/SPHARM_data/Tutorial_Output1/Mesh/SPHARM/my_data_pp_surf.vtk
ERROR: In /home/kitware/Dashboards/Nightly/S-450-E-b/SPHARM-PDM-build/VTK/IO/Legacy/vtkDataReader.cxx, line 466
vtkPolyDataReader (0x1f210f0): Unable to open file: /home/nm/SPHARM_data/Tutorial_Output1/Mesh/SPHARM/my_data_pp_para.vtk
regTemplate: my_data_pp_surfSPHARM.vtk
flipTemplate: my_data_pp_surfSPHARM.coef
Status: Start ParaToSPHARMMeshCLP /home/nm/SPHARM_data/Tutorial_Output1/Mesh/SPHARM/my_data_pp_para.vtk /home/nm/SPHARM_data/Tutorial_Output1/Mesh/SPHARM/my_data_pp_surf.vtk /home/nm/SPHARM_data/Tutorial_Output1/Mesh/SPHARM/my_data_pp_surf --regTemplateFileOn --regTemplate /home/nm/SPHARM_data/Tutorial_Output1/Template/my_data_pp_surfSPHARM.vtk --flipTemplateOn --flipTemplate /home/nm/SPHARM_data/Tutorial_Output1/Template/my_data_pp_surfSPHARM.coef --subdivLevel 10 --spharmDegree 15 --FinalFlip 0 --paraOut --phiIteration 100 --thetaIteration 100 --medialMesh
run: 'ParaToSPHARMMeshCLP' '''/home/nm/SPHARM_data/Tutorial_Output1/Mesh/SPHARM/my_data_pp_para.vtk' '/home/nm/SPHARM_data/Tutorial_Output1/Mesh/SPHARM/my_data_pp_surf.vtk' '/home/nm/SPHARM_data/Tutorial_Output1/Mesh/SPHARM/my_data_pp_surf' --regTemplateFileOn --regTemplate '/home/nm/SPHARM_data/Tutorial_Output1/Template/my_data_pp_surfSPHARM.vtk' --flipTemplateOn --flipTemplate '/home/nm/SPHARM_data/Tutorial_Output1/Template/my_data_pp_surfSPHARM.coef' --subdivLevel '10' --spharmDegree '15' --FinalFlip '0' --paraOut --phiIteration '100' --thetaIteration '100' --medialMesh''
Status: Finish: Execution time 1800ms
ParaToSPHARMMesh: ERROR: In /home/kitware/Dashboards/Nightly/S-450-E-b/SPHARM-PDM-build/VTK/IO/Legacy/vtkDataReader.cxx, line 466
vtkPolyDataReader (0x28a4b60): Unable to open file: /home/nm/SPHARM_data/Tutorial_Output1/Mesh/SPHARM/my_data_pp_surf.vtk
ERROR: In /home/kitware/Dashboards/Nightly/S-450-E-b/SPHARM-PDM-build/VTK/IO/Legacy/vtkDataReader.cxx, line 466
vtkPolyDataReader (0x28a4b60): Unable to open file: /home/nm/SPHARM_data/Tutorial_Output1/Mesh/SPHARM/my_data_pp_para.vtk
Generic Warning: In /home/kitware/Dashboards/Nightly/S-450-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-450-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-450-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-450-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-450-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/nm/SPHARM_data/Tutorial_Output1/Mesh/SPHARM/my_data_pp_surf_paraPhiHalf.txt
Case:/home/nm/SPHARM_data/origData/95453354_091001/my_data.nii
Doing Post Processing
Status: Start SegPostProcessCLP /home/nm/SPHARM_data/origData/95453354_091001/my_data.nii /home/nm/SPHARM_data/Tutorial_Output1/Mesh/PostProcess/my_data_pp.gipl.gz --rescale --space 0.5,0.5,0.5
run: 'SegPostProcessCLP' '''/home/nm/SPHARM_data/origData/95453354_091001/my_data.nii' '/home/nm/SPHARM_data/Tutorial_Output1/Mesh/PostProcess/my_data_pp.gipl.gz' --rescale --space '0.5,0.5,0.5'''
Status: Finish: Execution time 3001ms
Doing GenParaMesh
Status: Start GenParaMeshCLP --EulerFile --outEulerName /home/nm/SPHARM_data/Tutorial_Output1/EulerFiles/my_data_euler.txt --iter 126 --label 1 /home/nm/SPHARM_data/Tutorial_Output1/Mesh/PostProcess/my_data_pp.gipl.gz /home/nm/SPHARM_data/Tutorial_Output1/Mesh/SPHARM/my_data_pp_para.vtk /home/nm/SPHARM_data/Tutorial_Output1/Mesh/SPHARM/my_data_pp_surf.vtk
run: 'GenParaMeshCLP' ''--EulerFile --outEulerName '/home/nm/SPHARM_data/Tutorial_Output1/EulerFiles/my_data_euler.txt' --iter '126' --label '1' '/home/nm/SPHARM_data/Tutorial_Output1/Mesh/PostProcess/my_data_pp.gipl.gz' '/home/nm/SPHARM_data/Tutorial_Output1/Mesh/SPHARM/my_data_pp_para.vtk' '/home/nm/SPHARM_data/Tutorial_Output1/Mesh/SPHARM/my_data_pp_surf.vtk'''
Status: Finish: Execution time 7202ms
Doing ParaToSPHARMMesh
regTemplate: my_data_pp_surfSPHARM.vtk
flipTemplate: my_data_pp_surfSPHARM.coef
Case:/home/nm/SPHARM_data/origData/95491648_081204/my_data.nii
Doing Post Processing
Status: Start SegPostProcessCLP /home/nm/SPHARM_data/origData/95491648_081204/my_data.nii /home/nm/SPHARM_data/Tutorial_Output1/Mesh/PostProcess/my_data_pp.gipl.gz --rescale --space 0.5,0.5,0.5
run: 'SegPostProcessCLP' '''/home/nm/SPHARM_data/origData/95491648_081204/my_data.nii' '/home/nm/SPHARM_data/Tutorial_Output1/Mesh/PostProcess/my_data_pp.gipl.gz' --rescale --space '0.5,0.5,0.5'''
Status: Finish: Execution time 3002ms
Doing GenParaMesh
Doing ParaToSPHARMMesh
regTemplate: my_data_pp_surfSPHARM.vtk
flipTemplate: my_data_pp_surfSPHARM.coef
Case:/home/nm/SPHARM_data/origData/96892753_120209/my_data.nii
Doing Post Processing
Status: Start SegPostProcessCLP /home/nm/SPHARM_data/origData/96892753_120209/my_data.nii /home/nm/SPHARM_data/Tutorial_Output1/Mesh/PostProcess/my_data_pp.gipl.gz --rescale --space 0.5,0.5,0.5
run: 'SegPostProcessCLP' '''/home/nm/SPHARM_data/origData/96892753_120209/my_data.nii' '/home/nm/SPHARM_data/Tutorial_Output1/Mesh/PostProcess/my_data_pp.gipl.gz' --rescale --space '0.5,0.5,0.5'''
Status: Finish: Execution time 2703ms
Doing GenParaMesh
Doing ParaToSPHARMMesh
regTemplate: my_data_pp_surfSPHARM.vtk
flipTemplate: my_data_pp_surfSPHARM.coef
Executing BatchMake: Done!
Execute Meshmath...
Mapping parameters in SPHARM template meshes using MeshMath
Path for MeshMathTemplate: /home/nm/SPHARM_data/Tutorial_Output1/Template/
DONE COMPUTING SPHARM

And the error log:

Unable to open file: /home/nm/SPHARM_data/Tutorial_Output1/Mesh/SPHARM/my_data_pp_para.vtk
Error: Generic Warning: In /home/kitware/Dashboards/Nightly/S-450-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-450-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-450-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-450-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-450-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!