Hi everyone!

I used SPHARM slicer extension trying to follow the tutorial data analysis, but I didn't get para.vtk and surf.vtk in my outputs, and the Euler files all had 0. Although when looking at the error log, it seems that these files were indeed created (in red below). I am aware of Shahrokh's post (https://www.nitrc.org/forum/forum.php?th...) but it also seems to me that our problems might be different. I am using Slicer 4.5.0, and I do see the ".gipl.gz" files in the /Mesh/PostProcess" folder. Any insight is appreciated!

Thanks,
Yifan


Shape Analysis Module standard output:

------ Shape Analysis Module start -----
Computing ShapeAnalysisModule...
/home/dlabadmin/Desktop/SPHARM/Test_Apr2017/
/home/dlabadmin/Desktop/SPHARM/Test_Apr2017/ShapeAnalysisModule.bms
Number of Datas: 2
Executing BatchMake...
Case:/home/dlabadmin/Desktop/SPHARM/G1_20080528_KC_AMY_L.nii
Doing Post Processing
Status: Start SegPostProcessCLP /home/dlabadmin/Desktop/SPHARM/G1_20080528_KC_AMY_L.nii /home/dlabadmin/Desktop/SPHARM/Test_Apr2017/Mesh/PostProcess/G1_20080528_KC_AMY_L_pp.gipl.gz --rescale --space 0.5,0.5,0.5
run: 'SegPostProcessCLP' '''/home/dlabadmin/Desktop/SPHARM/G1_20080528_KC_AMY_L.nii' '/home/dlabadmin/Desktop/SPHARM/Test_Apr2017/Mesh/PostProcess/G1_20080528_KC_AMY_L_pp.gipl.gz' --rescale --space '0.5,0.5,0.5'''
Status: Finish: Execution time 15303ms
Doing GenParaMesh
Status: Start GenParaMeshCLP --EulerFile --outEulerName /home/dlabadmin/Desktop/SPHARM/Test_Apr2017/EulerFiles/G1_20080528_KC_AMY_L_euler.txt --iter 1000 --label 1 /home/dlabadmin/Desktop/SPHARM/Test_Apr2017/Mesh/PostProcess/G1_20080528_KC_AMY_L_pp.gipl.gz /home/dlabadmin/Desktop/SPHARM/Test_Apr2017/Mesh/SPHARM/G1_20080528_KC_AMY_L_pp_para.vtk /home/dlabadmin/Desktop/SPHARM/Test_Apr2017/Mesh/SPHARM/G1_20080528_KC_AMY_L_pp_surf.vtk
run: 'GenParaMeshCLP' ''--EulerFile --outEulerName '/home/dlabadmin/Desktop/SPHARM/Test_Apr2017/EulerFiles/G1_20080528_KC_AMY_L_euler.txt' --iter '1000' --label '1' '/home/dlabadmin/Desktop/SPHARM/Test_Apr2017/Mesh/PostProcess/G1_20080528_KC_AMY_L_pp.gipl.gz' '/home/dlabadmin/Desktop/SPHARM/Test_Apr2017/Mesh/SPHARM/G1_20080528_KC_AMY_L_pp_para.vtk' '/home/dlabadmin/Desktop/SPHARM/Test_Apr2017/Mesh/SPHARM/G1_20080528_KC_AMY_L_pp_surf.vtk'''
Status: Finish: Execution time 600ms
Doing ParaToSPHARMMesh
Creating Template
Status: Start ParaToSPHARMMeshCLP /home/dlabadmin/Desktop/SPHARM/Test_Apr2017/Mesh/SPHARM/G1_20080528_KC_AMY_L_pp_para.vtk /home/dlabadmin/Desktop/SPHARM/Test_Apr2017/Mesh/SPHARM/G1_20080528_KC_AMY_L_pp_surf.vtk /home/dlabadmin/Desktop/SPHARM/Test_Apr2017/Template/G1_20080528_KC_AMY_L_pp_surf --subdivLevel 10 --spharmDegree 15 --FinalFlip 0 --paraOut --phiIteration 100 --thetaIteration 100 --medialMesh
run: 'ParaToSPHARMMeshCLP' '''/home/dlabadmin/Desktop/SPHARM/Test_Apr2017/Mesh/SPHARM/G1_20080528_KC_AMY_L_pp_para.vtk' '/home/dlabadmin/Desktop/SPHARM/Test_Apr2017/Mesh/SPHARM/G1_20080528_KC_AMY_L_pp_surf.vtk' '/home/dlabadmin/Desktop/SPHARM/Test_Apr2017/Template/G1_20080528_KC_AMY_L_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 (0x29993d0): Unable to open file: /home/dlabadmin/Desktop/SPHARM/Test_Apr2017/Mesh/SPHARM/G1_20080528_KC_AMY_L_pp_surf.vtk
ERROR: In /home/kitware/Dashboards/Nightly/S-450-E-b/SPHARM-PDM-build/VTK/IO/Legacy/vtkDataReader.cxx, line 466
vtkPolyDataReader (0x29993d0): Unable to open file: /home/dlabadmin/Desktop/SPHARM/Test_Apr2017/Mesh/SPHARM/G1_20080528_KC_AMY_L_pp_para.vtk
regTemplate: G1_20080528_KC_AMY_L_pp_surfSPHARM.vtk
flipTemplate: G1_20080528_KC_AMY_L_pp_surfSPHARM.coef
Status: Start ParaToSPHARMMeshCLP /home/dlabadmin/Desktop/SPHARM/Test_Apr2017/Mesh/SPHARM/G1_20080528_KC_AMY_L_pp_para.vtk /home/dlabadmin/Desktop/SPHARM/Test_Apr2017/Mesh/SPHARM/G1_20080528_KC_AMY_L_pp_surf.vtk /home/dlabadmin/Desktop/SPHARM/Test_Apr2017/Mesh/SPHARM/G1_20080528_KC_AMY_L_pp_surf --regTemplateFileOn --regTemplate /home/dlabadmin/Desktop/SPHARM/Test_Apr2017/Template/G1_20080528_KC_AMY_L_pp_surfSPHARM.vtk --flipTemplateOn --flipTemplate /home/dlabadmin/Desktop/SPHARM/Test_Apr2017/Template/G1_20080528_KC_AMY_L_pp_surfSPHARM.coef --subdivLevel 10 --spharmDegree 15 --FinalFlip 0 --paraOut --phiIteration 100 --thetaIteration 100 --medialMesh
run: 'ParaToSPHARMMeshCLP' '''/home/dlabadmin/Desktop/SPHARM/Test_Apr2017/Mesh/SPHARM/G1_20080528_KC_AMY_L_pp_para.vtk' '/home/dlabadmin/Desktop/SPHARM/Test_Apr2017/Mesh/SPHARM/G1_20080528_KC_AMY_L_pp_surf.vtk' '/home/dlabadmin/Desktop/SPHARM/Test_Apr2017/Mesh/SPHARM/G1_20080528_KC_AMY_L_pp_surf' --regTemplateFileOn --regTemplate '/home/dlabadmin/Desktop/SPHARM/Test_Apr2017/Template/G1_20080528_KC_AMY_L_pp_surfSPHARM.vtk' --flipTemplateOn --flipTemplate '/home/dlabadmin/Desktop/SPHARM/Test_Apr2017/Template/G1_20080528_KC_AMY_L_pp_surfSPHARM.coef' --subdivLevel '10' --spharmDegree '15' --FinalFlip '0' --paraOut --phiIteration '100' --thetaIteration '100' --medialMesh''
Status: Finish: Execution time 1801ms
ParaToSPHARMMesh: ERROR: In /home/kitware/Dashboards/Nightly/S-450-E-b/SPHARM-PDM-build/VTK/IO/Legacy/vtkDataReader.cxx, line 466
vtkPolyDataReader (0x2c6d960): Unable to open file: /home/dlabadmin/Desktop/SPHARM/Test_Apr2017/Mesh/SPHARM/G1_20080528_KC_AMY_L_pp_surf.vtk
ERROR: In /home/kitware/Dashboards/Nightly/S-450-E-b/SPHARM-PDM-build/VTK/IO/Legacy/vtkDataReader.cxx, line 466
vtkPolyDataReader (0x2c6d960): Unable to open file: /home/dlabadmin/Desktop/SPHARM/Test_Apr2017/Mesh/SPHARM/G1_20080528_KC_AMY_L_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/dlabadmin/Desktop/SPHARM/Test_Apr2017/Mesh/SPHARM/G1_20080528_KC_AMY_L_pp_surf_paraPhiHalf.txt
Case:/home/dlabadmin/Desktop/SPHARM/G2_20080528_KC_AMY_L.nii
Doing Post Processing
Status: Start SegPostProcessCLP /home/dlabadmin/Desktop/SPHARM/G2_20080528_KC_AMY_L.nii /home/dlabadmin/Desktop/SPHARM/Test_Apr2017/Mesh/PostProcess/G2_20080528_KC_AMY_L_pp.gipl.gz --rescale --space 0.5,0.5,0.5
run: 'SegPostProcessCLP' '''/home/dlabadmin/Desktop/SPHARM/G2_20080528_KC_AMY_L.nii' '/home/dlabadmin/Desktop/SPHARM/Test_Apr2017/Mesh/PostProcess/G2_20080528_KC_AMY_L_pp.gipl.gz' --rescale --space '0.5,0.5,0.5'''
Status: Finish: Execution time 15303ms
Doing GenParaMesh
Status: Start GenParaMeshCLP --EulerFile --outEulerName /home/dlabadmin/Desktop/SPHARM/Test_Apr2017/EulerFiles/G2_20080528_KC_AMY_L_euler.txt --iter 1000 --label 1 /home/dlabadmin/Desktop/SPHARM/Test_Apr2017/Mesh/PostProcess/G2_20080528_KC_AMY_L_pp.gipl.gz /home/dlabadmin/Desktop/SPHARM/Test_Apr2017/Mesh/SPHARM/G2_20080528_KC_AMY_L_pp_para.vtk /home/dlabadmin/Desktop/SPHARM/Test_Apr2017/Mesh/SPHARM/G2_20080528_KC_AMY_L_pp_surf.vtk
run: 'GenParaMeshCLP' ''--EulerFile --outEulerName '/home/dlabadmin/Desktop/SPHARM/Test_Apr2017/EulerFiles/G2_20080528_KC_AMY_L_euler.txt' --iter '1000' --label '1' '/home/dlabadmin/Desktop/SPHARM/Test_Apr2017/Mesh/PostProcess/G2_20080528_KC_AMY_L_pp.gipl.gz' '/home/dlabadmin/Desktop/SPHARM/Test_Apr2017/Mesh/SPHARM/G2_20080528_KC_AMY_L_pp_para.vtk' '/home/dlabadmin/Desktop/SPHARM/Test_Apr2017/Mesh/SPHARM/G2_20080528_KC_AMY_L_pp_surf.vtk'''
Status: Finish: Execution time 600ms
Doing ParaToSPHARMMesh
regTemplate: G1_20080528_KC_AMY_L_pp_surfSPHARM.vtk
flipTemplate: G1_20080528_KC_AMY_L_pp_surfSPHARM.coef
Status: Start ParaToSPHARMMeshCLP /home/dlabadmin/Desktop/SPHARM/Test_Apr2017/Mesh/SPHARM/G2_20080528_KC_AMY_L_pp_para.vtk /home/dlabadmin/Desktop/SPHARM/Test_Apr2017/Mesh/SPHARM/G2_20080528_KC_AMY_L_pp_surf.vtk /home/dlabadmin/Desktop/SPHARM/Test_Apr2017/Mesh/SPHARM/G2_20080528_KC_AMY_L_pp_surf --regTemplateFileOn --regTemplate /home/dlabadmin/Desktop/SPHARM/Test_Apr2017/Template/G1_20080528_KC_AMY_L_pp_surfSPHARM.vtk --flipTemplateOn --flipTemplate /home/dlabadmin/Desktop/SPHARM/Test_Apr2017/Template/G1_20080528_KC_AMY_L_pp_surfSPHARM.coef --subdivLevel 10 --spharmDegree 15 --FinalFlip 0 --paraOut --phiIteration 100 --thetaIteration 100 --medialMesh
run: 'ParaToSPHARMMeshCLP' '''/home/dlabadmin/Desktop/SPHARM/Test_Apr2017/Mesh/SPHARM/G2_20080528_KC_AMY_L_pp_para.vtk' '/home/dlabadmin/Desktop/SPHARM/Test_Apr2017/Mesh/SPHARM/G2_20080528_KC_AMY_L_pp_surf.vtk' '/home/dlabadmin/Desktop/SPHARM/Test_Apr2017/Mesh/SPHARM/G2_20080528_KC_AMY_L_pp_surf' --regTemplateFileOn --regTemplate '/home/dlabadmin/Desktop/SPHARM/Test_Apr2017/Template/G1_20080528_KC_AMY_L_pp_surfSPHARM.vtk' --flipTemplateOn --flipTemplate '/home/dlabadmin/Desktop/SPHARM/Test_Apr2017/Template/G1_20080528_KC_AMY_L_pp_surfSPHARM.coef' --subdivLevel '10' --spharmDegree '15' --FinalFlip '0' --paraOut --phiIteration '100' --thetaIteration '100' --medialMesh''
Status: Finish: Execution time 1801ms
ParaToSPHARMMesh: ERROR: In /home/kitware/Dashboards/Nightly/S-450-E-b/SPHARM-PDM-build/VTK/IO/Legacy/vtkDataReader.cxx, line 466
vtkPolyDataReader (0x2ea2960): Unable to open file: /home/dlabadmin/Desktop/SPHARM/Test_Apr2017/Mesh/SPHARM/G2_20080528_KC_AMY_L_pp_surf.vtk
ERROR: In /home/kitware/Dashboards/Nightly/S-450-E-b/SPHARM-PDM-build/VTK/IO/Legacy/vtkDataReader.cxx, line 466
vtkPolyDataReader (0x2ea2960): Unable to open file: /home/dlabadmin/Desktop/SPHARM/Test_Apr2017/Mesh/SPHARM/G2_20080528_KC_AMY_L_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/dlabadmin/Desktop/SPHARM/Test_Apr2017/Mesh/SPHARM/G2_20080528_KC_AMY_L_pp_surf_paraPhiHalf.txt
Executing BatchMake: Done!
Execute Meshmath...
Mapping parameters in SPHARM template meshes using MeshMath
Path for MeshMathTemplate: /home/dlabadmin/Desktop/SPHARM/Test_Apr2017/Template/
DONE COMPUTING SPHARM

Hi Yifan,

Sorry you are jumping into trouble. You see commandline standard output messages for all commands because, with the current implementation, they will always try to run. If the Euler files are != than 2 everything indicates the topology is wrong. 

Do you see any outputs in the Mesh/PostProcess folder? Are there any postprocessed segmentations?


Thank you!
Beatriz

Hi, Beatriz

Thank you so much for your reply! Sorry that I didn't see your reply earlier and I nearly gave up on using SPHARM. Seeing your reply has given me new hope :D.
The Mesh/PostProcess folder is empty, and there's incomplete (I believe) outputs in the Mesh/SPHARM folder:
groupA_01_hippo_pp_surfMedialAxisScalars.csv
groupA_01_hippo_pp_surf_medialMeshArea.txt
groupA_01_hippo_pp_surf_medialMeshPartialArea.txt
groupA_01_hippo_pp_surf_medialMeshPartialRadius.txt
groupA_01_hippo_pp_surf_medialMeshRadius.txt
groupA_01_hippo_pp_surf_paraPhi.txt
groupA_01_hippo_pp_surf_paraTheta.txt
groupA_01_hippo_pp_surf_para.vtk
groupA_01_hippo_pp_surfSPHARM.coef
groupA_01_hippo_pp_surfSPHARM_ellalign.coef
groupA_01_hippo_pp_surfSPHARM_ellalign.vtk
groupA_01_hippo_pp_surfSPHARMMedialAxis.vtk
groupA_01_hippo_pp_surfSPHARMMedialMesh.vtk
groupA_01_hippo_pp_surfSPHARM_procalign.vtk
groupA_01_hippo_pp_surfSPHARM.vtk
groupA_02_hippo_pp_surfMedialAxisScalars.csv
groupA_02_hippo_pp_surf_medialMeshArea.txt
groupA_02_hippo_pp_surf_medialMeshPartialArea.txt
groupA_02_hippo_pp_surf_medialMeshPartialRadius.txt
groupA_02_hippo_pp_surf_medialMeshRadius.txt
groupA_02_hippo_pp_surf_paraPhi.txt
groupA_02_hippo_pp_surf_paraTheta.txt
groupA_02_hippo_pp_surf_para.vtk
groupA_02_hippo_pp_surfSPHARM.coef
groupA_02_hippo_pp_surfSPHARM_ellalign.coef
groupA_02_hippo_pp_surfSPHARM_ellalign.vtk
groupA_02_hippo_pp_surfSPHARMMedialAxis.vtk
groupA_02_hippo_pp_surfSPHARMMedialMesh.vtk
groupA_02_hippo_pp_surfSPHARM_procalign.vtk
groupA_02_hippo_pp_surfSPHARM.vtk
groupB_01_hippo_pp_surfMedialAxisScalars.csv
groupB_01_hippo_pp_surf_medialMeshArea.txt
groupB_01_hippo_pp_surf_medialMeshPartialArea.txt
groupB_01_hippo_pp_surf_medialMeshPartialRadius.txt
groupB_01_hippo_pp_surf_medialMeshRadius.txt
groupB_01_hippo_pp_surf_paraPhi.txt
groupB_01_hippo_pp_surf_paraTheta.txt
groupB_01_hippo_pp_surf_para.vtk
groupB_01_hippo_pp_surfSPHARM.coef
groupB_01_hippo_pp_surfSPHARM_ellalign.coef
groupB_01_hippo_pp_surfSPHARM_ellalign.vtk
groupB_01_hippo_pp_surfSPHARMMedialAxis.vtk
groupB_01_hippo_pp_surfSPHARMMedialMesh.vtk
groupB_01_hippo_pp_surfSPHARM_procalign.vtk
groupB_01_hippo_pp_surfSPHARM.vtk
groupB_02_hippo_pp_surfMedialAxisScalars.csv
groupB_02_hippo_pp_surf_medialMeshArea.txt
groupB_02_hippo_pp_surf_medialMeshPartialArea.txt
groupB_02_hippo_pp_surf_medialMeshPartialRadius.txt
groupB_02_hippo_pp_surf_medialMeshRadius.txt
groupB_02_hippo_pp_surf_paraPhi.txt
groupB_02_hippo_pp_surf_paraTheta.txt
groupB_02_hippo_pp_surf_para.vtk
groupB_02_hippo_pp_surfSPHARM.coef
groupB_02_hippo_pp_surfSPHARM_ellalign.coef
groupB_02_hippo_pp_surfSPHARM_ellalign.vtk
groupB_02_hippo_pp_surfSPHARMMedialAxis.vtk
groupB_02_hippo_pp_surfSPHARMMedialMesh.vtk
groupB_02_hippo_pp_surfSPHARM_procalign.vtk
groupB_02_hippo_pp_surfSPHARM.vtk

I only had 2 subjects in this analysis. Thanks in advance for your help!

Best,
Yifan

Hi Yifan,


I see. It does not make any sense that Mesh/PostProcess is empty and MEsh/SPHARM has results. The second depends on the first.
Could you please create a completely new output folder and re-run the whole module? Also, what operating system and version of SPHARM are you using?


Thank you,
Beatriz

Hi, Beatriz

I downloaded again the sample dataset (ShapeAnalysis_Data_Example.zip from 2010-05-20) and ran the analysis on the first files in each group. This time I have no outputs in the EulerFiles folder, no outputs in the Mesh/PostProcess, still outputs in the Mesh/SPHARM folder (attached).
I'm using a Ubuntu 12.4 LTS, and SPHARM as the Slicer extension, and Slicer 4.5.0-1.
Thanks so much for your help!

Best,
Yifan

Hi Yifan

I see, that is indeed weird.
Do these files contain any information? Can you visualize them?
Thanks!

Beatriz