Dear all spharm-pdm users,
For the above my problem (error about cannot find the bms file), I solved it.

First, I found that the bms file were generated at the same folder in where the Slicer3 were run in the command line, not in GUI double clicking.
For example, when I run the Slicer3 at /usr/local/bin, the bms were generated at /usr/local/bin.
So, I realized that I have to run Slicer3 in the BatchMake_Applications folder.

However, other error were occurred when I run Slicer3.
I attached the error log. the error is about the XML parsing.
I think it is not the run time error of ShapeAnaysisModule. It's just about the running of Slicer3 in commandline.

The more serious problem for me is the following error messages.
From the below log, I guess that there's no problem to process 1) input data, 2) post processing, 3) genparamesh,
4) paratospharmmesh...

In actual,
"Execute Meshmath... Error: Could not run MeshMath" would be a problem I think.

Please give me any advice or tips. Thanks.

-----------------------------------------------------------------------------
------ Shape Analysis Module start -----


Computing ShapeAnalysisModule...

/usr/local/bin/spharm/ShapeAnalysisTest/ShapeAnalysis_Results
/usr/local/bin/spharm/ShapeAnalysisTest/ShapeAnalysis_Results/
192

ShapeAnalysisModule_id11026.bms
ShapeAnalysisModule_id11026.bms
Number of Datas: 1
Executing BatchMake...


Case:/usr/local/bin/TutorialData/origData/groupA_01_hippo.gipl.gz

Doing Post Processing
Status: Start SegPostProcessCLP /usr/local/bin/TutorialData/origData/groupA_01_hippo.gipl.gz /usr/local/bin/spharm/ShapeAnalysisTest/ShapeAnalysis_Results/Mesh/PostProcess/groupA_01_hippo_pp.gipl.gz --space 0.5,0.5,0.5
run: 'SegPostProcessCLP' '''/usr/local/bin/TutorialData/origData/groupA_01_hippo.gipl.gz' '/usr/local/bin/spharm/ShapeAnalysisTest/ShapeAnalysis_Results/Mesh/PostProcess/groupA_01_hippo_pp.gipl.gz' --space '0.5,0.5,0.5'''
Status: Finish: Execution time 300ms

Doing GenParaMesh
Status: Start GenParaMeshCLP --EulerFile --outEulerName /usr/local/bin/spharm/ShapeAnalysisTest/ShapeAnalysis_Results/EulerFiles/groupA_01_hippo_euler.txt --iter 10 --label 1 /usr/local/bin/spharm/ShapeAnalysisTest/ShapeAnalysis_Results/Mesh/PostProcess/groupA_01_hippo_pp.gipl.gz /usr/local/bin/spharm/ShapeAnalysisTest/ShapeAnalysis_Results/Mesh/SPHARM/groupA_01_hippo_pp_para.vtk /usr/local/bin/spharm/ShapeAnalysisTest/ShapeAnalysis_Results/Mesh/SPHARM/groupA_01_hippo_pp_surf.vtk
run: 'GenParaMeshCLP' ''--EulerFile --outEulerName '/usr/local/bin/spharm/ShapeAnalysisTest/ShapeAnalysis_Results/EulerFiles/groupA_01_hippo_euler.txt' --iter '10' --label '1' '/usr/local/bin/spharm/ShapeAnalysisTest/ShapeAnalysis_Results/Mesh/PostProcess/groupA_01_hippo_pp.gipl.gz' '/usr/local/bin/spharm/ShapeAnalysisTest/ShapeAnalysis_Results/Mesh/SPHARM/groupA_01_hippo_pp_para.vtk' '/usr/local/bin/spharm/ShapeAnalysisTest/ShapeAnalysis_Results/Mesh/SPHARM/groupA_01_hippo_pp_surf.vtk'''
Status: Finish: Execution time 300ms

Doing ParaToSPHARMMesh
Creating Template


Status: Start ParaToSPHARMMeshCLP /usr/local/bin/spharm/ShapeAnalysisTest/ShapeAnalysis_Results/Mesh/SPHARM/groupA_01_hippo_pp_para.vtk /usr/local/bin/spharm/ShapeAnalysisTest/ShapeAnalysis_Results/Mesh/SPHARM/groupA_01_hippo_pp_surf.vtk /usr/local/bin/spharm/ShapeAnalysisTest/ShapeAnalysis_Results/Template/groupA_01_hippo_pp_surf --subdivLevel 10 --spharmDegree 15 --FinalFlip 0 --paraOut
run: 'ParaToSPHARMMeshCLP' '''/usr/local/bin/spharm/ShapeAnalysisTest/ShapeAnalysis_Results/Mesh/SPHARM/groupA_01_hippo_pp_para.vtk' '/usr/local/bin/spharm/ShapeAnalysisTest/ShapeAnalysis_Results/Mesh/SPHARM/groupA_01_hippo_pp_surf.vtk' '/usr/local/bin/spharm/ShapeAnalysisTest/ShapeAnalysis_Results/Template/groupA_01_hippo_pp_surf' --subdivLevel '10' --spharmDegree '15' --FinalFlip '0' --paraOut''
Status: Finish: Execution time 301ms

regTemplate:
flipTemplate:

Status: Start ParaToSPHARMMeshCLP /usr/local/bin/spharm/ShapeAnalysisTest/ShapeAnalysis_Results/Mesh/SPHARM/groupA_01_hippo_pp_para.vtk /usr/local/bin/spharm/ShapeAnalysisTest/ShapeAnalysis_Results/Mesh/SPHARM/groupA_01_hippo_pp_surf.vtk /usr/local/bin/spharm/ShapeAnalysisTest/ShapeAnalysis_Results/Mesh/SPHARM/groupA_01_hippo_pp_surf --regTemplateFileOn --regTemplate /usr/local/bin/spharm/ShapeAnalysisTest/ShapeAnalysis_Results/Template/ --flipTemplateOn --flipTemplate /usr/local/bin/spharm/ShapeAnalysisTest/ShapeAnalysis_Results/Template/ --subdivLevel 10 --spharmDegree 15 --FinalFlip 0 --paraOut
run: 'ParaToSPHARMMeshCLP' '''/usr/local/bin/spharm/ShapeAnalysisTest/ShapeAnalysis_Results/Mesh/SPHARM/groupA_01_hippo_pp_para.vtk' '/usr/local/bin/spharm/ShapeAnalysisTest/ShapeAnalysis_Results/Mesh/SPHARM/groupA_01_hippo_pp_surf.vtk' '/usr/local/bin/spharm/ShapeAnalysisTest/ShapeAnalysis_Results/Mesh/SPHARM/groupA_01_hippo_pp_surf' --regTemplateFileOn --regTemplate '/usr/local/bin/spharm/ShapeAnalysisTest/ShapeAnalysis_Results/Template/' --flipTemplateOn --flipTemplate '/usr/local/bin/spharm/ShapeAnalysisTest/ShapeAnalysis_Results/Template/' --subdivLevel '10' --spharmDegree '15' --FinalFlip '0' --paraOut''
Status: Finish: Execution time 301ms

Executing BatchMake: Done!

ShapeAnalysisModule_id11026.bms


Execute Meshmath...

Error: Could not run MeshMath:
No such file or directory
Error: Could not run MeshMath:
No such file or directory
Error: Could not run MeshMath:
No such file or directory
Error: Could not run MeshMath:
No such file or directory
Error: Could not run MeshMath:
No such file or directory
Error: Could not run MeshMath:
No such file or directory
meshmath template
mrml /usr/local/bin/spharm/ShapeAnalysisTest/ShapeAnalysis_Results/MRML/ShapeAnalysisModuleMRMLscene_allVTK_Phi.mrml
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