Hi All,

I am new to spharm and am a bit confused with my output, I hope you can help.

I am using the using the shape analysis module in Slicer3. I have followed the tutorial "TutorialContest_ShapeAnalysisModule_2011". The program seems to have created all my outputs as specified here http://www.nitrc.org/plugins/mwiki/index... except the 3 MRML files.

The status on the Slicer GUI says: completed with errors

Is there some way to tell what the error was and how I can fix it?

Thanks
Cathy

Hi Cathy, welcome!


When the MRML scene hasnt been created there are several things you can test:

1) Do you have all the output files associated to all the input data? Even if only one is missing your MRML scene wont create.
2) Is your MeshMath binary working? i.e. when you type 'MeshMath --help', do you get a help message prompted?


Let me know about the outcomes of these simple tests, we will try to troubleshoot your problem.
Regards,

BEATRIZ

Hi Beatriz,

Thanks for the reply. So, I just re-ran the analysis with fewer subjects to make troubleshooting easier (3 patients and 3 controls). This time the slicer GUI says the status is completed but the MRML files still did not create.

1)I've checked and all the output data has been created for all the input files and I can view them in Slicer using "File -> add data .." I opened the files created in Mesh/SPHARM/
2) I also typed MeshMath --help and I get the help message prompt so seems to be working.

Any other suggestions greatly appreciated!!

Thanks,
Cathy

Hi Cathy,


Can you look into the Slicer error message you get when you do not obtain any mrml outputs?
Right lower corner, you should see an red circle icon with a white cross on it in the Slicer graphic user interface.
Could you copy and paste the outputs you get from the module?


Thanks!
BEATRIZ

Hi Beatriz,

Here is the full output from the Slicer including the error message pasted below. Hope you can help! Cathy :

-------------------------------------------------------------------------------------------

Type: Information
Time: Mon Nov 21 14:25:33 2011
Description: Shape Analysis Module completed without errors


Type: Error
Time: Mon Nov 21 14:25:33 2011
Description: ERROR: In /build/buildd/slicer-3.6.3~svn16592/Modules/CommandLineModule/vtkCommandLineModuleLogic.cxx, line 1499
vtkCommandLineModuleLogic (0x6c194c0): Shape Analysis Module standard error:

Error: Could not run CreateMRML:
No such file or directory
Error: Could not run CreateMRML:
No such file or directory
Error: Could not run CreateMRML:
No such file or directory
Error: Could not run CreateMRML:
No such file or directory
Error: Could not run CreateMRML:
No such file or directory
Error: Could not run CreateMRML:
No such file or directory




Type: Information
Time: Mon Nov 21 14:25:33 2011
Description: Shape Analysis Module standard output:

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


Computing ShapeAnalysisModule...

/home/dara/CS/spharm/FEP_Caud_Left_test/output
/home/dara/CS/spharm/FEP_Caud_Left_test/output/
/home/dara/CS/spharm/FEP_Caud_Left_test/output/ShapeAnalysisModule.bms
Number of Datas: 6
    Executing BatchMake...


Case:/home/dara/CS/spharm/FEP_Caud_Left_test/orig/cL_003MC.gipl

Doing Post Processing
Status: Start SegPostProcessCLP /home/dara/CS/spharm/FEP_Caud_Left_test/orig/cL_003MC.gipl /home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/PostProcess/cL_003MC_pp.gipl.gz --space 0.5,0.5,0.5
 run: 'SegPostProcessCLP' '''/home/dara/CS/spharm/FEP_Caud_Left_test/orig/cL_003MC.gipl' '/home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/PostProcess/cL_003MC_pp.gipl.gz' --space '0.5,0.5,0.5'''
Status: Finish: Execution time 4504ms

Doing GenParaMesh
Status: Start GenParaMeshCLP --EulerFile --outEulerName /home/dara/CS/spharm/FEP_Caud_Left_test/output/EulerFiles/cL_003MC_euler.txt --iter 1000 --label 1 /home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/PostProcess/cL_003MC_pp.gipl.gz /home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/cL_003MC_pp_para.vtk /home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/cL_003MC_pp_surf.vtk
 run: 'GenParaMeshCLP' ''--EulerFile --outEulerName '/home/dara/CS/spharm/FEP_Caud_Left_test/output/EulerFiles/cL_003MC_euler.txt' --iter '1000' --label '1' '/home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/PostProcess/cL_003MC_pp.gipl.gz' '/home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/cL_003MC_pp_para.vtk' '/home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/cL_003MC_pp_surf.vtk'''
Status: Finish: Execution time 36312ms

Doing ParaToSPHARMMesh
Creating Template


Status: Start ParaToSPHARMMeshCLP /home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/cL_003MC_pp_para.vtk /home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/cL_003MC_pp_surf.vtk /home/dara/CS/spharm/FEP_Caud_Left_test/output/Template/cL_003MC_pp_surf --subdivLevel 10 --spharmDegree 15 --FinalFlip 0 --paraOut
 run: 'ParaToSPHARMMeshCLP' '''/home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/cL_003MC_pp_para.vtk' '/home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/cL_003MC_pp_surf.vtk' '/home/dara/CS/spharm/FEP_Caud_Left_test/output/Template/cL_003MC_pp_surf' --subdivLevel '10' --spharmDegree '15' --FinalFlip '0' --paraOut''
Status: Finish: Execution time 3601ms

regTemplate: cL_003MC_pp_surfSPHARM.vtk
flipTemplate: cL_003MC_pp_surfSPHARM.coef

Status: Start ParaToSPHARMMeshCLP /home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/cL_003MC_pp_para.vtk /home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/cL_003MC_pp_surf.vtk /home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/cL_003MC_pp_surf --regTemplateFileOn --regTemplate /home/dara/CS/spharm/FEP_Caud_Left_test/output/Template/cL_003MC_pp_surfSPHARM.vtk --flipTemplateOn --flipTemplate /home/dara/CS/spharm/FEP_Caud_Left_test/output/Template/cL_003MC_pp_surfSPHARM.coef --subdivLevel 10 --spharmDegree 15 --FinalFlip 0 --paraOut
 run: 'ParaToSPHARMMeshCLP' '''/home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/cL_003MC_pp_para.vtk' '/home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/cL_003MC_pp_surf.vtk' '/home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/cL_003MC_pp_surf' --regTemplateFileOn --regTemplate '/home/dara/CS/spharm/FEP_Caud_Left_test/output/Template/cL_003MC_pp_surfSPHARM.vtk' --flipTemplateOn --flipTemplate '/home/dara/CS/spharm/FEP_Caud_Left_test/output/Template/cL_003MC_pp_surfSPHARM.coef' --subdivLevel '10' --spharmDegree '15' --FinalFlip '0' --paraOut''
Status: Finish: Execution time 4502ms
/home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/cL_003MC_pp_surf_paraPhiHalf.txt

Case:/home/dara/CS/spharm/FEP_Caud_Left_test/orig/fL_133AW.gipl

Doing Post Processing
Status: Start SegPostProcessCLP /home/dara/CS/spharm/FEP_Caud_Left_test/orig/fL_133AW.gipl /home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/PostProcess/fL_133AW_pp.gipl.gz --space 0.5,0.5,0.5
 run: 'SegPostProcessCLP' '''/home/dara/CS/spharm/FEP_Caud_Left_test/orig/fL_133AW.gipl' '/home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/PostProcess/fL_133AW_pp.gipl.gz' --space '0.5,0.5,0.5'''
Status: Finish: Execution time 4503ms

Doing GenParaMesh
Status: Start GenParaMeshCLP --EulerFile --outEulerName /home/dara/CS/spharm/FEP_Caud_Left_test/output/EulerFiles/fL_133AW_euler.txt --iter 1000 --label 1 /home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/PostProcess/fL_133AW_pp.gipl.gz /home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/fL_133AW_pp_para.vtk /home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/fL_133AW_pp_surf.vtk
 run: 'GenParaMeshCLP' ''--EulerFile --outEulerName '/home/dara/CS/spharm/FEP_Caud_Left_test/output/EulerFiles/fL_133AW_euler.txt' --iter '1000' --label '1' '/home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/PostProcess/fL_133AW_pp.gipl.gz' '/home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/fL_133AW_pp_para.vtk' '/home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/fL_133AW_pp_surf.vtk'''
Status: Finish: Execution time 31210ms

Doing ParaToSPHARMMesh

regTemplate: cL_003MC_pp_surfSPHARM.vtk
flipTemplate: cL_003MC_pp_surfSPHARM.coef

Status: Start ParaToSPHARMMeshCLP /home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/fL_133AW_pp_para.vtk /home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/fL_133AW_pp_surf.vtk /home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/fL_133AW_pp_surf --regTemplateFileOn --regTemplate /home/dara/CS/spharm/FEP_Caud_Left_test/output/Template/cL_003MC_pp_surfSPHARM.vtk --flipTemplateOn --flipTemplate /home/dara/CS/spharm/FEP_Caud_Left_test/output/Template/cL_003MC_pp_surfSPHARM.coef --subdivLevel 10 --spharmDegree 15 --FinalFlip 0 --paraOut
 run: 'ParaToSPHARMMeshCLP' '''/home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/fL_133AW_pp_para.vtk' '/home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/fL_133AW_pp_surf.vtk' '/home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/fL_133AW_pp_surf' --regTemplateFileOn --regTemplate '/home/dara/CS/spharm/FEP_Caud_Left_test/output/Template/cL_003MC_pp_surfSPHARM.vtk' --flipTemplateOn --flipTemplate '/home/dara/CS/spharm/FEP_Caud_Left_test/output/Template/cL_003MC_pp_surfSPHARM.coef' --subdivLevel '10' --spharmDegree '15' --FinalFlip '0' --paraOut''
Status: Finish: Execution time 4201ms
/home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/fL_133AW_pp_surf_paraPhiHalf.txt

Case:/home/dara/CS/spharm/FEP_Caud_Left_test/orig/cL_030GOC.gipl

Doing Post Processing
Status: Start SegPostProcessCLP /home/dara/CS/spharm/FEP_Caud_Left_test/orig/cL_030GOC.gipl /home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/PostProcess/cL_030GOC_pp.gipl.gz --space 0.5,0.5,0.5
 run: 'SegPostProcessCLP' '''/home/dara/CS/spharm/FEP_Caud_Left_test/orig/cL_030GOC.gipl' '/home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/PostProcess/cL_030GOC_pp.gipl.gz' --space '0.5,0.5,0.5'''
Status: Finish: Execution time 4514ms

Doing GenParaMesh
Status: Start GenParaMeshCLP --EulerFile --outEulerName /home/dara/CS/spharm/FEP_Caud_Left_test/output/EulerFiles/cL_030GOC_euler.txt --iter 1000 --label 1 /home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/PostProcess/cL_030GOC_pp.gipl.gz /home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/cL_030GOC_pp_para.vtk /home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/cL_030GOC_pp_surf.vtk
 run: 'GenParaMeshCLP' ''--EulerFile --outEulerName '/home/dara/CS/spharm/FEP_Caud_Left_test/output/EulerFiles/cL_030GOC_euler.txt' --iter '1000' --label '1' '/home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/PostProcess/cL_030GOC_pp.gipl.gz' '/home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/cL_030GOC_pp_para.vtk' '/home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/cL_030GOC_pp_surf.vtk'''
Status: Finish: Execution time 59118ms

Doing ParaToSPHARMMesh

regTemplate: cL_003MC_pp_surfSPHARM.vtk
flipTemplate: cL_003MC_pp_surfSPHARM.coef

Status: Start ParaToSPHARMMeshCLP /home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/cL_030GOC_pp_para.vtk /home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/cL_030GOC_pp_surf.vtk /home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/cL_030GOC_pp_surf --regTemplateFileOn --regTemplate /home/dara/CS/spharm/FEP_Caud_Left_test/output/Template/cL_003MC_pp_surfSPHARM.vtk --flipTemplateOn --flipTemplate /home/dara/CS/spharm/FEP_Caud_Left_test/output/Template/cL_003MC_pp_surfSPHARM.coef --subdivLevel 10 --spharmDegree 15 --FinalFlip 0 --paraOut
 run: 'ParaToSPHARMMeshCLP' '''/home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/cL_030GOC_pp_para.vtk' '/home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/cL_030GOC_pp_surf.vtk' '/home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/cL_030GOC_pp_surf' --regTemplateFileOn --regTemplate '/home/dara/CS/spharm/FEP_Caud_Left_test/output/Template/cL_003MC_pp_surfSPHARM.vtk' --flipTemplateOn --flipTemplate '/home/dara/CS/spharm/FEP_Caud_Left_test/output/Template/cL_003MC_pp_surfSPHARM.coef' --subdivLevel '10' --spharmDegree '15' --FinalFlip '0' --paraOut''
Status: Finish: Execution time 4802ms
/home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/cL_030GOC_pp_surf_paraPhiHalf.txt

Case:/home/dara/CS/spharm/FEP_Caud_Left_test/orig/cL_018AM.gipl

Doing Post Processing
Status: Start SegPostProcessCLP /home/dara/CS/spharm/FEP_Caud_Left_test/orig/cL_018AM.gipl /home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/PostProcess/cL_018AM_pp.gipl.gz --space 0.5,0.5,0.5
 run: 'SegPostProcessCLP' '''/home/dara/CS/spharm/FEP_Caud_Left_test/orig/cL_018AM.gipl' '/home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/PostProcess/cL_018AM_pp.gipl.gz' --space '0.5,0.5,0.5'''
Status: Finish: Execution time 4202ms

Doing GenParaMesh
Status: Start GenParaMeshCLP --EulerFile --outEulerName /home/dara/CS/spharm/FEP_Caud_Left_test/output/EulerFiles/cL_018AM_euler.txt --iter 1000 --label 1 /home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/PostProcess/cL_018AM_pp.gipl.gz /home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/cL_018AM_pp_para.vtk /home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/cL_018AM_pp_surf.vtk
 run: 'GenParaMeshCLP' ''--EulerFile --outEulerName '/home/dara/CS/spharm/FEP_Caud_Left_test/output/EulerFiles/cL_018AM_euler.txt' --iter '1000' --label '1' '/home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/PostProcess/cL_018AM_pp.gipl.gz' '/home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/cL_018AM_pp_para.vtk' '/home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/cL_018AM_pp_surf.vtk'''
Status: Finish: Execution time 42314ms

Doing ParaToSPHARMMesh

regTemplate: cL_003MC_pp_surfSPHARM.vtk
flipTemplate: cL_003MC_pp_surfSPHARM.coef

Status: Start ParaToSPHARMMeshCLP /home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/cL_018AM_pp_para.vtk /home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/cL_018AM_pp_surf.vtk /home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/cL_018AM_pp_surf --regTemplateFileOn --regTemplate /home/dara/CS/spharm/FEP_Caud_Left_test/output/Template/cL_003MC_pp_surfSPHARM.vtk --flipTemplateOn --flipTemplate /home/dara/CS/spharm/FEP_Caud_Left_test/output/Template/cL_003MC_pp_surfSPHARM.coef --subdivLevel 10 --spharmDegree 15 --FinalFlip 0 --paraOut
 run: 'ParaToSPHARMMeshCLP' '''/home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/cL_018AM_pp_para.vtk' '/home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/cL_018AM_pp_surf.vtk' '/home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/cL_018AM_pp_surf' --regTemplateFileOn --regTemplate '/home/dara/CS/spharm/FEP_Caud_Left_test/output/Template/cL_003MC_pp_surfSPHARM.vtk' --flipTemplateOn --flipTemplate '/home/dara/CS/spharm/FEP_Caud_Left_test/output/Template/cL_003MC_pp_surfSPHARM.coef' --subdivLevel '10' --spharmDegree '15' --FinalFlip '0' --paraOut''
Status: Finish: Execution time 4502ms
/home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/cL_018AM_pp_surf_paraPhiHalf.txt

Case:/home/dara/CS/spharm/FEP_Caud_Left_test/orig/fL_027DK.gipl

Doing Post Processing
Status: Start SegPostProcessCLP /home/dara/CS/spharm/FEP_Caud_Left_test/orig/fL_027DK.gipl /home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/PostProcess/fL_027DK_pp.gipl.gz --space 0.5,0.5,0.5
 run: 'SegPostProcessCLP' '''/home/dara/CS/spharm/FEP_Caud_Left_test/orig/fL_027DK.gipl' '/home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/PostProcess/fL_027DK_pp.gipl.gz' --space '0.5,0.5,0.5'''
Status: Finish: Execution time 4502ms

Doing GenParaMesh
Status: Start GenParaMeshCLP --EulerFile --outEulerName /home/dara/CS/spharm/FEP_Caud_Left_test/output/EulerFiles/fL_027DK_euler.txt --iter 1000 --label 1 /home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/PostProcess/fL_027DK_pp.gipl.gz /home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/fL_027DK_pp_para.vtk /home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/fL_027DK_pp_surf.vtk
 run: 'GenParaMeshCLP' ''--EulerFile --outEulerName '/home/dara/CS/spharm/FEP_Caud_Left_test/output/EulerFiles/fL_027DK_euler.txt' --iter '1000' --label '1' '/home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/PostProcess/fL_027DK_pp.gipl.gz' '/home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/fL_027DK_pp_para.vtk' '/home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/fL_027DK_pp_surf.vtk'''
Status: Finish: Execution time 51617ms

Doing ParaToSPHARMMesh

regTemplate: cL_003MC_pp_surfSPHARM.vtk
flipTemplate: cL_003MC_pp_surfSPHARM.coef

Status: Start ParaToSPHARMMeshCLP /home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/fL_027DK_pp_para.vtk /home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/fL_027DK_pp_surf.vtk /home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/fL_027DK_pp_surf --regTemplateFileOn --regTemplate /home/dara/CS/spharm/FEP_Caud_Left_test/output/Template/cL_003MC_pp_surfSPHARM.vtk --flipTemplateOn --flipTemplate /home/dara/CS/spharm/FEP_Caud_Left_test/output/Template/cL_003MC_pp_surfSPHARM.coef --subdivLevel 10 --spharmDegree 15 --FinalFlip 0 --paraOut
 run: 'ParaToSPHARMMeshCLP' '''/home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/fL_027DK_pp_para.vtk' '/home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/fL_027DK_pp_surf.vtk' '/home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/fL_027DK_pp_surf' --regTemplateFileOn --regTemplate '/home/dara/CS/spharm/FEP_Caud_Left_test/output/Template/cL_003MC_pp_surfSPHARM.vtk' --flipTemplateOn --flipTemplate '/home/dara/CS/spharm/FEP_Caud_Left_test/output/Template/cL_003MC_pp_surfSPHARM.coef' --subdivLevel '10' --spharmDegree '15' --FinalFlip '0' --paraOut''
Status: Finish: Execution time 4502ms
/home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/fL_027DK_pp_surf_paraPhiHalf.txt

Case:/home/dara/CS/spharm/FEP_Caud_Left_test/orig/fL_035MH.gipl

Doing Post Processing
Status: Start SegPostProcessCLP /home/dara/CS/spharm/FEP_Caud_Left_test/orig/fL_035MH.gipl /home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/PostProcess/fL_035MH_pp.gipl.gz --space 0.5,0.5,0.5
 run: 'SegPostProcessCLP' '''/home/dara/CS/spharm/FEP_Caud_Left_test/orig/fL_035MH.gipl' '/home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/PostProcess/fL_035MH_pp.gipl.gz' --space '0.5,0.5,0.5'''
Status: Finish: Execution time 4507ms

Doing GenParaMesh
Status: Start GenParaMeshCLP --EulerFile --outEulerName /home/dara/CS/spharm/FEP_Caud_Left_test/output/EulerFiles/fL_035MH_euler.txt --iter 1000 --label 1 /home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/PostProcess/fL_035MH_pp.gipl.gz /home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/fL_035MH_pp_para.vtk /home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/fL_035MH_pp_surf.vtk
 run: 'GenParaMeshCLP' ''--EulerFile --outEulerName '/home/dara/CS/spharm/FEP_Caud_Left_test/output/EulerFiles/fL_035MH_euler.txt' --iter '1000' --label '1' '/home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/PostProcess/fL_035MH_pp.gipl.gz' '/home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/fL_035MH_pp_para.vtk' '/home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/fL_035MH_pp_surf.vtk'''
Status: Finish: Execution time 51616ms

Doing ParaToSPHARMMesh

regTemplate: cL_003MC_pp_surfSPHARM.vtk
flipTemplate: cL_003MC_pp_surfSPHARM.coef

Status: Start ParaToSPHARMMeshCLP /home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/fL_035MH_pp_para.vtk /home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/fL_035MH_pp_surf.vtk /home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/fL_035MH_pp_surf --regTemplateFileOn --regTemplate /home/dara/CS/spharm/FEP_Caud_Left_test/output/Template/cL_003MC_pp_surfSPHARM.vtk --flipTemplateOn --flipTemplate /home/dara/CS/spharm/FEP_Caud_Left_test/output/Template/cL_003MC_pp_surfSPHARM.coef --subdivLevel 10 --spharmDegree 15 --FinalFlip 0 --paraOut
 run: 'ParaToSPHARMMeshCLP' '''/home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/fL_035MH_pp_para.vtk' '/home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/fL_035MH_pp_surf.vtk' '/home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/fL_035MH_pp_surf' --regTemplateFileOn --regTemplate '/home/dara/CS/spharm/FEP_Caud_Left_test/output/Template/cL_003MC_pp_surfSPHARM.vtk' --flipTemplateOn --flipTemplate '/home/dara/CS/spharm/FEP_Caud_Left_test/output/Template/cL_003MC_pp_surfSPHARM.coef' --subdivLevel '10' --spharmDegree '15' --FinalFlip '0' --paraOut''
Status: Finish: Execution time 4801ms
/home/dara/CS/spharm/FEP_Caud_Left_test/output/Mesh/SPHARM/fL_035MH_pp_surf_paraPhiHalf.txt

    Executing BatchMake: Done!

/home/dara/CS/spharm/FEP_Caud_Left_test/output/ShapeAnalysisModule.bms


Execute Meshmath...

meshmath template
mrml /home/dara/CS/spharm/FEP_Caud_Left_test/output/MRML/ShapeAnalysisModuleMRMLscene_allVTK_Phi.mrml

Error: Could not run CreateMRML:
No such file or directory
mrml /home/dara/CS/spharm/FEP_Caud_Left_test/output/MRML/ShapeAnalysisModuleMRMLscene_allVTK_Theta.mrml

Error: Could not run CreateMRML:
No such file or directory
mrml /home/dara/CS/spharm/FEP_Caud_Left_test/output/MRML/Ellalign/ShapeAnalysisModuleMRMLscene_allVTK_Phi.mrml

Error: Could not run CreateMRML:
No such file or directory
mrml /home/dara/CS/spharm/FEP_Caud_Left_test/output/MRML/Ellalign/ShapeAnalysisModuleMRMLscene_allVTK_Theta.mrml

Error: Could not run CreateMRML:
No such file or directory
mrml /home/dara/CS/spharm/FEP_Caud_Left_test/output/MRML/Procalign/ShapeAnalysisModuleMRMLscene_allVTK_Phi.mrml

Error: Could not run CreateMRML:
No such file or directory
mrml /home/dara/CS/spharm/FEP_Caud_Left_test/output/MRML/Procalign/ShapeAnalysisModuleMRMLscene_allVTK_Theta.mrml

Error: Could not run CreateMRML:
No such file or directory


Type: Information
Time: Mon Nov 21 14:20:01 2011
Description: Shape Analysis Module command line:

/usr/local/spharm/ShapeAnalysisModule --sx 0.5 --sy 0.5 --sz 0.5 --label 1 --NumberofIterations 1000 --SubdivLevelValue 10 --SPHARMDegreeValue 15 --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/dara/CS/spharm/FEP_Caud_Left_test/FEP_Left_Caud.csv /home/dara/CS/spharm/FEP_Caud_Left_test/output


Type: Information
Time: Mon Nov 21 14:20:01 2011
Description: CommandLineModule

Type: Information
Time: Mon Nov 21 14:20:01 2011
Description: /usr/local/spharm/ShapeAnalysisModule

Type: Information
Time: Mon Nov 21 14:20:01 2011
Description: Found CommandLine Module, target is

Hi Cathy,


Just as an update, we have found a bug in our code thanks to your inquiry. We are working in solving this as soon as possible, but in the meantime you should have all the inputs computed as listed here http://www.nitrc.org/plugins/mwiki/index.php/spharm-pdm:Pipeline_Doc_V1.9#Output_file_description_for_ShapeAnalysisModule to continue your analysis. The only problem we have located has to do with MRML scenes.


Thanks a lot for your questions and your indirect help to improve our module!
Regards,

BEATRIZ

Hi Beatriz,

Great, thanks for letting me know, glad I could help (indirectly!).
I would appreciate if you could let me know when this bug has been fixed so I can continue the analysis.

All the best,
Cathy