[fsl@fslvm6 ~]$ ShapeAnalysisModule --sx 0.5 --sy 0.5 --sz 0.5 --label 1 --NumberofIterations 10 --SubdivLevelValue 10 --SPHARMDegreeValue 15 --columVolumeFile 0 --varX 10 --varY 10 --varZ 10 --regTemplate None --flipTemplate None --paraOutTemplate --noFlip --HorizontalGridPara 1 --VerticalGridPara 2 --DoParticlesCorrespondence --UseProcalign /home/fsl/Slicer-4.3.1-linux-amd64/SpharmInput/InputFile.csv /home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3/
------ Shape Analysis Module start -----


Computing ShapeAnalysisModule...

/home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3/
/home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//
/home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//ShapeAnalysisModule.bms
/home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//ShapeAnalysisModule.bms
Number of Datas: 4
	Executing BatchMake...


Case:/home/fsl/Slicer-4.3.1-linux-amd64/SpharmInput/origData/groupA_01_hippo.gipl.gz

Doing Post Processing
Status: Start SegPostProcessCLP /home/fsl/Slicer-4.3.1-linux-amd64/SpharmInput/origData/groupA_01_hippo.gipl.gz /home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/PostProcess/groupA_01_hippo_pp.gipl.gz --space 0.5,0.5,0.5
 run: 'SegPostProcessCLP' '''/home/fsl/Slicer-4.3.1-linux-amd64/SpharmInput/origData/groupA_01_hippo.gipl.gz' '/home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/PostProcess/groupA_01_hippo_pp.gipl.gz' --space '0.5,0.5,0.5'''
Status: Finish: Execution time 903ms

Doing GenParaMesh
Status: Start GenParaMeshCLP --EulerFile --outEulerName /home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//EulerFiles/groupA_01_hippo_euler.txt --iter 10 --label 1 /home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/PostProcess/groupA_01_hippo_pp.gipl.gz /home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/SPHARM/groupA_01_hippo_pp_para.vtk /home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/SPHARM/groupA_01_hippo_pp_surf.vtk
 run: 'GenParaMeshCLP' ''--EulerFile --outEulerName '/home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//EulerFiles/groupA_01_hippo_euler.txt' --iter '10' --label '1' '/home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/PostProcess/groupA_01_hippo_pp.gipl.gz' '/home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/SPHARM/groupA_01_hippo_pp_para.vtk' '/home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/SPHARM/groupA_01_hippo_pp_surf.vtk'''
Status: Finish: Execution time 6615ms

Doing ParaToSPHARMMesh
Creating Template


Status: Start ParaToSPHARMMeshCLP /home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/SPHARM/groupA_01_hippo_pp_para.vtk /home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/SPHARM/groupA_01_hippo_pp_surf.vtk /home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Template/groupA_01_hippo_pp_surf --subdivLevel 10 --spharmDegree 15 --FinalFlip 0 --paraOut --phiIteration 100 --thetaIteration 100 --medialMesh
 run: 'ParaToSPHARMMeshCLP' '''/home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/SPHARM/groupA_01_hippo_pp_para.vtk' '/home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/SPHARM/groupA_01_hippo_pp_surf.vtk' '/home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Template/groupA_01_hippo_pp_surf' --subdivLevel '10' --spharmDegree '15' --FinalFlip '0' --paraOut --phiIteration '100' --thetaIteration '100' --medialMesh''
Status: Finish: Execution time 6906ms

regTemplate: groupA_01_hippo_pp_surfSPHARM.vtk
flipTemplate: groupA_01_hippo_pp_surfSPHARM.coef

Status: Start ParaToSPHARMMeshCLP /home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/SPHARM/groupA_01_hippo_pp_para.vtk /home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/SPHARM/groupA_01_hippo_pp_surf.vtk /home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/SPHARM/groupA_01_hippo_pp_surf --regTemplateFileOn --regTemplate /home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Template/groupA_01_hippo_pp_surfSPHARM.vtk --flipTemplateOn --flipTemplate /home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Template/groupA_01_hippo_pp_surfSPHARM.coef --subdivLevel 10 --spharmDegree 15 --FinalFlip 0 --paraOut --phiIteration 100 --thetaIteration 100 --medialMesh
 run: 'ParaToSPHARMMeshCLP' '''/home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/SPHARM/groupA_01_hippo_pp_para.vtk' '/home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/SPHARM/groupA_01_hippo_pp_surf.vtk' '/home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/SPHARM/groupA_01_hippo_pp_surf' --regTemplateFileOn --regTemplate '/home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Template/groupA_01_hippo_pp_surfSPHARM.vtk' --flipTemplateOn --flipTemplate '/home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Template/groupA_01_hippo_pp_surfSPHARM.coef' --subdivLevel '10' --spharmDegree '15' --FinalFlip '0' --paraOut --phiIteration '100' --thetaIteration '100' --medialMesh''
Status: Finish: Execution time 7207ms
/home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/SPHARM/groupA_01_hippo_pp_surf_paraPhiHalf.txt

Case:/home/fsl/Slicer-4.3.1-linux-amd64/SpharmInput/origData/groupA_02_hippo.gipl.gz

Doing Post Processing
Status: Start SegPostProcessCLP /home/fsl/Slicer-4.3.1-linux-amd64/SpharmInput/origData/groupA_02_hippo.gipl.gz /home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/PostProcess/groupA_02_hippo_pp.gipl.gz --space 0.5,0.5,0.5
 run: 'SegPostProcessCLP' '''/home/fsl/Slicer-4.3.1-linux-amd64/SpharmInput/origData/groupA_02_hippo.gipl.gz' '/home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/PostProcess/groupA_02_hippo_pp.gipl.gz' --space '0.5,0.5,0.5'''
Status: Finish: Execution time 301ms

Doing GenParaMesh
Status: Start GenParaMeshCLP --EulerFile --outEulerName /home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//EulerFiles/groupA_02_hippo_euler.txt --iter 10 --label 1 /home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/PostProcess/groupA_02_hippo_pp.gipl.gz /home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/SPHARM/groupA_02_hippo_pp_para.vtk /home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/SPHARM/groupA_02_hippo_pp_surf.vtk
 run: 'GenParaMeshCLP' ''--EulerFile --outEulerName '/home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//EulerFiles/groupA_02_hippo_euler.txt' --iter '10' --label '1' '/home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/PostProcess/groupA_02_hippo_pp.gipl.gz' '/home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/SPHARM/groupA_02_hippo_pp_para.vtk' '/home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/SPHARM/groupA_02_hippo_pp_surf.vtk'''
Status: Finish: Execution time 4805ms

Doing ParaToSPHARMMesh

regTemplate: groupA_01_hippo_pp_surfSPHARM.vtk
flipTemplate: groupA_01_hippo_pp_surfSPHARM.coef

Status: Start ParaToSPHARMMeshCLP /home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/SPHARM/groupA_02_hippo_pp_para.vtk /home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/SPHARM/groupA_02_hippo_pp_surf.vtk /home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/SPHARM/groupA_02_hippo_pp_surf --regTemplateFileOn --regTemplate /home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Template/groupA_01_hippo_pp_surfSPHARM.vtk --flipTemplateOn --flipTemplate /home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Template/groupA_01_hippo_pp_surfSPHARM.coef --subdivLevel 10 --spharmDegree 15 --FinalFlip 0 --paraOut --phiIteration 100 --thetaIteration 100 --medialMesh
 run: 'ParaToSPHARMMeshCLP' '''/home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/SPHARM/groupA_02_hippo_pp_para.vtk' '/home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/SPHARM/groupA_02_hippo_pp_surf.vtk' '/home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/SPHARM/groupA_02_hippo_pp_surf' --regTemplateFileOn --regTemplate '/home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Template/groupA_01_hippo_pp_surfSPHARM.vtk' --flipTemplateOn --flipTemplate '/home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Template/groupA_01_hippo_pp_surfSPHARM.coef' --subdivLevel '10' --spharmDegree '15' --FinalFlip '0' --paraOut --phiIteration '100' --thetaIteration '100' --medialMesh''
Status: Finish: Execution time 6310ms
/home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/SPHARM/groupA_02_hippo_pp_surf_paraPhiHalf.txt

Case:/home/fsl/Slicer-4.3.1-linux-amd64/SpharmInput/origData/groupB_01_hippo.gipl.gz

Doing Post Processing
Status: Start SegPostProcessCLP /home/fsl/Slicer-4.3.1-linux-amd64/SpharmInput/origData/groupB_01_hippo.gipl.gz /home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/PostProcess/groupB_01_hippo_pp.gipl.gz --space 0.5,0.5,0.5
 run: 'SegPostProcessCLP' '''/home/fsl/Slicer-4.3.1-linux-amd64/SpharmInput/origData/groupB_01_hippo.gipl.gz' '/home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/PostProcess/groupB_01_hippo_pp.gipl.gz' --space '0.5,0.5,0.5'''
Status: Finish: Execution time 301ms

Doing GenParaMesh
Status: Start GenParaMeshCLP --EulerFile --outEulerName /home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//EulerFiles/groupB_01_hippo_euler.txt --iter 10 --label 1 /home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/PostProcess/groupB_01_hippo_pp.gipl.gz /home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/SPHARM/groupB_01_hippo_pp_para.vtk /home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/SPHARM/groupB_01_hippo_pp_surf.vtk
 run: 'GenParaMeshCLP' ''--EulerFile --outEulerName '/home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//EulerFiles/groupB_01_hippo_euler.txt' --iter '10' --label '1' '/home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/PostProcess/groupB_01_hippo_pp.gipl.gz' '/home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/SPHARM/groupB_01_hippo_pp_para.vtk' '/home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/SPHARM/groupB_01_hippo_pp_surf.vtk'''
Status: Finish: Execution time 6010ms

Doing ParaToSPHARMMesh

regTemplate: groupA_01_hippo_pp_surfSPHARM.vtk
flipTemplate: groupA_01_hippo_pp_surfSPHARM.coef

Status: Start ParaToSPHARMMeshCLP /home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/SPHARM/groupB_01_hippo_pp_para.vtk /home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/SPHARM/groupB_01_hippo_pp_surf.vtk /home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/SPHARM/groupB_01_hippo_pp_surf --regTemplateFileOn --regTemplate /home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Template/groupA_01_hippo_pp_surfSPHARM.vtk --flipTemplateOn --flipTemplate /home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Template/groupA_01_hippo_pp_surfSPHARM.coef --subdivLevel 10 --spharmDegree 15 --FinalFlip 0 --paraOut --phiIteration 100 --thetaIteration 100 --medialMesh
 run: 'ParaToSPHARMMeshCLP' '''/home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/SPHARM/groupB_01_hippo_pp_para.vtk' '/home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/SPHARM/groupB_01_hippo_pp_surf.vtk' '/home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/SPHARM/groupB_01_hippo_pp_surf' --regTemplateFileOn --regTemplate '/home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Template/groupA_01_hippo_pp_surfSPHARM.vtk' --flipTemplateOn --flipTemplate '/home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Template/groupA_01_hippo_pp_surfSPHARM.coef' --subdivLevel '10' --spharmDegree '15' --FinalFlip '0' --paraOut --phiIteration '100' --thetaIteration '100' --medialMesh''
Status: Finish: Execution time 6616ms
/home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/SPHARM/groupB_01_hippo_pp_surf_paraPhiHalf.txt

Case:/home/fsl/Slicer-4.3.1-linux-amd64/SpharmInput/origData/groupB_02_hippo.gipl.gz

Doing Post Processing
Status: Start SegPostProcessCLP /home/fsl/Slicer-4.3.1-linux-amd64/SpharmInput/origData/groupB_02_hippo.gipl.gz /home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/PostProcess/groupB_02_hippo_pp.gipl.gz --space 0.5,0.5,0.5
 run: 'SegPostProcessCLP' '''/home/fsl/Slicer-4.3.1-linux-amd64/SpharmInput/origData/groupB_02_hippo.gipl.gz' '/home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/PostProcess/groupB_02_hippo_pp.gipl.gz' --space '0.5,0.5,0.5'''
Status: Finish: Execution time 300ms

Doing GenParaMesh
Status: Start GenParaMeshCLP --EulerFile --outEulerName /home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//EulerFiles/groupB_02_hippo_euler.txt --iter 10 --label 1 /home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/PostProcess/groupB_02_hippo_pp.gipl.gz /home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/SPHARM/groupB_02_hippo_pp_para.vtk /home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/SPHARM/groupB_02_hippo_pp_surf.vtk
 run: 'GenParaMeshCLP' ''--EulerFile --outEulerName '/home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//EulerFiles/groupB_02_hippo_euler.txt' --iter '10' --label '1' '/home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/PostProcess/groupB_02_hippo_pp.gipl.gz' '/home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/SPHARM/groupB_02_hippo_pp_para.vtk' '/home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/SPHARM/groupB_02_hippo_pp_surf.vtk'''
Status: Finish: Execution time 6007ms

Doing ParaToSPHARMMesh

regTemplate: groupA_01_hippo_pp_surfSPHARM.vtk
flipTemplate: groupA_01_hippo_pp_surfSPHARM.coef

Status: Start ParaToSPHARMMeshCLP /home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/SPHARM/groupB_02_hippo_pp_para.vtk /home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/SPHARM/groupB_02_hippo_pp_surf.vtk /home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/SPHARM/groupB_02_hippo_pp_surf --regTemplateFileOn --regTemplate /home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Template/groupA_01_hippo_pp_surfSPHARM.vtk --flipTemplateOn --flipTemplate /home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Template/groupA_01_hippo_pp_surfSPHARM.coef --subdivLevel 10 --spharmDegree 15 --FinalFlip 0 --paraOut --phiIteration 100 --thetaIteration 100 --medialMesh
 run: 'ParaToSPHARMMeshCLP' '''/home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/SPHARM/groupB_02_hippo_pp_para.vtk' '/home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/SPHARM/groupB_02_hippo_pp_surf.vtk' '/home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/SPHARM/groupB_02_hippo_pp_surf' --regTemplateFileOn --regTemplate '/home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Template/groupA_01_hippo_pp_surfSPHARM.vtk' --flipTemplateOn --flipTemplate '/home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Template/groupA_01_hippo_pp_surfSPHARM.coef' --subdivLevel '10' --spharmDegree '15' --FinalFlip '0' --paraOut --phiIteration '100' --thetaIteration '100' --medialMesh''
Status: Finish: Execution time 6611ms
/home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//Mesh/SPHARM/groupB_02_hippo_pp_surf_paraPhiHalf.txt

	Executing BatchMake: Done!



Execute Meshmath...

meshmath template
 
Run the Particle Correspondence
ParticleModule --columMeshFile 5 --sx 0.5 --sy 0.5 --sz 0.5 --HorizontalGridPara 1 --VerticalGridPara 2 /home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//OutputGroupFile/ShapeAnalysisModule_OutputFileVersion1.csv /home/fsl/Slicer-4.3.1-linux-amd64/SpharmOutput3//ParticleCorrespondence  
 
Modify output csv 0 seconds) 
DONE COMPUTING SPHARM