Hi Beatriz,

Thanks a lot for your reaction and thanks for updating.

I followed the turorial but I still have troubles. I hope you can help me. Here is the script I used (I used both slicer 3.6 and 4.1.1 and SPHARM-PDM v1.11 and v1.10.12 for testing purposes). Please ask if you need more information.

#OS Ubuntu 11.10 (64-bit)

#install batchmake
git clone git://batchmake.org/BatchMake.git
cd BatchMakeBin
ccmake ../BatchMake
make
sudo make install

#using SPHARM-PDM v1.11 (updated version with BatchMake_Applications directory)
#Set the environnement variable BatchmakeShapeAnalysisModule_Dir
export BatchmakeShapeAnalysisModule_Dir=/home/elwannabe/Documenten/HJ/TEST1/SPHARM1_11_precompiled/spharm-pdm_linux64/BatchMake_Applications

#Add the external applications 
export PATH=/home/elwannabe/Documenten/HJ/TEST1/SPHARM1_11_precompiled/spharm-pdm_linux64/:${PATH}

#using Slicer3 v3.6
#view --> Application Settings --> Module Settings --> add a present --> /home/elwannabe/Documenten/HJ/TEST1/SPHARM1_11_precompiled/spharm-pdm_linux64/
#close slicer

#Run analysis with tutorial data from http://www.nitrc.org/docman/index.php?gr...

#run SPHARM-PDM using gui of Slicer3
Under 'Shape Analysis module' only Mancova Shape Analysis Tool, Particle module and SegPostProcess where showed. In addition ShapeAnalysisMANCOVA_wizard were showed under Statistics. No ShapeAnalysisModule was showed.

#using slicer v4.1.1 --> same result

#I checked all modules manually using the command-line --> only StatNonParamTestPDM give an error but I understand from the forum that this function is not actively developed.

#run SPHARM-PDM from commandline
ShapeAnalysisModule --sx 0.5 --sy 0.5 --sz 0.5 --label 1 --NumberofIterations 100 --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/elwannabe/Documenten/HJ/TEST1/Data/Input/InputFile_ShapeAnalaysis_4data.csv /home/elwannabe/Documenten/HJ/TEST1/Data/Output

#ANALYSIS COMPLETED WITH ERRORS (see in attachment report1)

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#using SPHARM-PDM v1.10.12
#Set the environnement variable BatchmakeShapeAnalysisModule_Dir
export BatchmakeShapeAnalysisModule_Dir=/home/elwannabe/Documenten/HJ/TEST1/SPHARM1_10_12_precompiled/spharm-pdm_linux64/BatchMake_Applications

#Add the external applications
export PATH=/home/elwannabe/Documenten/HJ/TEST1/SPHARM1_10_12_precompiled/spharm-pdm_linux64/:${PATH}

#using Slicer3 v3.6
#view --> Application Settings --> Module Settings --> add a present --> /home/elwannabe/Documenten/HJ/TEST1/SPHARM1_10_12_precompiled/spharm-pdm_linux64/
#also remove v1.11 from module settings (/home/elwannabe/Documenten/HJ/TEST1/SPHARM1_11_precompiled/spharm-pdm_linux64/)
#close slicer

#Run analysis with tutorial data from http://www.nitrc.org/docman/index.php?gr...

#run SPHARM-PDM v1.10.12 using gui of Slicer3
#ERROR after 5 seconds running (see in attachment report2)

#run SPHARM-PDM v1.10.12 using gui of slicer v4.1.1 --> same result

#run SPHARM-PDM from commandline
ShapeAnalysisModule --sx 0.5 --sy 0.5 --sz 0.5 --label 1 --NumberofIterations 100 --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/elwannabe/Documenten/HJ/TEST1/Data/Input/InputFile_ShapeAnalaysis_4data.csv /home/elwannabe/Documenten/HJ/TEST1/Data/Output

#ONLY ERRORS (see in attachment report3)