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help > Error using SPHARM module in Slicer CLI
Nov 3, 2014 04:11 AM | Vincent Koppelmans
Error using SPHARM module in Slicer CLI
Hi all,
I have binary segmentations of the third ventricle of multiple subjects collected over multiple time points. I am trying to get SPHARM to run, but I receive some errors.
I am using the SPHARM module in Slicer v. 4.3.1 r22599 running on Mac OSX 10.9.5
This is the syntax I used:
#!/bin/bash
# 3D Slcier Shape Analysis Module on 2 subjects
# Module: Automatic SPHARM Shape Analysis in 3D Slicer
I have attached my log file. The errors seem to occur during ParaToSPHARMMeshCLP. Does anybody know how I could fix this?
Best,
Vincent
I have binary segmentations of the third ventricle of multiple subjects collected over multiple time points. I am trying to get SPHARM to run, but I receive some errors.
I am using the SPHARM module in Slicer v. 4.3.1 r22599 running on Mac OSX 10.9.5
This is the syntax I used:
#!/bin/bash
# 3D Slcier Shape Analysis Module on 2 subjects
# Module: Automatic SPHARM Shape Analysis in 3D Slicer
# Environment
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/Applications/Slicer.app/Contents/lib/Slicer-4.3
export PATH=${PATH}:/Applications/Slicer.app/Contents/MacOS
export PATH=${PATH}:/Applications/Slicer.app/Contents/lib/Slicer-4.3/cli-modules
export PATH=${PATH}:/Applications/Slicer.app/Contents/Extensions-22599/SPHARM-PDM/lib/Slicer-4.3/cli-modules
export PATH=${PATH}:/Applications/Slicer.app/Contents/Extensions-22599/SPHARM-PDM/lib/Slicer-4.3/ExternalBin
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/Applications/Slicer.app/Contents/lib/Slicer-4.3
export PATH=${PATH}:/Applications/Slicer.app/Contents/MacOS
export PATH=${PATH}:/Applications/Slicer.app/Contents/lib/Slicer-4.3/cli-modules
export PATH=${PATH}:/Applications/Slicer.app/Contents/Extensions-22599/SPHARM-PDM/lib/Slicer-4.3/cli-modules
export PATH=${PATH}:/Applications/Slicer.app/Contents/Extensions-22599/SPHARM-PDM/lib/Slicer-4.3/ExternalBin
export LC_NUMERIC=en_GB.UTF-8
DIR=/Volumes/Data/tmp/Shape/
mkdir -p ${DIR}/output
mkdir -p ${DIR}/output
ShapeAnalysisModule \
--RescaleSegPostProcess \
--sx 0.5 \
--sy 0.5 \
--sz 0.5 \
--label 1 \
--NumberofIterations 1000 \
--SubdivLevelValue 10 \
--SPHARMDegreeValue 15 \
--thetaIterationValue 100 \
--phiIterationValue 100 \
--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 \
${DIR}/data.csv \
${DIR}/output \
&> ${DIR}/output/log.txt
--RescaleSegPostProcess \
--sx 0.5 \
--sy 0.5 \
--sz 0.5 \
--label 1 \
--NumberofIterations 1000 \
--SubdivLevelValue 10 \
--SPHARMDegreeValue 15 \
--thetaIterationValue 100 \
--phiIterationValue 100 \
--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 \
${DIR}/data.csv \
${DIR}/output \
&> ${DIR}/output/log.txt
exit
I have attached my log file. The errors seem to occur during ParaToSPHARMMeshCLP. Does anybody know how I could fix this?
Best,
Vincent
Threaded View
| Title | Author | Date |
|---|---|---|
| Vincent Koppelmans | Nov 3, 2014 | |
| Beatriz Paniagua | Nov 4, 2014 | |
| Vincent Koppelmans | Dec 3, 2014 | |