Dear Beatriz,

I'm using your Rodent Thickness pipeline to estimate the cortical thickness in a sample of mice. Following the pipeline, I entered all necessary information in the GUI and measureThicknessFilter, ImageMath, SegPostProcessCLP, GenParaMeshCLP and ParaToSPHARMMeshCLP worked fine to me.
I encountered one problem when I used shapeworks.py. could you help me to solve it, please?

Thank you for your collaboration.

Marco

run: '/usr/bin/python' '/RodentThickness_package_v1.1_with_vtk_and_python/pythonscript/shapeworks.py' '/Rodent_Thickness/test8/Processing/2.shapeworks/inputimage.txt' '/Rodent_Thickness/test8/Processing/2.shapeworks/inputsurfacemodels.txt' '-c' '/Rodent_Thickness/test8/Processing/2.shapeworks/outputCorrespondence.txt' '-w' '/Rodent_Thickness/test8/Processing/2.shapeworks/outputWarped.txt' '--workingDir' '/Rodent_Thickness/test8/Processing/2.shapeworks' '--pathShapeWorksRun' '/RodentThickness_package_v1.1_with_vtk_and_python/Application/ShapeWorksRun' '--pathShapeWorksGroom' '/RodentThickness_package_v1.1_with_vtk_and_python/Application/ShapeWorksGroom' '--pathImageMath' '/RodentThickness_package_v1.1_with_vtk_and_python/Application/ImageMath' '--pathBinaryToDistanceMap' '/RodentThickness_package_v1.1_with_vtk_and_python/Application/BinaryToDistanceMap'
Status: Finish: Execution time 600ms
Error: terminate called after throwing an instance of 'itk::ImageFileReaderException'
Error: what(): /NIRAL/work/mjacquem/CorticalSlicer/ITKv4-install/include/ITK-4.4/itkImageFileReader.hxx:143:
Error: Could not create IO object for file 000.DT.nrrd
Error: The file doesn't exist.
Error: Filename = 000.DT.nrrd
Error: Aborted (core dumped)
Error: sh: 1: ImageStat: not found
Error: Traceback (most recent call last):
Error: File "/RodentThickness_package_v1.1_with_vtk_and_python/pythonscript/shapeworks.py", line 232, in
Error: main(opts, args)
Error: File "/RodentThickness_package_v1.1_with_vtk_and_python/pythonscript/shapeworks.py", line 190, in main
Error: vtk2lpts(inputImages,inputSurfaces, inputPoints)
Error: File "/RodentThickness_package_v1.1_with_vtk_and_python/pythonscript/shapeworks.py", line 48, in vtk2lpts
Error: pixsize=voxelSize(fim)
Error: File "/RodentThickness_package_v1.1_with_vtk_and_python/pythonscript/shapeworks.py", line 124, in voxelSize
Error: spacing = [ float(i) for i in pixdims[0].split(" ")[1:] ]
Error: IndexError: list index out of range
| Running Failed...