Hi Francois,
Hi Beatriz,

thanks a lot for the ImageStat. Recently, I have encountered another problem with shapeworks.py.

I think it has something to do with itkImageFileReader.hxx. Colud you please help me to diagnose the problem?

thanks a lot for your support!

Marco

/usr/bin/python /home/imaging/tools/RodentThickness/RodentThickness_package_v1.1_with_vtk_and_python/pythonscript/shapeworks.py /MRI-G/experiments/ex-vivo/cortical_thickness/output_GUI2/Processing/2.shapeworks/inputimage.txt /MRI-G/experiments/ex-vivo/cortical_thickness/output_GUI2/Processing/2.shapeworks/inputsurfacemodels.txt -c /MRI-G/experiments/ex-vivo/cortical_thickness/output_GUI2/Processing/2.shapeworks/outputCorrespondence.txt -w /MRI-G/experiments/ex-vivo/cortical_thickness/output_GUI2/Processing/2.shapeworks/outputWarped.txt --workingDir /MRI-G/experiments/ex-vivo/cortical_thickness/output_GUI2/Processing/2.shapeworks --pathShapeWorksRun /home/imaging/tools/RodentThickness/RodentThickness_package_v1.1_with_vtk_and_python/Application/ShapeWorksRun --pathShapeWorksGroom /home/imaging/tools/RodentThickness/RodentThickness_package_v1.1_with_vtk_and_python/Application/ShapeWorksGroom --pathImageMath /home/imaging/tools/RodentThickness/RodentThickness_package_v1.1_with_vtk_and_python/Application/ImageMath --pathBinaryToDistanceMap /home/imaging/tools/RodentThickness/RodentThickness_package_v1.1_with_vtk_and_python/Application/BinaryToDistanceMap

Executing /home/imaging/tools/RodentThickness/RodentThickness_package_v1.1_with_vtk_and_python/Application/ImageMath /MRI-G/experiments/ex-vivo/cortical_thickness/output_GUI2/Processing/1.MeasurementandSPHARM/1.labelMapNCsegmentationSegPostProcess.nrrd -type short -changeSp 1.25,1.25,1.25 -outfile 000.DT.nrrd ...
SPACING: 1.25 | 1.25 | 1.25

Executing /home/imaging/tools/RodentThickness/RodentThickness_package_v1.1_with_vtk_and_python/Application/BinaryToDistanceMap --binaryInput 000.DT.nrrd --smoothing 1.25 --output 000.DT.nrrd ...
image read
distance map computed
smoothing: 1.25
smoothing completed

Converting /MRI-G/experiments/ex-vivo/cortical_thickness/output_GUI2/Processing/1.MeasurementandSPHARM/1.ip.SPHARM.vtk into 000.initial.lpts [1002 points] ...
ITK exception caught in main

itk::ImageFileReaderException (0x1bc6a00)
Location: "void itk::ImageFileReader::GenerateOutputInformation() [with TOutputImage = itk::Image, ConvertPixelTraits = itk::DefaultConvertPixelTraits]"
File: /home/imaging/tools/antsbin/ITKv4/Modules/IO/ImageBase/include/itkImageFileReader.hxx
Line: 143
Description: Could not create IO object for file /MRI-G/experiments/ex-vivo/cortical_thickness/output_GUI2/Processing/1.MeasurementandSPHARM/1.labelMapNCsegmentationSegPostProcess.nrrd
Tried to create one of the following:
You probably failed to set a file suffix, or
set the suffix to an unsupported type.
Traceback (most recent call last):
File "/home/imaging/tools/RodentThickness/RodentThickness_package_v1.1_with_vtk_and_python/pythonscript/shapeworks.py", line 232, in
main(opts, args)
File "/home/imaging/tools/RodentThickness/RodentThickness_package_v1.1_with_vtk_and_python/pythonscript/shapeworks.py", line 190, in main
vtk2lpts(inputImages,inputSurfaces, inputPoints)
File "/home/imaging/tools/RodentThickness/RodentThickness_package_v1.1_with_vtk_and_python/pythonscript/shapeworks.py", line 48, in vtk2lpts
pixsize=voxelSize(fim)
File "/home/imaging/tools/RodentThickness/RodentThickness_package_v1.1_with_vtk_and_python/pythonscript/shapeworks.py", line 124, in voxelSize
spacing = [ float(i) for i in pixdims[0].split(" ")[1:] ]
IndexError: list index out of range