I am trying to run the lobe segmentation workflow from inside the container with:
python /ChestImagingPlatform/cip_python/nipype/workflows/lung_lobe_segmentation_workflow.py --in_ct /hdd_scratch3/br888855/own_nrrd_convert/test_write__20181017192209_3314255955.nrrd --out /hdd_scratch3/br888855/own_nrrd_convert/CIPlungSegWorkflow_labelmask.nrrd
The workflow throws the following error:
RuntimeError: Command:
GeneratePartialLungLabelMap --ict "/hdd_scratch3/br888855/own_nrrd_convert/test_write__20181017192209_3314255955.nrrd" --olm "/tmp/tmpQG60_7/cid_partialLungLabelMap.nrrd"
Standard output:
Clipping low CT image values...
Clipping upper CT image values...
Executing partial lung filter...
Standard error:
Exception caught segmenting lungs:
itk::ExceptionObject (0xd86be0)
Location: "unknown"
File: /ChestImagingPlatform-build/ITKv4/Modules/Core/Common/src/itkMultiThreader.cxx
Line: 399
Description: itk::ERROR: MultiThreader(0xc88700): Exception occurred during SingleMethodExecute
/ChestImagingPlatform-build/ITKv4/Modules/Segmentation/ConnectedComponents/include/itkConnectedComponentImageFilter.hxx:347:
itk::ERROR: ConnectedComponentImageFilter(0xcafe80): Number of objects greater than maximum of output pixel type
Return code: 15
Interface GeneratePartialLungLabelMap failed to run.
I think this happens because the image I am using is quite large (~1,000 slices) and the issue should be solvable by changing the output data type of itkConnectedComponentImageFilter. I am, however, not able to do this or edit the container.
Hello,
I am trying to run the lobe segmentation workflow from inside the container with: python /ChestImagingPlatform/cip_python/nipype/workflows/lung_lobe_segmentation_workflow.py --in_ct /hdd_scratch3/br888855/own_nrrd_convert/test_write__20181017192209_3314255955.nrrd --out /hdd_scratch3/br888855/own_nrrd_convert/CIPlungSegWorkflow_labelmask.nrrd
The workflow throws the following error:
RuntimeError: Command: GeneratePartialLungLabelMap --ict "/hdd_scratch3/br888855/own_nrrd_convert/test_write__20181017192209_3314255955.nrrd" --olm "/tmp/tmpQG60_7/cid_partialLungLabelMap.nrrd" Standard output: Clipping low CT image values... Clipping upper CT image values... Executing partial lung filter... Standard error: Exception caught segmenting lungs: itk::ExceptionObject (0xd86be0) Location: "unknown" File: /ChestImagingPlatform-build/ITKv4/Modules/Core/Common/src/itkMultiThreader.cxx Line: 399 Description: itk::ERROR: MultiThreader(0xc88700): Exception occurred during SingleMethodExecute /ChestImagingPlatform-build/ITKv4/Modules/Segmentation/ConnectedComponents/include/itkConnectedComponentImageFilter.hxx:347: itk::ERROR: ConnectedComponentImageFilter(0xcafe80): Number of objects greater than maximum of output pixel type
Return code: 15 Interface GeneratePartialLungLabelMap failed to run.
I think this happens because the image I am using is quite large (~1,000 slices) and the issue should be solvable by changing the output data type of itkConnectedComponentImageFilter. I am, however, not able to do this or edit the container.
Any help /advice greatly appreciated!