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acil-bwh / ChestImagingPlatform

Chest Imaging Platform (CIP)
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lobe segmentation workflow issue on docker version #37

Open brangl opened 3 years ago

brangl commented 3 years ago

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!