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acil-bwh / ChestImagingPlatform

Chest Imaging Platform (CIP)
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GeneratePartialLungLabelMap exception #5

Closed rjosest closed 9 years ago

rjosest commented 9 years ago

I run into an interesting exception that might highlight some underlying problem with GeneratePartialLungLabelMap exception.

The experiment is as follows. When I execute: GeneratePartialLungLabelMap -c 026658003996_INSP_STD_L3_ECLIPSE.nhdr -o tmp.nrrd --lsr 4

Things run as expected

However, if you execute: GeneratePartialLungLabelMap -c 026658003996_INSP_STD_L3_ECLIPSE.nhdr -o tmp.nrrd --lsr 4 --lcv -1100 --lrv 1024 --ucv 1024 --urv 1024

I get the following error: Reading CT from file... Clipping low CT image values... Clipping upper CT image values... Executing partial lung filter... Exception caught segmenting lungs: itk::ExceptionObject (0x7f8155b00a98) Location: "unknown" File: /Users/rjosest/src/devel/ChestImagingPlatformPrivate-build/ITKv4/Modules/Core/Common/include/itkExtractImageFilter.hxx Line: 99 Description: itk::ERROR: ExtractImageFilter(0x7f8155b00080): Extraction Region not consistent with output image Writing lung mask image... Exception caught while writing lung mask: itk::ExceptionObject (0x7f8156a00a98) Location: "unknown" File: /Users/rjosest/src/devel/ChestImagingPlatformPrivate-build/ITKv4/Modules/Core/Common/include/itkExtractImageFilter.hxx Line: 99 Description: itk::ERROR: ExtractImageFilter(0x7f8156a00080): Extraction Region not consistent with output image DONE.

jcross186 commented 9 years ago

I was able to reproduce this behavior. However, if you set --lrv to -1024, everything works as expected. Will close this issue.