Lung CT segmenter from Chest Imaging Platform bad quality image and segmentation

Khaldoun · February 20, 2026, 1:22pm

Problem report for 3D Slicer 5.10.0 win-amd64: [please describe expected and actual behavior]

Since the last update of Total Segmentator the Lung CT segmenter module in Chest Imaging Platform is producing very blurry segmentation of the lung lobes as it is shown in the screen capture below while it was perfectly functionning previously without changing any thing on hardware (Windows 11, no GPU and CPU forced on desktop computer with 13th Gen Intel(R) Core™ i5-13500 2.50GHz; 16.0 Go RAM, and INterl(R) UHD GRaphics 770 128 MB.

Below is the screen shot of the result applied to Chest CT from sample data down load

and below copy of the log message

Thank you for your help as I am using Lung CT Segmenter on a daily practice in my hospital

[DEBUG][Qt] 20.02.2026 09:22:47 (unknown:0) - Session start time …: 20260220_092247
[DEBUG][Qt] 20.02.2026 09:22:47 (unknown:0) - Slicer version …: 5.10.0 (revision 34045 / a2b6d08) win-amd64 - installed release
[DEBUG][Qt] 20.02.2026 09:22:47 (unknown:0) - Operating system …: Windows / Professional / (Build 26200, Code Page 65001) - 64-bit
[DEBUG][Qt] 20.02.2026 09:22:47 (unknown:0) - Memory …: 16072 MB physical, 34496 MB virtual
[DEBUG][Qt] 20.02.2026 09:22:47 (unknown:0) - CPU …: GenuineIntel , 20 cores, 20 logical processors
[DEBUG][Qt] 20.02.2026 09:22:47 (unknown:0) - VTK configuration …: OpenGL2 rendering, TBB threading
[DEBUG][Qt] 20.02.2026 09:22:47 (unknown:0) - Qt configuration …: version 5.15.2, with SSL, requested OpenGL 3.2 (core profile)
[DEBUG][Qt] 20.02.2026 09:22:47 (unknown:0) - DCMTK configuration …: version 3.6.8, no SSL
[DEBUG][Qt] 20.02.2026 09:22:47 (unknown:0) - Internationalization …: disabled, language=
[DEBUG][Qt] 20.02.2026 09:22:47 (unknown:0) - Developer mode …: disabled
[DEBUG][Qt] 20.02.2026 09:22:47 (unknown:0) - Application path …: C:/Users/538827/AppData/Local/slicer.org/3D Slicer 5.10.0/bin
[DEBUG][Qt] 20.02.2026 09:22:47 (unknown:0) - Additional module paths ..: slicer.org/Extensions-34045/AirwaySegmentation/lib/Slicer-5.10/cli-modules, slicer.org/Extensions-34045/AirwaySegmentation/lib/Slicer-5.10/qt-scripted-modules, slicer.org/Extensions-34045/PyTorch/lib/Slicer-5.10/qt-scripted-modules, slicer.org/Extensions-34045/SegmentEditorExtraEffects/lib/Slicer-5.10/qt-loadable-modules, slicer.org/Extensions-34045/SegmentEditorExtraEffects/lib/Slicer-5.10/qt-scripted-modules, slicer.org/Extensions-34045/SurfaceWrapSolidify/lib/Slicer-5.10/qt-scripted-modules, slicer.org/Extensions-34045/LungCTAnalyzer/lib/Slicer-5.10/qt-scripted-modules, slicer.org/Extensions-34045/MarkupsToModel/lib/Slicer-5.10/qt-loadable-modules, slicer.org/Extensions-34045/NNUNet/lib/Slicer-5.10/qt-scripted-modules, slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules, slicer.org/Extensions-34045/SlicerPythonTestRunner/lib/Slicer-5.10/qt-scripted-modules, slicer.org/Extensions-34045/MONAIAuto3DSeg/lib/Slicer-5.10/qt-scripted-modules, slicer.org/Extensions-34045/NNInteractive/lib/Slicer-5.10/qt-scripted-modules, slicer.org/Extensions-34045/NvidiaAIAssistedAnnotation/lib/Slicer-5.10/qt-scripted-modules, slicer.org/Extensions-34045/PETTumorSegmentation/lib/Slicer-5.10/qt-loadable-modules, slicer.org/Extensions-34045/PETTumorSegmentation/lib/Slicer-5.10/qt-scripted-modules
[INFO][Stream] 20.02.2026 09:22:48 (unknown:0) -
[DEBUG][Python] 20.02.2026 09:22:51 [Python] (C:\Users\538827\AppData\Local\slicer.org\3D Slicer 5.10.0\lib\Slicer-5.10\qt-scripted-modules\SubjectHierarchyPlugins\AbstractScriptedSubjectHierarchyPlugin.py:40) - Scripted subject hierarchy plugin registered: SegmentEditor
[DEBUG][Python] 20.02.2026 09:22:51 [Python] (C:\Users\538827\AppData\Local\slicer.org\3D Slicer 5.10.0\lib\Slicer-5.10\qt-scripted-modules\SubjectHierarchyPlugins\AbstractScriptedSubjectHierarchyPlugin.py:40) - Scripted subject hierarchy plugin registered: SegmentStatistics
[DEBUG][Qt] 20.02.2026 09:22:51 (unknown:0) - Switch to module: “Welcome”
[WARNING][VTK] 20.02.2026 09:22:51 [vtkSlicerTerminologiesModuleLogic (00000284F7398D40)] (vtkSlicerTerminologiesModuleLogic.cxx:3370) - LoadAnatomicContextFromFile is deprecated. Use LoadRegionContextFromFile instead.
[INFO][Python] 20.02.2026 09:22:52 [Python] (C:/Users/538827/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/NvidiaAIAssistedAnnotation/lib/Slicer-5.10/qt-scripted-modules/SegmentEditorNvidiaAIAA.py:32) - This plugin dir: C:/Users/538827/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/NvidiaAIAssistedAnnotation/lib/Slicer-5.10/qt-scripted-modules
[WARNING][VTK] 20.02.2026 09:22:52 [vtkSlicerTerminologiesModuleLogic (00000284F7398D40)] (vtkSlicerTerminologiesModuleLogic.cxx:3370) - LoadAnatomicContextFromFile is deprecated. Use LoadRegionContextFromFile instead.
[DEBUG][Qt] 20.02.2026 10:55:54 (unknown:0) - Switch to module: “SampleData”
[DEBUG][Qt] 20.02.2026 10:56:27 (unknown:0) - Switch to module: “DICOM”
[DEBUG][Qt] 20.02.2026 10:56:34 (unknown:0) - Switch to module: “Welcome”
[DEBUG][Qt] 20.02.2026 10:56:35 (unknown:0) - Switch to module: “SampleData”
[DEBUG][Python] 20.02.2026 10:56:36 [Python] (C:/Users/538827/AppData/Local/slicer.org/3D Slicer 5.10.0/bin/../lib/Slicer-5.10/qt-scripted-modules/SampleData.py:461) - Verifying checksum
[DEBUG][Python] 20.02.2026 10:56:36 [Python] (C:/Users/538827/AppData/Local/slicer.org/3D Slicer 5.10.0/bin/../lib/Slicer-5.10/qt-scripted-modules/SampleData.py:461) - File already exists and checksum is OK - reusing it.
[DEBUG][Python] 20.02.2026 10:56:36 [Python] (C:/Users/538827/AppData/Local/slicer.org/3D Slicer 5.10.0/bin/../lib/Slicer-5.10/qt-scripted-modules/SampleData.py:461) - Requesting load CTChest from C:/Users/538827/AppData/Local/slicer.org/Slicer/cache/SlicerIO/CT-chest.nrrd …
[DEBUG][Qt] 20.02.2026 10:56:37 (unknown:0) - “Volume” Reader has successfully read the file “C:/Users/538827/AppData/Local/slicer.org/Slicer/cache/SlicerIO/CT-chest.nrrd” “[0.36s]”
[DEBUG][Python] 20.02.2026 10:56:37 [Python] (C:/Users/538827/AppData/Local/slicer.org/3D Slicer 5.10.0/bin/../lib/Slicer-5.10/qt-scripted-modules/SampleData.py:461) - Load finished
[DEBUG][Qt] 20.02.2026 10:57:00 (unknown:0) - Switch to module: “LungCTSegmenter”
[INFO][VTK] 20.02.2026 10:57:11 [vtkSlicerCLIModuleLogic (00000284F88484E0)] (C:\D\S\S-0\Base\Logic\vtkSlicerCLIModuleLogic.cxx:844) - Found CommandLine Module, target is C:/Users/538827/AppData/Local/slicer.org/3D Slicer 5.10.0/bin/../lib/Slicer-5.10/cli-modules/ResampleScalarVolume.exe
[INFO][VTK] 20.02.2026 10:57:11 [vtkSlicerCLIModuleLogic (00000284F88484E0)] (C:\D\S\S-0\Base\Logic\vtkSlicerCLIModuleLogic.cxx:862) - ModuleType: CommandLineModule
[INFO][VTK] 20.02.2026 10:57:12 [vtkSlicerCLIModuleLogic (00000284F88484E0)] (C:\D\S\S-0\Base\Logic\vtkSlicerCLIModuleLogic.cxx:1690) - Resample Scalar Volume command line:

C:/Users/538827/AppData/Local/slicer.org/3D Slicer 5.10.0/bin/../lib/Slicer-5.10/cli-modules/ResampleScalarVolume.exe --spacing 2.0,2.0,2.0 --interpolation linear C:/Users/538827/AppData/Local/Temp/Slicer/CAAIE_vtkMRMLScalarVolumeNodeB.nrrd C:/Users/538827/AppData/Local/Temp/Slicer/CAAIE_vtkMRMLScalarVolumeNodeC.nrrd
[INFO][VTK] 20.02.2026 10:57:12 [vtkSlicerCLIModuleLogic (00000284F88484E0)] (C:\D\S\S-0\Base\Logic\vtkSlicerCLIModuleLogic.cxx:1894) - Resample Scalar Volume completed without errors
[WARNING][Qt] 20.02.2026 10:57:12 (unknown:0) - QLayout::addChildLayout: layout “” already has a parent
[WARNING][Qt] 20.02.2026 10:57:12 (unknown:0) - libpng warning: iCCP: known incorrect sRGB profile
[WARNING][Qt] 20.02.2026 10:57:12 (unknown:0) - ctkSliderWidget::setSingleStep() 0 is out of bounds. 0 1000 1
[INFO][Python] 20.02.2026 10:57:12 [Python] (C:/Users/538827/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/LungCTAnalyzer/lib/Slicer-5.10/qt-scripted-modules/LungCTSegmenter.py:1555) - StartSegmentation completed in 1.28 seconds
[INFO][Python] 20.02.2026 10:57:13 [Python] (C:/Users/538827/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/LungCTAnalyzer/lib/Slicer-5.10/qt-scripted-modules/LungCTSegmenter.py:1126) - Saving markups in temp directory …
[INFO][Stream] 20.02.2026 10:57:19 (unknown:0) - Torch version:
[INFO][Python] 20.02.2026 10:57:19 [Python] (C:/Users/538827/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/PyTorch/lib/Slicer-5.10/qt-scripted-modules/PyTorchUtils.py:153) - Importing torch…
[INFO][Python] 20.02.2026 10:57:21 [Python] (C:/Users/538827/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/PyTorch/lib/Slicer-5.10/qt-scripted-modules/PyTorchUtils.py:190) - PyTorch 2.10.0+cpu imported successfully
[INFO][Python] 20.02.2026 10:57:21 [Python] (C:/Users/538827/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/PyTorch/lib/Slicer-5.10/qt-scripted-modules/PyTorchUtils.py:191) - CUDA available: False
[INFO][Stream] 20.02.2026 10:57:21 (unknown:0) - 2.10.0+cpu
[INFO][Python] 20.02.2026 10:57:21 [Python] (C:/Users/538827/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/LungCTAnalyzer/lib/Slicer-5.10/qt-scripted-modules/LungCTSegmenter.py:2296) - Pytorch CUDA is not available. AI will use CPU processing.
[INFO][Python] 20.02.2026 10:57:21 [Python] (C:\Users\538827\AppData\Local\slicer.org\3D Slicer 5.10.0\bin\Python\slicer\util.py:3146) - Warning: Pytorch CUDA is not found on your system. The AI processing will last 3-10 minutes. Are you sure you want to continue AI segmentation?
[WARNING][Qt] 20.02.2026 11:26:22 (unknown:0) - ctkSliderWidget::setSingleStep() 0 is out of bounds. 0 100 1
[INFO][Python] 20.02.2026 11:26:23 [Python] (C:/Users/538827/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:677) - Processing started
[INFO][Python] 20.02.2026 11:26:23 [Python] (C:/Users/538827/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:677) - Writing input file to C:/Users/538827/AppData/Local/Temp/Slicer/__SlicerTemp__2026-02-20_11+26+23.843/total-segmentator-input.nii
[INFO][Python] 20.02.2026 11:26:24 [Python] (C:/Users/538827/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:677) - Creating segmentations with TotalSegmentator AI…
[INFO][Python] 20.02.2026 11:26:24 [Python] (C:/Users/538827/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:677) - Total Segmentator arguments: [‘-i’, ‘C:/Users/538827/AppData/Local/Temp/Slicer/__SlicerTemp__2026-02-20_11+26+23.843/total-segmentator-input.nii’, ‘-o’, ‘C:/Users/538827/AppData/Local/Temp/Slicer/__SlicerTemp__2026-02-20_11+26+23.843/segmentation’, ‘–ml’, ‘–task’, ‘total’, ‘–fastest’]
[INFO][Python] 20.02.2026 11:26:45 [Python] (C:/Users/538827/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:677) -
[INFO][Python] 20.02.2026 11:26:46 [Python] (C:/Users/538827/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:677) - 0%| | 0/4 [00:00<?, ?it/s]
[INFO][Python] 20.02.2026 11:26:46 [Python] (C:/Users/538827/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:677) - 25%|##5 | 1/4 [00:00<00:02, 1.29it/s]
[INFO][Python] 20.02.2026 11:26:47 [Python] (C:/Users/538827/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:677) - 50%|##### | 2/4 [00:01<00:01, 1.45it/s]
[INFO][Python] 20.02.2026 11:26:47 [Python] (C:/Users/538827/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:677) - 75%|#######5 | 3/4 [00:01<00:00, 1.62it/s]
[INFO][Python] 20.02.2026 11:26:47 [Python] (C:/Users/538827/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:677) - 100%|##########| 4/4 [00:02<00:00, 1.75it/s]
[INFO][Python] 20.02.2026 11:26:47 [Python] (C:/Users/538827/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:677) - 100%|##########| 4/4 [00:02<00:00, 1.64it/s]
[INFO][Python] 20.02.2026 11:26:52 [Python] (C:/Users/538827/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:677) - No GPU detected. Running on CPU. This can be very slow. The ‘–fast’ or the --roi_subset option can help to reduce runtime.
[INFO][Python] 20.02.2026 11:26:52 [Python] (C:/Users/538827/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:677) -
[INFO][Python] 20.02.2026 11:26:52 [Python] (C:/Users/538827/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:677) - If you use this tool please cite: https://pubs.rsna.org/doi/10.1148/ryai.230024
[INFO][Python] 20.02.2026 11:26:52 [Python] (C:/Users/538827/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:677) -
[INFO][Python] 20.02.2026 11:26:52 [Python] (C:/Users/538827/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:677) - Using ‘fastest’ option: resampling to lower resolution (6mm)
[INFO][Python] 20.02.2026 11:26:52 [Python] (C:/Users/538827/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:677) - Resampling…
[INFO][Python] 20.02.2026 11:26:52 [Python] (C:/Users/538827/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:677) - Resampled in 1.64s
[INFO][Python] 20.02.2026 11:26:52 [Python] (C:/Users/538827/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:677) - Predicting…
[INFO][Python] 20.02.2026 11:26:52 [Python] (C:/Users/538827/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:677) - Predicted in 14.09s
[INFO][Python] 20.02.2026 11:26:52 [Python] (C:/Users/538827/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:677) - Resampling…
[INFO][Python] 20.02.2026 11:26:52 [Python] (C:/Users/538827/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:677) - Saving segmentations…
[INFO][Python] 20.02.2026 11:26:52 [Python] (C:/Users/538827/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:677) - Saved in 0.43s
[INFO][Python] 20.02.2026 11:26:53 [Python] (C:/Users/538827/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:677) - Importing segmentation results…
[INFO][VTK] 20.02.2026 11:26:53 [vtkMRMLSegmentationStorageNode (00000285137BD930)] (C:\D\S\S-0\Libs\MRML\Core\vtkMRMLSegmentationStorageNode.cxx:608) - ReferenceImageExtentOffset attribute was not found in NRRD segmentation file. Assume no offset.
[INFO][Python] 20.02.2026 11:26:53 [Python] (C:/Users/538827/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:677) - Processing completed in 30.01 seconds
[INFO][Python] 20.02.2026 11:26:53 [Python] (C:/Users/538827/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:677) - Cleaning up temporary folder…
[ERROR][VTK] 20.02.2026 12:42:59 [vtkCompositeDataPipeline (000002849F0468C0)] (vtkDemandDrivenPipeline.cxx:677) - Input port 0 of algorithm vtkTransformPolyDataFilter (000002848908F130) has 0 connections but is not optional.
[ERROR][VTK] 20.02.2026 12:42:59 [vtkCompositeDataPipeline (000002849F0468C0)] (vtkDemandDrivenPipeline.cxx:677) - Input port 0 of algorithm vtkTransformPolyDataFilter (000002848908F130) has 0 connections but is not optional.
[ERROR][VTK] 20.02.2026 12:42:59 [vtkCompositeDataPipeline (000002849F0468C0)] (vtkDemandDrivenPipeline.cxx:677) - Input port 0 of algorithm vtkTransformPolyDataFilter (000002848908F130) has 0 connections but is not optional.
[ERROR][VTK] 20.02.2026 12:42:59 [vtkCompositeDataPipeline (000002849F0468C0)] (vtkDemandDrivenPipeline.cxx:677) - Input port 0 of algorithm vtkTransformPolyDataFilter (000002848908F130) has 0 connections but is not optional.
[ERROR][VTK] 20.02.2026 12:43:00 [vtkCompositeDataPipeline (000002849F0468C0)] (vtkDemandDrivenPipeline.cxx:677) - Input port 0 of algorithm vtkTransformPolyDataFilter (000002848908F130) has 0 connections but is not optional.
[ERROR][VTK] 20.02.2026 12:43:00 [vtkCompositeDataPipeline (000002849F0468C0)] (vtkDemandDrivenPipeline.cxx:677) - Input port 0 of algorithm vtkTransformPolyDataFilter (000002848908F130) has 0 connections but is not optional.
[ERROR][VTK] 20.02.2026 12:43:00 [vtkCompositeDataPipeline (000002849F0468C0)] (vtkDemandDrivenPipeline.cxx:677) - Input port 0 of algorithm vtkTransformPolyDataFilter (000002848908F130) has 0 connections but is not optional.
[ERROR][VTK] 20.02.2026 12:43:00 [vtkCompositeDataPipeline (000002849F0468C0)] (vtkDemandDrivenPipeline.cxx:677) - Input port 0 of algorithm vtkTransformPolyDataFilter (000002848908F130) has 0 connections but is not optional.
[INFO][Stream] 20.02.2026 12:43:00 (unknown:0) - Reference: left deep back muscle
[ERROR][VTK] 20.02.2026 12:43:00 [vtkCompositeDataPipeline (000002849F0468C0)] (vtkDemandDrivenPipeline.cxx:677) - Input port 0 of algorithm vtkTransformPolyDataFilter (000002848908F130) has 0 connections but is not optional.
[WARNING][Qt] 20.02.2026 12:43:00 (unknown:0) - ctkSliderWidget::setSingleStep() 0 is out of bounds. 0 100 1
[INFO][Stream] 20.02.2026 12:43:01 (unknown:0) - Mean radiodensity of trachea = -787.13 HU
[INFO][Stream] 20.02.2026 12:43:01 (unknown:0) - Mean radiodensity of deep back muscle muscle = 38.24 HU
[WARNING][VTK] 20.02.2026 12:43:01 [vtkMRMLMarkupsFiducialNode (00000284FECA49C0)] (vtkMRMLMarkupsFiducialNode.h:113) - vtkMRMLMarkupsFiducialNode::AddFiducialFromArray method is deprecated, please use AddControlPoint instead
[INFO][Python] 20.02.2026 12:43:02 [Python] (C:/Users/538827/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/LungCTAnalyzer/lib/Slicer-5.10/qt-scripted-modules/LungCTSegmenter.py:2565) - Segmentation done.
[ERROR][VTK] 20.02.2026 12:43:03 [vtkImageData (0000028516D7D780)] (vtkImageData.cxx:2082) - GetPointer: Pixel (0, 0, 0) not in current extent: (0, -1, 0, -1, 0, -1)
[ERROR][Python] 20.02.2026 12:43:03 [Python] (C:\Users\538827\AppData\Local\slicer.org\3D Slicer 5.10.0\lib\Slicer-5.10\qt-scripted-modules\SegmentStatisticsPlugins\LabelmapSegmentStatisticsPlugin.py:177) - Could not calculate centroid_ras!
[INFO][Stream] 20.02.2026 12:43:03 (unknown:0) - Median radiodensity of lungs = -865.00 HU
[INFO][Stream] 20.02.2026 12:43:03 (unknown:0) - MaximumThreshold: -865.0
[INFO][Stream] 20.02.2026 12:43:03 (unknown:0) - MinimumThreshold: -3024.0
[INFO][Stream] 20.02.2026 12:43:03 (unknown:0) - IJK trachea markup
[INFO][Stream] 20.02.2026 12:43:03 (unknown:0) - [261, 234, 108]
[INFO][Python] 20.02.2026 12:43:14 [Python] (C:/Users/538827/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/LungCTAnalyzer/lib/Slicer-5.10/qt-scripted-modules/LungCTSegmenter.py:2925) - ApplySegmentation completed in 6361.95 seconds
[INFO][Stream] 20.02.2026 12:43:14 (unknown:0) - Segmentation completed in 6361.95 seconds
[WARNING][VTK] 20.02.2026 12:43:15 [vtkMRMLSegmentationDisplayNode (000002848B674010)] (vtkMRMLSegmentationDisplayNode.cxx:294) - vtkMRMLSegmentationDisplayNode::GetSegmentDisplayProperties: no display properties are found for segment ID=, return default
[DEBUG][Qt] 20.02.2026 12:44:17 (unknown:0) - Switch to module: “Data”
[DEBUG][Qt] 20.02.2026 13:24:59 (unknown:0) - Switch to module: “Welcome”
[DEBUG][Qt] 20.02.2026 13:25:00 (unknown:0) - Switch to module: “SampleData”
[DEBUG][Qt] 20.02.2026 14:17:47 (unknown:0) - Switch to module: “Welcome”
[DEBUG][Qt] 20.02.2026 14:17:48 (unknown:0) - Switch to module: “SampleData”

pieper · February 20, 2026, 4:16pm

I’m not sure why this resolution would have changed, by you could try reporting on github issues for either TotalSegmentator or the Slicer extension.

In the meantime you could just install the older release version.

jamesobutler · February 20, 2026, 5:26pm

^Isn’t this just using the new --fastest option which is the lower resolution (6mm) option?

It was part of latest commit of SlicerTotalSegmentator:

github.com/lassoan/SlicerTotalSegmentator

Update TotalSegmentator to v2.12.0

committed 02:33PM - 12 Feb 26 UTC

mhalle

+972 -59

Summary: Update version pin to v2.12.0 (commit a4a906) and bump minimum depende…ncy versions (torch>=2.1.2, nnunetv2>=2.3.1). Add 5 new segmentation tasks: - craniofacial_structures - abdominal_muscles - teeth (77 classes) - trunk_cavities - brain_aneurysm (TOF MRI) Expose new CLI options in the UI: fastest mode (6mm), robust cropping, remove small blobs, and higher-order resampling. Add Apple Silicon (MPS) GPU device detection and pass --device mps when available. Add SNOMED-CT mappings and terminology entries for all new structures (~109 new labels). Fix pre-existing bug where Fast mode default used wrong case ("True" vs "true"), and fix pericardium SNOMED code collision with breast (76752008 -> 76848001). Detailed report: --- # Porting SlicerTotalSegmentator to TotalSegmentator v2.12.0 ## Overview This document describes the changes made to port the SlicerTotalSegmentator 3D Slicer extension from its previous TotalSegmentator version (~v2.6.0/v2.9.0 depending on Python version) to **TotalSegmentator v2.12.0**. The work is tracked in PR #81 on `lassoan/SlicerTotalSegmentator`. --- ## What Was Done ### 1. Version Pin Update **File:** `TotalSegmentator/TotalSegmentator.py` (line ~400) The extension previously maintained two separate commit-hash pins depending on the Python version: - Python < 3.12 (Slicer 5.8-): commit `25a8586` (~v2.6.0) - Python >= 3.12 (Slicer 5.9+): commit `0a1c3c3` (~v2.9.0) Both were replaced with a single pin to v2.12.0: ```python self.totalSegmentatorPythonPackageDownloadUrl = \ "https://github.com/wasserth/TotalSegmentator/archive/a4a9060012a4b7c39d15fe93772af3f7c1239fbf.zip" # v2.12.0 ``` The Python-version branching was removed because v2.12.0 supports both Python 3.9 and 3.12+. ### 2. Dependency Version Bumps **File:** `TotalSegmentator/TotalSegmentator.py` (lines ~809, ~819) | Dependency | Previous Min | New Min | |-----------|-------------|---------| | torch | >= 2.0.0 | >= 2.1.2 | | nnunetv2 | >= 2.2.1 | >= 2.3.1 | These match the requirements of TotalSegmentator v2.12.0. ### 3. Seven New Segmentation Tasks **File:** `TotalSegmentator/TotalSegmentator.py` (lines ~476-483) Five new tasks were added: | Task ID | Title | Modality | Labels | License | Notes | |---------|-------|----------|--------|---------|-------| | `craniofacial_structures` | head: craniofacial structures | CT | 7 | Open | New | | `abdominal_muscles` | abdominal muscles | CT | 22 | Open | New, bilateral muscles | | `teeth` | teeth | CT | 77 | Open | New, FDI-numbered teeth + pulps | | `trunk_cavities` | trunk cavities | CT | 4 | Open | New | | `brain_aneurysm` | brain: aneurysm (TOF MRI) | **MR** | 1 | Open | New, TOF MRI only | **Total new labels across all 7 tasks: 127** None of the new tasks support `fast` or `fastest` mode. The `teeth` task internally cascades through `craniofacial_structures` for cropping, but this is handled entirely by TotalSegmentator itself -- no Slicer-side logic needed. ### 4. SNOMED-CT Mappings **File:** `TotalSegmentator/Resources/totalsegmentator_snomed_mapping.csv` Added ~109 new rows mapping TotalSegmentator structure names to SNOMED-CT codes. Each row specifies: - Structure name (must match TotalSegmentator's `class_map` label exactly) - Category (Anatomical Structure, Morphologically Altered Structure, etc.) - Type (SNOMED code for the anatomical structure) - Type modifier (laterality: Left/Right where applicable) - Region and region modifier (for non-anatomical categories like dental pulp) - Display color (RGB) **Breakdown by task:** | Task | New CSV Rows | Notes | |------|-------------|-------| | `craniofacial_structures` | 6 | `skull` already existed | | `abdominal_muscles` | 20 | `trapezius_right/left` already existed from `headneck_muscles` | | `teeth` | 77 | Jawbones, canals, 32 teeth, 32 pulps, bridge/crown/implant, pharynx | | `trunk_cavities` | 4 | abdominal_cavity, thoracic_cavity, pericardium, mediastinum | | `brain_aneurysm` | 1 | Uses "Morphologically Altered Structure" category | | `ventricle_parts` | 0 | All 12 labels already had mappings | | `aortic_sinuses` | 0 | All 4 labels already had mappings | **Cross-reference verification:** A script was run to confirm that every label in TotalSegmentator's `class_map` for all 7 tasks has a corresponding CSV entry. No missing or duplicate names exist. ### 5. Terminology JSON **File:** `TotalSegmentator/Resources/SegmentationCategoryTypeModifier-TotalSegmentator.term.json` Added terminology entries for all new structures under the appropriate categories: - **Anatomical Structure** (SCT 123037004): ~30 new Type entries including mandible, maxilla, maxillary sinus (paired), frontal sinus, head, tooth types (central incisor through third molar, all paired), muscles (pectoralis major, rectus abdominis, latissimus dorsi, external/internal oblique, erector spinae, transversospinalis, psoas major, quadratus lumborum -- all paired), dental structures (dental pulp, inferior alveolar nerve, lingual canal, dental prosthesis, dental crown, implant), and cavities (abdominal, thoracic, pericardium, mediastinum). - **Morphologically Altered Structure** (SCT 49755003): 1 new entry for cerebral aneurysm. Each entry includes `recommendedDisplayRGBValue`, `3dSlicerLabel`, laterality modifiers where applicable, and SNOMED concept IDs. ### 6. New UI Controls **File:** `TotalSegmentator/Resources/UI/TotalSegmentator.ui` Added the following widgets: | Widget | Section | Type | Notes | |--------|---------|------|-------| | `fastestCheckBox` + `fastestNotAvailableLabel` | Inputs | Checkbox + Label | Only visible for `total` and `total_mr` | | `robustCropCheckBox` | Advanced | Checkbox | "Use 3mm model for cropping" | | `removeSmallBlobsCheckBox` | Advanced | Checkbox | "Remove regions < 0.2 ml" | | `higherOrderResamplingCheckBox` | Advanced | Checkbox | "Smoother but more memory" | The `fastest` row follows the same visibility pattern as the existing `fast` row: checkbox shown when supported, "not available" label shown otherwise. ### 7. Python Logic Updates **File:** `TotalSegmentator/TotalSegmentator.py` #### Widget connections (lines ~106-113) All new checkboxes connected to `updateParameterNodeFromGUI`. #### Parameter node persistence (lines ~216-269) All new parameters (`Fastest`, `RobustCrop`, `RemoveSmallBlobs`, `HigherOrderResampling`, `Statistics`) are read from and written to the MRML parameter node, preserving user settings across scene save/load. #### `isFastestModeSupportedForTask()` (line ~593) New method mirroring the existing `isFastModeSupportedForTask()`. #### `process()` signature (line ~983) Extended with keyword arguments: `fastest`, `robustCrop`, `removeSmallBlobs`, `higherOrderResampling`, `statistics`. #### `processVolume()` CLI argument building (lines ~1143-1166) - `--fastest` and `--fast` are mutually exclusive (fastest takes priority) - `--device` flag supports `gpu` (default), `cpu`, and `mps` - New flags: `--robust_crop`, `--remove_small_blobs`, `--higher_order_resampling`, `--statistics` ### 8. Apple Silicon (MPS) Device Detection **File:** `TotalSegmentator/TotalSegmentator.py` (lines ~1028-1056) Added detection of Apple Metal Performance Shaders (MPS) as a third GPU backend alongside CUDA: ```python cuda = torch.cuda if torch.backends.cuda.is_built() and torch.cuda.is_available() else None mps = hasattr(torch.backends, 'mps') and torch.backends.mps.is_available() hasGPU = cuda is not None or mps ``` Device selection priority: user-forced CPU > MPS > CUDA GPU. The "no GPU" and "low GPU memory" interactive warnings were updated to account for both `fast` and `fastest` modes. The GPU memory check only applies to CUDA (MPS does not expose a comparable memory reporting API). ### 9. Bug Fixes #### Fix 1: Pericardium SNOMED code collision (Critical) The `pericardium` entry in the CSV used SNOMED code `76752008`, which is actually "Breast structure" (already used by the `breast` entry on line 301). Changed to `76848001` (Pericardial sac structure) in both the CSV and the terminology JSON. #### Fix 2: Orphaned trapezius CSV entries (Medium) Added `trapezius_right_abdominal` and `trapezius_left_abdominal` entries, but TotalSegmentator's `abdominal_muscles` class_map uses `trapezius_right` and `trapezius_left` -- which were already mapped from the `headneck_muscles` task. The `_abdominal` suffixed entries would never match any output. Removed them. #### Fix 3: Fast mode default case mismatch (Medium, pre-existing) `setDefaultParameters()` set `"True"` (capital T) for the Fast parameter, but `updateGUIFromParameterNode()` compared against `"true"` (lowercase). This meant the Fast checkbox was effectively OFF by default on first module load. Changed to lowercase `"true"`. --- ## What Remains To Be Done ### High Priority #### Terminology Completeness Audit While all 127 new labels have SNOMED mappings, a thorough audit should verify: - All SNOMED codes are semantically correct (not just syntactically valid) - The `implant` entry (teeth task) uses "Anatomical Structure" category but should arguably use "Physical object" (260787004) for consistency with `hip_implant`. Low impact since DICOM master list fallback handles it. - Dental pulp Region entries reference specific tooth types via SNOMED -- these should be spot-checked against the SNOMED CT browser. ### Medium Priority #### Modality Auto-Detection for Task Filtering The task metadata already includes `modalities` (CT, MR). After the user selects an input volume, the module could: - Detect whether the volume is CT or MR (from DICOM metadata or volume properties) - Filter or highlight the task dropdown to show only compatible tasks - Show a warning if the user selects a task incompatible with the input modality (e.g., `brain_aneurysm` on a CT volume) This is a UI convenience enhancement, not a functional requirement. ### Low Priority #### Expose `--body_seg` Option Controls whether to use body segmentation for cropping. Advanced users might want to disable this for non-standard anatomies. #### Expose `--quiet` / `--verbose` Logging Levels TotalSegmentator supports `--quiet` and `--verbose` flags. Could be tied to Slicer's logging level. ## Reference Material | Source | Purpose | |--------|---------| | `TotalSegmentator/totalsegmentator/python_api.py` | Task definitions (resample, trainer, crop, model, folds) | | `TotalSegmentator/totalsegmentator/map_to_binary.py` | Label value-to-name mappings per task | | `TotalSegmentator/totalsegmentator/bin/TotalSegmentator.py` | CLI argument definitions | | `TotalSegmentator/CHANGELOG.md` | Version history v2.9.0 through v2.12.0 | ## Testing The following should be verified before merging: 1. Load extension in Slicer -- all tasks appear in dropdown including 7 new ones 2. Trigger package install -- confirms v2.12.0 is downloaded 3. Run `total` task on a CT volume -- basic segmentation works end-to-end 4. Run a new task (e.g., `trunk_cavities`) -- segments load with correct names/colors 5. `fastest` checkbox visible only for `total` and `total_mr` 6. Advanced options pass correct CLI flags 7. Fast checkbox defaults to ON for new parameter nodes 8. On Apple Silicon: MPS detection works and `--device mps` is passed --- Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com> Co-Authored-By: Andras Lasso <lasso@queensu.ca>

Khaldoun · February 20, 2026, 7:06pm

Hi Steve, thank you for your quick reply. I will try reporting on github issues for both even if I a not used to it but I will give it a try. Meantime, I am back to the latest relase version that I have kept installed ! Thank you once more

Khaldoun · February 20, 2026, 7:12pm

Hi James, Thank you for your quick reply and suggestion. As I told Steve I am phycisian with poor knowledge in python and github etc.. even if I am learning and improving but you are probably right so I will try to use the faster, fast and normal option on the Chest CT demo with total segmentator and see what it will look like. Still I dont know how to set “normal” on Lung CT Segment module in Chest Imaging Platform. Thaks again

lassoan · February 21, 2026, 9:43pm

Yes, as the log shows, the fastest (6mm voxel) is used.

The problem was due to indeed a backward incompatible API change when I updated TotalSegmentator. I’ve fixed it now. If you update TotalSegmentator extension tomorrow or later the quality should be back to normal.

Topic		Replies	Views
New extension: Fully automatic whole-body CT segmentation in 2 minutes using TotalSegmentator Support feature , segmentation , ai	61	35999	May 3, 2025
Not able to segment using TotalSegmentator Support segmentation , totalsegmentator	10	419	November 10, 2023
Failed to export file after total segmentation (fast, on CPU) Support	7	373	June 27, 2023
TotalSegmentator error at first run: Command ...Python\Scripts\TotalSegmentator... returned non-zero exit status 120 Support segmentation	29	3629	August 1, 2024
Failed to compute results - Total Segmentator Support	6	268	June 6, 2025

Lung CT segmenter from Chest Imaging Platform bad quality image and segmentation

Related topics