Problem report for Slicer 5.2.2 win-amd64: Hello, I am new to 3D Slicer (version 5.2.2) I ran totalsegmentator (fast on CPU) and then tried to export file, but failed. Thanks for any help
Logs
[DEBUG][Qt] 03.06.2023 17:45:37 (unknown:0) - Session start time …: 2023-06-03 17:45:37
[DEBUG][Qt] 03.06.2023 17:45:37 (unknown:0) - Slicer version …: 5.2.2 (revision 31382 / fb46bd1) win-amd64 - installed release
[DEBUG][Qt] 03.06.2023 17:45:37 (unknown:0) - Operating system …: Windows / Personal / (Build 19045, Code Page 65001) - 64-bit
[DEBUG][Qt] 03.06.2023 17:45:37 (unknown:0) - Memory …: 16234 MB physical, 18666 MB virtual
[DEBUG][Qt] 03.06.2023 17:45:37 (unknown:0) - CPU …: GenuineIntel , 12 cores, 12 logical processors
[DEBUG][Qt] 03.06.2023 17:45:37 (unknown:0) - VTK configuration …: OpenGL2 rendering, TBB threading
[DEBUG][Qt] 03.06.2023 17:45:37 (unknown:0) - Qt configuration …: version 5.15.2, with SSL, requested OpenGL 3.2 (compatibility profile)
[DEBUG][Qt] 03.06.2023 17:45:37 (unknown:0) - Internationalization …: disabled, language=
[DEBUG][Qt] 03.06.2023 17:45:37 (unknown:0) - Developer mode …: disabled
[DEBUG][Qt] 03.06.2023 17:45:37 (unknown:0) - Application path …: C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/bin
[DEBUG][Qt] 03.06.2023 17:45:37 (unknown:0) - Additional module paths …: NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules, NA-MIC/Extensions-31382/PyTorch/lib/Slicer-5.2/qt-scripted-modules, NA-MIC/Extensions-31382/SequenceRegistration/lib/Slicer-5.2/qt-scripted-modules, NA-MIC/Extensions-31382/SlicerElastix/lib/Slicer-5.2/qt-scripted-modules, NA-MIC/Extensions-31382/SlicerVMTK/lib/Slicer-5.2/qt-loadable-modules, NA-MIC/Extensions-31382/SlicerVMTK/lib/Slicer-5.2/qt-scripted-modules, NA-MIC/Extensions-31382/MarkupsToModel/lib/Slicer-5.2/qt-loadable-modules, NA-MIC/Extensions-31382/RVesselX/lib/Slicer-5.2/qt-scripted-modules, NA-MIC/Extensions-31382/ExtraMarkups/lib/Slicer-5.2/qt-loadable-modules, NA-MIC/Extensions-31382/MeshStatisticsExtension/lib/Slicer-5.2/qt-scripted-modules, NA-MIC/Extensions-31382/ModelToModelDistance/lib/Slicer-5.2/cli-modules, NA-MIC/Extensions-31382/DebuggingTools/lib/Slicer-5.2/qt-scripted-modules, NA-MIC/Extensions-31382/MONAILabel/lib/Slicer-5.2/qt-scripted-modules, NA-MIC/Extensions-31382/DensityLungSegmentation/lib/Slicer-5.2/qt-scripted-modules, NA-MIC/Extensions-31382/SurfaceWrapSolidify/lib/Slicer-5.2/qt-scripted-modules, NA-MIC/Extensions-31382/SegmentEditorExtraEffects/lib/Slicer-5.2/qt-loadable-modules, NA-MIC/Extensions-31382/SegmentEditorExtraEffects/lib/Slicer-5.2/qt-scripted-modules, NA-MIC/Extensions-31382/NvidiaAIAssistedAnnotation/lib/Slicer-5.2/qt-scripted-modules, NA-MIC/Extensions-31382/HDBrainExtraction/lib/Slicer-5.2/qt-scripted-modules, NA-MIC/Extensions-31382/Sandbox/lib/Slicer-5.2/qt-loadable-modules, NA-MIC/Extensions-31382/Sandbox/lib/Slicer-5.2/qt-scripted-modules, NA-MIC/Extensions-31382/SegmentMesher/lib/Slicer-5.2/qt-scripted-modules, NA-MIC/Extensions-31382/SegmentRegistration/lib/Slicer-5.2/qt-scripted-modules, NA-MIC/Extensions-31382/SlicerProstate/lib/Slicer-5.2/cli-modules, NA-MIC/Extensions-31382/SlicerProstate/lib/Slicer-5.2/qt-scripted-modules, NA-MIC/Extensions-31382/SlicerOpenAnatomy/lib/Slicer-5.2/qt-scripted-modules, NA-MIC/Extensions-31382/SlicerRT/lib/Slicer-5.2/cli-modules, NA-MIC/Extensions-31382/SlicerRT/lib/Slicer-5.2/qt-loadable-modules, NA-MIC/Extensions-31382/SlicerRT/lib/Slicer-5.2/qt-scripted-modules, NA-MIC/Extensions-31382/SlicerDevelopmentToolbox/lib/Slicer-5.2/qt-scripted-modules, NA-MIC/Extensions-31382/QuantitativeReporting/lib/Slicer-5.2/qt-scripted-modules, NA-MIC/Extensions-31382/DCMQI/lib/Slicer-5.2/cli-modules, NA-MIC/Extensions-31382/PETDICOMExtension/lib/Slicer-5.2/cli-modules, NA-MIC/Extensions-31382/PETDICOMExtension/lib/Slicer-5.2/qt-scripted-modules
[CRITICAL][Qt] 03.06.2023 17:45:44 (unknown:0) - Error(s):
CLI executable: C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/SlicerVMTK/lib/Slicer-5.2/qt-loadable-modules/vtkvmtk.py
The process failed to start. Either the invoked program is missing, or you may have insufficient permissions to invoke the program.
[CRITICAL][Qt] 03.06.2023 17:45:44 (unknown:0) - Fail to instantiate module “vtkvmtk”
[CRITICAL][Qt] 03.06.2023 17:45:44 (unknown:0) - The following modules failed to be instantiated:
[CRITICAL][Qt] 03.06.2023 17:45:44 (unknown:0) - vtkvmtk
[DEBUG][Python] 03.06.2023 17:45:46 [Python] (C:\Users\Simone\AppData\Local\NA-MIC\Slicer-5.2.2\lib\Slicer-5.2\qt-scripted-modules\SubjectHierarchyPlugins\AbstractScriptedSubjectHierarchyPlugin.py:38) - Scripted subject hierarchy plugin registered: Annotations
[CRITICAL][Stream] 03.06.2023 17:45:48 (unknown:0) - Failed to load vtkSlicerStenosisMeasurement3DModuleLogicPython: No module named vtkSlicerShapeModuleMRMLPython
[DEBUG][Python] 03.06.2023 17:45:49 [Python] (C:\Users\Simone\AppData\Local\NA-MIC\Slicer-5.2.2\lib\Slicer-5.2\qt-scripted-modules\SubjectHierarchyPlugins\AbstractScriptedSubjectHierarchyPlugin.py:38) - Scripted subject hierarchy plugin registered: SegmentEditor
[DEBUG][Python] 03.06.2023 17:45:50 [Python] (C:\Users\Simone\AppData\Local\NA-MIC\Slicer-5.2.2\lib\Slicer-5.2\qt-scripted-modules\SubjectHierarchyPlugins\AbstractScriptedSubjectHierarchyPlugin.py:38) - Scripted subject hierarchy plugin registered: SegmentStatistics
[DEBUG][Qt] 03.06.2023 17:45:50 (unknown:0) - Switch to module: “Welcome”
[INFO][Python] 03.06.2023 17:45:51 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/NvidiaAIAssistedAnnotation/lib/Slicer-5.2/qt-scripted-modules/SegmentEditorNvidiaAIAA.py:32) - This plugin dir: C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/NvidiaAIAssistedAnnotation/lib/Slicer-5.2/qt-scripted-modules
[INFO][VTK] 03.06.2023 17:45:51 [vtkMRMLVolumeArchetypeStorageNode (00000237BAB4B310)] (D:\D\S\S-0\Libs\MRML\Core\vtkMRMLVolumeArchetypeStorageNode.cxx:513) - Loaded volume from file: C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/SlicerVMTK/lib/Slicer-5.2/qt-scripted-modules/Resources/Vesselness.png. Dimensions: 65x50x1. Number of components: 3. Pixel type: unsigned char.
[DEBUG][Qt] 03.06.2023 17:46:30 (unknown:0) - Switch to module: “DICOM”
[DEBUG][Python] 03.06.2023 17:46:35 [Python] (C:\Users\Simone\AppData\Local\NA-MIC\Slicer-5.2.2\NA-MIC\Extensions-31382\QuantitativeReporting\lib\Slicer-5.2\qt-scripted-modules\base\DICOMPluginBase.py:52) - DICOMParametricMapPluginClass : Caching files
[DEBUG][Python] 03.06.2023 17:46:36 [Python] (C:\Users\Simone\AppData\Local\NA-MIC\Slicer-5.2.2\NA-MIC\Extensions-31382\QuantitativeReporting\lib\Slicer-5.2\qt-scripted-modules\base\DICOMPluginBase.py:49) - DICOMParametricMapPluginClass : Using cached files
[WARNING][Python] 03.06.2023 17:46:39 [Python] (C:\Users\Simone\AppData\Local\NA-MIC\Slicer-5.2.2\lib\Slicer-5.2\qt-scripted-modules\DICOMLib\DICOMUtils.py:697) - Geometric issues were found with 1 of the series. Please use caution.
[DEBUG][Python] 03.06.2023 17:46:39 [Python] (C:\Users\Simone\AppData\Local\NA-MIC\Slicer-5.2.2\NA-MIC\Extensions-31382\QuantitativeReporting\lib\Slicer-5.2\qt-scripted-modules\base\DICOMPluginBase.py:52) - DICOMSegmentationPluginClass : Caching files
[DEBUG][Python] 03.06.2023 17:46:40 [Python] (C:\Users\Simone\AppData\Local\NA-MIC\Slicer-5.2.2\NA-MIC\Extensions-31382\QuantitativeReporting\lib\Slicer-5.2\qt-scripted-modules\base\DICOMPluginBase.py:49) - DICOMSegmentationPluginClass : Using cached files
[DEBUG][Python] 03.06.2023 17:46:40 [Python] (C:\Users\Simone\AppData\Local\NA-MIC\Slicer-5.2.2\NA-MIC\Extensions-31382\QuantitativeReporting\lib\Slicer-5.2\qt-scripted-modules\base\DICOMPluginBase.py:52) - DICOMTID1500PluginClass : Caching files
[DEBUG][Python] 03.06.2023 17:46:50 [Python] (C:\Users\Simone\AppData\Local\NA-MIC\Slicer-5.2.2\NA-MIC\Extensions-31382\QuantitativeReporting\lib\Slicer-5.2\qt-scripted-modules\base\DICOMPluginBase.py:49) - DICOMTID1500PluginClass : Using cached files
[WARNING][Python] 03.06.2023 17:47:04 [Python] (C:\Users\Simone\AppData\Local\NA-MIC\Slicer-5.2.2\lib\Slicer-5.2\qt-scripted-modules\DICOMLib\DICOMBrowser.py:555) - Warning in DICOM plugin Scalar Volume when examining loadable 12: Venosa 1.5 Br59 1 Osteo: Images are not equally spaced (a difference of 1 vs 1 in spacings was detected). Slicer will apply a transform to this series trying to regularize the volume. Please use caution.
[INFO][Python] 03.06.2023 17:47:04 [Python] (C:\Users\Simone\AppData\Local\NA-MIC\Slicer-5.2.2\bin\Python\slicer\util.py:2736) - Warnings detected during load. Examine data in Advanced mode for details. Load anyway?
[INFO][Python] 03.06.2023 17:48:18 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/bin/…/lib/Slicer-5.2/qt-scripted-modules/DICOMScalarVolumePlugin.py:393) - Loading with imageIOName: GDCM
[WARNING][ITK] 03.06.2023 17:48:28 (unknown:0) - WARNING: In D:\D\S\S-0-build\ITK\Modules\IO\ImageBase\include\itkImageSeriesReader.hxx, line 478
ImageSeriesReader (00000237BF977AE0): Non uniform sampling or missing slices detected, maximum nonuniformity:1.95963
[WARNING][Python] 03.06.2023 17:48:29 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/bin/…/lib/Slicer-5.2/qt-scripted-modules/DICOMScalarVolumePlugin.py:837) - Irregular volume geometry detected (maximum error of 4.13354 mm is above tolerance threshold of 0.001 mm). Adding acquisition transform to regularize geometry.
[DEBUG][Python] 03.06.2023 17:49:31 [Python] (C:\Users\Simone\AppData\Local\NA-MIC\Slicer-5.2.2\NA-MIC\Extensions-31382\QuantitativeReporting\lib\Slicer-5.2\qt-scripted-modules\base\DICOMPluginBase.py:49) - DICOMParametricMapPluginClass : Using cached files
[DEBUG][Python] 03.06.2023 17:49:31 [Python] (C:\Users\Simone\AppData\Local\NA-MIC\Slicer-5.2.2\NA-MIC\Extensions-31382\QuantitativeReporting\lib\Slicer-5.2\qt-scripted-modules\base\DICOMPluginBase.py:49) - DICOMParametricMapPluginClass : Using cached files
[DEBUG][Python] 03.06.2023 17:49:31 [Python] (C:\Users\Simone\AppData\Local\NA-MIC\Slicer-5.2.2\NA-MIC\Extensions-31382\QuantitativeReporting\lib\Slicer-5.2\qt-scripted-modules\base\DICOMPluginBase.py:49) - DICOMSegmentationPluginClass : Using cached files
[DEBUG][Python] 03.06.2023 17:49:31 [Python] (C:\Users\Simone\AppData\Local\NA-MIC\Slicer-5.2.2\NA-MIC\Extensions-31382\QuantitativeReporting\lib\Slicer-5.2\qt-scripted-modules\base\DICOMPluginBase.py:49) - DICOMSegmentationPluginClass : Using cached files
[DEBUG][Python] 03.06.2023 17:49:31 [Python] (C:\Users\Simone\AppData\Local\NA-MIC\Slicer-5.2.2\NA-MIC\Extensions-31382\QuantitativeReporting\lib\Slicer-5.2\qt-scripted-modules\base\DICOMPluginBase.py:49) - DICOMTID1500PluginClass : Using cached files
[DEBUG][Python] 03.06.2023 17:49:31 [Python] (C:\Users\Simone\AppData\Local\NA-MIC\Slicer-5.2.2\NA-MIC\Extensions-31382\QuantitativeReporting\lib\Slicer-5.2\qt-scripted-modules\base\DICOMPluginBase.py:49) - DICOMTID1500PluginClass : Using cached files
[WARNING][Python] 03.06.2023 17:49:45 [Python] (C:\Users\Simone\AppData\Local\NA-MIC\Slicer-5.2.2\lib\Slicer-5.2\qt-scripted-modules\DICOMLib\DICOMBrowser.py:555) - Warning in DICOM plugin Scalar Volume when examining loadable 12: Venosa 1.5 Br59 1 Osteo: Images are not equally spaced (a difference of 1 vs 1 in spacings was detected). Slicer will apply a transform to this series trying to regularize the volume. Please use caution.
[INFO][Python] 03.06.2023 17:49:45 [Python] (C:\Users\Simone\AppData\Local\NA-MIC\Slicer-5.2.2\bin\Python\slicer\util.py:2736) - Warnings detected during load. Examine data in Advanced mode for details. Load anyway?
[INFO][Python] 03.06.2023 17:49:47 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/bin/…/lib/Slicer-5.2/qt-scripted-modules/DICOMScalarVolumePlugin.py:393) - Loading with imageIOName: GDCM
[WARNING][ITK] 03.06.2023 17:49:56 (unknown:0) - WARNING: In D:\D\S\S-0-build\ITK\Modules\IO\ImageBase\include\itkImageSeriesReader.hxx, line 478
ImageSeriesReader (00000237BF979A60): Non uniform sampling or missing slices detected, maximum nonuniformity:1.95963
[WARNING][Python] 03.06.2023 17:49:58 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/bin/…/lib/Slicer-5.2/qt-scripted-modules/DICOMScalarVolumePlugin.py:837) - Irregular volume geometry detected (maximum error of 4.13354 mm is above tolerance threshold of 0.001 mm). Adding acquisition transform to regularize geometry.
[DEBUG][Qt] 03.06.2023 17:50:05 (unknown:0) - Switch to module: “Segmentations”
[DEBUG][Qt] 03.06.2023 17:50:22 (unknown:0) - Switch to module: “TotalSegmentator”
[DEBUG][Python] 03.06.2023 17:50:31 [Python] (C:\Users\Simone\AppData\Local\NA-MIC\Slicer-5.2.2\lib\Python\Lib\site-packages\matplotlib_init_.py:337) - matplotlib data path: C:\Users\Simone\AppData\Local\NA-MIC\Slicer-5.2.2\lib\Python\Lib\site-packages\matplotlib\mpl-data
[DEBUG][Python] 03.06.2023 17:50:31 [Python] (C:\Users\Simone\AppData\Local\NA-MIC\Slicer-5.2.2\lib\Python\Lib\site-packages\matplotlib_init_.py:337) - CONFIGDIR=C:\Users\Simone.matplotlib
[DEBUG][Python] 03.06.2023 17:50:31 [Python] (C:\Users\Simone\AppData\Local\NA-MIC\Slicer-5.2.2\lib\Python\Lib\site-packages\matplotlib_init_.py:1505) - interactive is False
[DEBUG][Python] 03.06.2023 17:50:31 [Python] (C:\Users\Simone\AppData\Local\NA-MIC\Slicer-5.2.2\lib\Python\Lib\site-packages\matplotlib_init_.py:1506) - platform is win32
[INFO][Python] 03.06.2023 17:50:31 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py:521) - Processing started
[INFO][Python] 03.06.2023 17:50:31 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py:521) - Writing input file to C:/Users/Simone/AppData/Local/Temp/Slicer/__SlicerTemp__2023-06-03_17+50+31.634/total-segmentator-input.nii
[INFO][Python] 03.06.2023 17:50:32 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py:521) - Creating segmentations with TotalSegmentator AI…
[INFO][Python] 03.06.2023 17:50:32 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py:521) - Total Segmentator arguments: [‘-i’, ‘C:/Users/Simone/AppData/Local/Temp/Slicer/__SlicerTemp__2023-06-03_17+50+31.634/total-segmentator-input.nii’, ‘-o’, ‘C:/Users/Simone/AppData/Local/Temp/Slicer/__SlicerTemp__2023-06-03_17+50+31.634/segmentation’, ‘–ml’, ‘–task’, ‘total’, ‘–fast’]
[INFO][Python] 03.06.2023 17:51:16 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py:521) -
[INFO][Python] 03.06.2023 17:51:16 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py:521) -
[INFO][Python] 03.06.2023 17:51:16 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py:521) - Please cite the following paper when using nnUNet:
[INFO][Python] 03.06.2023 17:51:16 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py:521) -
[INFO][Python] 03.06.2023 17:51:16 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py:521) - Isensee, F., Jaeger, P.F., Kohl, S.A.A. et al. “nnU-Net: a self-configuring method for deep learning-based biomedical image segmentation.” Nat Methods (2020). nnU-Net: a self-configuring method for deep learning-based biomedical image segmentation | Nature Methods
[INFO][Python] 03.06.2023 17:51:17 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py:521) -
[INFO][Python] 03.06.2023 17:51:17 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py:521) -
[INFO][Python] 03.06.2023 17:51:17 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py:521) - If you have questions or suggestions, feel free to open an issue at GitHub - MIC-DKFZ/nnUNet
[INFO][Python] 03.06.2023 17:51:17 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py:521) -
[INFO][Python] 03.06.2023 17:51:17 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py:521) - preprocessing C:\Users\Simone\AppData\Local\Temp\nnunet_tmp_79zcp9bd\s01.nii.gz
[INFO][Python] 03.06.2023 17:51:17 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py:521) - using preprocessor GenericPreprocessor
[INFO][Python] 03.06.2023 17:51:17 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py:521) - before crop: (1, 224, 117, 117) after crop: (1, 224, 117, 117) spacing: [3. 3. 3.]
[INFO][Python] 03.06.2023 17:51:17 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py:521) -
[INFO][Python] 03.06.2023 17:51:17 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py:521) - no resampling necessary
[INFO][Python] 03.06.2023 17:51:17 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py:521) - no resampling necessary
[INFO][Python] 03.06.2023 17:51:17 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py:521) - before: {‘spacing’: array([3., 3., 3.]), ‘spacing_transposed’: array([3., 3., 3.]), ‘data.shape (data is transposed)’: (1, 224, 117, 117)}
[INFO][Python] 03.06.2023 17:51:17 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py:521) - after: {‘spacing’: array([3., 3., 3.]), ‘data.shape (data is resampled)’: (1, 224, 117, 117)}
[INFO][Python] 03.06.2023 17:51:17 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py:521) -
[INFO][Python] 03.06.2023 17:51:17 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py:521) - (1, 224, 117, 117)
[INFO][Python] 03.06.2023 17:51:17 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py:521) - This worker has ended successfully, no errors to report
[INFO][Python] 03.06.2023 17:51:17 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py:521) - C:\Users\Simone\AppData\Local\NA-MIC\Slicer-5.2.2\lib\Python\Lib\site-packages\torch\cuda\amp\grad_scaler.py:120: UserWarning: torch.cuda.amp.GradScaler is enabled, but CUDA is not available. Disabling.
[INFO][Python] 03.06.2023 17:51:17 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py:521) - warnings.warn(“torch.cuda.amp.GradScaler is enabled, but CUDA is not available. Disabling.”)
[INFO][Python] 03.06.2023 17:51:17 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py:521) - C:\Users\Simone\AppData\Local\NA-MIC\Slicer-5.2.2\lib\Python\Lib\site-packages\torch\amp\autocast_mode.py:204: UserWarning: User provided device_type of ‘cuda’, but CUDA is not available. Disabling
[INFO][Python] 03.06.2023 17:51:17 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py:521) - warnings.warn(‘User provided device_type of 'cuda', but CUDA is not available. Disabling’)
[INFO][Python] 03.06.2023 17:53:45 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py:521) -
[INFO][Python] 03.06.2023 17:53:45 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py:521) -
[INFO][Python] 03.06.2023 17:53:45 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py:521) - Please cite the following paper when using nnUNet:
[INFO][Python] 03.06.2023 17:53:45 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py:521) -
[INFO][Python] 03.06.2023 17:53:45 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py:521) - Isensee, F., Jaeger, P.F., Kohl, S.A.A. et al. “nnU-Net: a self-configuring method for deep learning-based biomedical image segmentation.” Nat Methods (2020). nnU-Net: a self-configuring method for deep learning-based biomedical image segmentation | Nature Methods
[INFO][Python] 03.06.2023 17:53:45 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py:521) -
[INFO][Python] 03.06.2023 17:53:45 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py:521) -
[INFO][Python] 03.06.2023 17:53:45 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py:521) - If you have questions or suggestions, feel free to open an issue at GitHub - MIC-DKFZ/nnUNet
[INFO][Python] 03.06.2023 17:53:45 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py:521) -
[INFO][Python] 03.06.2023 17:53:45 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py:521) - force_separate_z: None interpolation order: 0
[INFO][Python] 03.06.2023 17:54:10 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py:521) -
[INFO][Python] 03.06.2023 17:54:10 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py:521) - If you use this tool please cite: [2208.05868] TotalSegmentator: robust segmentation of 104 anatomical structures in CT images
[INFO][Python] 03.06.2023 17:54:10 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py:521) -
[INFO][Python] 03.06.2023 17:54:10 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py:521) - No GPU detected. Running on CPU. This can be very slow. The ‘–fast’ option can help to some extend.
[INFO][Python] 03.06.2023 17:54:10 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py:521) - Using ‘fast’ option: resampling to lower resolution (3mm)
[INFO][Python] 03.06.2023 17:54:10 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py:521) - Resampling…
[INFO][Python] 03.06.2023 17:54:10 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py:521) - Resampled in 15.60s
[INFO][Python] 03.06.2023 17:54:10 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py:521) - Predicting…
[INFO][Python] 03.06.2023 17:54:10 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py:521) - Predicted in 164.26s
[INFO][Python] 03.06.2023 17:54:10 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py:521) - Resampling…
[INFO][Python] 03.06.2023 17:54:10 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py:521) - Saving segmentations…
[INFO][Python] 03.06.2023 17:54:10 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py:521) - Saved in 10.85s
[INFO][Python] 03.06.2023 17:54:11 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py:521) - Importing segmentation results…
[INFO][VTK] 03.06.2023 17:54:11 [vtkMRMLSegmentationStorageNode (00000237BCF8E790)] (D:\D\S\S-0\Libs\MRML\Core\vtkMRMLSegmentationStorageNode.cxx:624) - ReferenceImageExtentOffset attribute was not found in NRRD segmentation file. Assume no offset.
[INFO][Python] 03.06.2023 17:54:33 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py:521) - Cleaning up temporary folder…
[INFO][Python] 03.06.2023 17:54:33 [Python] (C:/Users/Simone/AppData/Local/NA-MIC/Slicer-5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py:521) - Processing completed in 242.40 seconds
[DEBUG][Qt] 03.06.2023 17:54:44 (unknown:0) - Switch to module: “SegmentEditor”
[WARNING][Qt] 03.06.2023 17:54:44 (unknown:0) - QLayout::addChildLayout: layout “” already has a parent
[WARNING][Qt] 03.06.2023 17:54:56 (unknown:0) - ctkSliderWidget::setSingleStep() 0 is out of bounds. 0 100 1
[DEBUG][Qt] 03.06.2023 17:55:00 (unknown:0) - Switch to module: “Segmentations”
[CRITICAL][Qt] 03.06.2023 17:56:20 (unknown:0) - double __cdecl qSlicerSubjectHierarchyFolderPlugin::canOwnSubjectHierarchyItem(__int64) const : Input item is invalid
[WARNING][VTK] 03.06.2023 17:56:20 [vtkMRMLSubjectHierarchyNode (00000237B9D66510)] (D:\D\S\S-0\Libs\MRML\Core\vtkMRMLSubjectHierarchyNode.cxx:2102) - GetItemDataNode: Invalid item ID given