Operating system: Windows 10
Slicer version: 4.10.2
Expected behavior: Load segmentation DICOM images
Actual behavior: Unable to load, with error message
Hi,
I am trying to open a DICOM file with segmentation of an MRI in slicer, unsuccessfully. I have checked a couple post on similar issues before, but it seems to be a different issue. The segmentation was generated on a Siemens workstation.
I have the following toolboxes
QuantiativeReporting
SlicerRT
SlicerDevelopmentToolbox
The log is below.
Any suggestions?
Thank you.
[DEBUG][Qt] 18.12.2020 22:36:44 [] (unknown:0) - Session start time …: 2020-12-18 22:36:44
[DEBUG][Qt] 18.12.2020 22:36:44 [] (unknown:0) - Slicer version …: 4.10.2 (revision 28257) win-amd64 - installed release
[DEBUG][Qt] 18.12.2020 22:36:44 [] (unknown:0) - Operating system …: Windows / Professional / (Build 9200) - 64-bit
[DEBUG][Qt] 18.12.2020 22:36:44 [] (unknown:0) - Memory …: 8035 MB physical, 15715 MB virtual
[DEBUG][Qt] 18.12.2020 22:36:44 [] (unknown:0) - CPU …: GenuineIntel , 8 cores, 8 logical processors
[DEBUG][Qt] 18.12.2020 22:36:44 [] (unknown:0) - VTK configuration …: OpenGL2 rendering, TBB threading
[DEBUG][Qt] 18.12.2020 22:36:44 [] (unknown:0) - Developer mode enabled …: yes
[DEBUG][Qt] 18.12.2020 22:36:44 [] (unknown:0) - Prefer executable CLI …: yes
[DEBUG][Qt] 18.12.2020 22:36:44 [] (unknown:0) - Additional module paths …: C:/Users/mohaas01/AppData/Roaming/NA-MIC/Extensions-28257/SlicerDevelopmentToolbox/lib/Slicer-4.10/qt-scripted-modules, C:/Users/mohaas01/AppData/Roaming/NA-MIC/Extensions-28257/SlicerRT/lib/Slicer-4.10/cli-modules, C:/Users/mohaas01/AppData/Roaming/NA-MIC/Extensions-28257/SlicerRT/lib/Slicer-4.10/qt-loadable-modules, C:/Users/mohaas01/AppData/Roaming/NA-MIC/Extensions-28257/SlicerRT/lib/Slicer-4.10/qt-scripted-modules, C:/Users/mohaas01/AppData/Roaming/NA-MIC/Extensions-28257/DCMQI/lib/Slicer-4.10/cli-modules, C:/Users/mohaas01/AppData/Roaming/NA-MIC/Extensions-28257/QuantitativeReporting/lib/Slicer-4.10/qt-scripted-modules
[DEBUG][Python] 18.12.2020 22:36:56 [Python] (C:\Program Files\Slicer 4.10.2\lib\Slicer-4.10\qt-scripted-modules\SubjectHierarchyPlugins\AbstractScriptedSubjectHierarchyPlugin.py:36) - Scripted subject hierarchy plugin registered: Annotations
[DEBUG][Python] 18.12.2020 22:36:59 [Python] (C:\Program Files\Slicer 4.10.2\lib\Slicer-4.10\qt-scripted-modules\SubjectHierarchyPlugins\AbstractScriptedSubjectHierarchyPlugin.py:36) - Scripted subject hierarchy plugin registered: SegmentEditor
[DEBUG][Python] 18.12.2020 22:36:59 [Python] (C:\Program Files\Slicer 4.10.2\lib\Slicer-4.10\qt-scripted-modules\SubjectHierarchyPlugins\AbstractScriptedSubjectHierarchyPlugin.py:36) - Scripted subject hierarchy plugin registered: SegmentStatistics
[DEBUG][Qt] 18.12.2020 22:36:59 [] (unknown:0) - Switch to module: “Welcome”
[WARNING][Qt] 18.12.2020 22:39:27 [] (unknown:0) - An OpenGL Core Profile was requested, but it is not supported on the current platform. Falling back to a non-Core profile. Note that this might cause rendering issues.
[WARNING][Qt] 18.12.2020 22:39:27 [] (unknown:0) - QPixmap::scaled: Pixmap is a null pixmap
[WARNING][Qt] 18.12.2020 22:39:27 [] (unknown:0) - QPixmap::scaled: Pixmap is a null pixmap
[WARNING][Qt] 18.12.2020 22:39:27 [] (unknown:0) - Remote debugging server started successfully. Try pointing a Chromium-based browser to http://127.0.0.1:1337
[DEBUG][Qt] 18.12.2020 22:41:51 [] (unknown:0) - Switch to module: “DICOM”
[DEBUG][Qt] 18.12.2020 22:41:54 [] (unknown:0) - Deleting 1 patients
[DEBUG][Qt] 18.12.2020 22:41:54 [] (unknown:0) - SQLITE: removing seriesInstanceUID 1.3.12.2.1107.5.4.5.164247.30000020072022243746900000203
[DEBUG][Qt] 18.12.2020 22:41:54 [] (unknown:0) - SQLITE: removing seriesInstanceUID 1.3.12.2.1107.5.4.5.164247.30000020072022243746900000397
[CRITICAL][Stream] 18.12.2020 22:42:09 [] (unknown:0) - DICOM dataset contains some encoding that we never thought we would see(ISO 2022 IR 100). Using default encoding.
[CRITICAL][Stream] 18.12.2020 22:42:09 [] (unknown:0) - DICOM dataset contains some encoding that we never thought we would see(ISO 2022 IR 100). Using default encoding.
[CRITICAL][Stream] 18.12.2020 22:42:09 [] (unknown:0) - DICOM dataset contains some encoding that we never thought we would see(ISO 2022 IR 100). Using default encoding.
[CRITICAL][Stream] 18.12.2020 22:42:09 [] (unknown:0) - DICOM dataset contains some encoding that we never thought we would see(ISO 2022 IR 100). Using default encoding.
[DEBUG][Qt] 18.12.2020 22:42:09 [] (unknown:0) - New patient inserted: 109
[DEBUG][Qt] 18.12.2020 22:42:09 [] (unknown:0) - New patient inserted as : 109
[DEBUG][Qt] 18.12.2020 22:42:09 [] (unknown:0) - Need to insert new study: “1.3.12.2.1107.5.4.5.164247.30000020072022243746900000202”
[CRITICAL][Stream] 18.12.2020 22:42:09 [] (unknown:0) - DICOM dataset contains some encoding that we never thought we would see(ISO 2022 IR 100). Using default encoding.
[CRITICAL][Stream] 18.12.2020 22:42:09 [] (unknown:0) - DICOM dataset contains some encoding that we never thought we would see(ISO 2022 IR 100). Using default encoding.
[CRITICAL][Stream] 18.12.2020 22:42:09 [] (unknown:0) - DICOM dataset contains some encoding that we never thought we would see(ISO 2022 IR 100). Using default encoding.
[DEBUG][Qt] 18.12.2020 22:42:09 [] (unknown:0) - Study Added
[DEBUG][Qt] 18.12.2020 22:42:09 [] (unknown:0) - Need to insert new series: “1.3.12.2.1107.5.4.5.164247.30000020072022243746900000397”
[DEBUG][Qt] 18.12.2020 22:42:09 [] (unknown:0) - Series Added
[DEBUG][Qt] 18.12.2020 22:42:09 [] (unknown:0) - “DICOM indexer has successfully processed 1 files [0.19s]”
[INFO][Python] 18.12.2020 22:42:11 [Python] (C:\Program Files\Slicer 4.10.2\lib\Slicer-4.10\qt-scripted-modules\DICOMLib\DICOMWidgets.py:471) - Imported a DICOM directory, checking for extensions
[INFO][Stream] 18.12.2020 22:42:11 [] (unknown:0) - Imported a DICOM directory, checking for extensions
[DEBUG][Python] 18.12.2020 22:42:37 [Python] (C:\Users\mohaas01\AppData\Roaming\NA-MIC\Extensions-28257\QuantitativeReporting\lib\Slicer-4.10\qt-scripted-modules\base\DICOMPluginBase.py:52) - DICOMParametricMapPluginClass : Caching files
[DEBUG][Python] 18.12.2020 22:42:37 [Python] (C:\Users\mohaas01\AppData\Roaming\NA-MIC\Extensions-28257\QuantitativeReporting\lib\Slicer-4.10\qt-scripted-modules\base\DICOMPluginBase.py:52) - DICOMParametricMapPluginClass : Caching files
[DEBUG][Python] 18.12.2020 22:42:44 [Python] (C:\Users\mohaas01\AppData\Roaming\NA-MIC\Extensions-28257\QuantitativeReporting\lib\Slicer-4.10\qt-scripted-modules\base\DICOMPluginBase.py:49) - DICOMParametricMapPluginClass : Using cached files
[DEBUG][Python] 18.12.2020 22:42:44 [Python] (C:\Users\mohaas01\AppData\Roaming\NA-MIC\Extensions-28257\QuantitativeReporting\lib\Slicer-4.10\qt-scripted-modules\base\DICOMPluginBase.py:49) - DICOMParametricMapPluginClass : Using cached files
[DEBUG][Python] 18.12.2020 22:42:44 [Python] (C:/Program Files/Slicer 4.10.2/bin/…/lib/Slicer-4.10/qt-scripted-modules/MultiVolumeImporterPlugin.py:455) - MultiVolumeImportPlugin::examine
[DEBUG][Python] 18.12.2020 22:42:47 [Python] (C:/Program Files/Slicer 4.10.2/bin/…/lib/Slicer-4.10/qt-scripted-modules/MultiVolumeImporterPlugin.py:495) - DICOMMultiVolumePlugin found 1 multivolumes!
[DEBUG][Python] 18.12.2020 22:42:48 [Python] (C:/Program Files/Slicer 4.10.2/bin/…/lib/Slicer-4.10/qt-scripted-modules/MultiVolumeImporterPlugin.py:455) - MultiVolumeImportPlugin::examine
[DEBUG][Python] 18.12.2020 22:43:24 [Python] (C:/Program Files/Slicer 4.10.2/bin/…/lib/Slicer-4.10/qt-scripted-modules/MultiVolumeImporterPlugin.py:495) - DICOMMultiVolumePlugin found 1 multivolumes!
[DEBUG][Python] 18.12.2020 22:43:55 [Python] (C:/Program Files/Slicer 4.10.2/bin/…/lib/Slicer-4.10/qt-scripted-modules/MultiVolumeImporterPlugin.py:165) - MultiVolumeImportPlugin:examineMultiseries
[DEBUG][Python] 18.12.2020 22:44:07 [Python] (C:/Program Files/Slicer 4.10.2/bin/…/lib/Slicer-4.10/qt-scripted-modules/MultiVolumeImporterPlugin.py:170) - DICOMMultiVolumePlugin found 0 multivolumes!
[INFO][Stream] 18.12.2020 22:44:12 [] (unknown:0) - reg inside examine
[DEBUG][Python] 18.12.2020 22:44:13 [Python] (C:\Users\mohaas01\AppData\Roaming\NA-MIC\Extensions-28257\QuantitativeReporting\lib\Slicer-4.10\qt-scripted-modules\base\DICOMPluginBase.py:52) - DICOMSegmentationPluginClass : Caching files
[DEBUG][Python] 18.12.2020 22:44:13 [Python] (C:/Users/mohaas01/AppData/Roaming/NA-MIC/Extensions-28257/QuantitativeReporting/lib/Slicer-4.10/qt-scripted-modules/DICOMSegmentationPlugin.py:60) - DICOM SEG modality found
[DEBUG][Python] 18.12.2020 22:44:13 [Python] (C:/Users/mohaas01/AppData/Roaming/NA-MIC/Extensions-28257/QuantitativeReporting/lib/Slicer-4.10/qt-scripted-modules/DICOMSegmentationPlugin.py:60) - DICOM SEG modality found
[DEBUG][Python] 18.12.2020 22:44:13 [Python] (C:\Users\mohaas01\AppData\Roaming\NA-MIC\Extensions-28257\QuantitativeReporting\lib\Slicer-4.10\qt-scripted-modules\base\DICOMPluginBase.py:52) - DICOMSegmentationPluginClass : Caching files
[DEBUG][Python] 18.12.2020 22:44:20 [Python] (C:\Users\mohaas01\AppData\Roaming\NA-MIC\Extensions-28257\QuantitativeReporting\lib\Slicer-4.10\qt-scripted-modules\base\DICOMPluginBase.py:52) - DICOMTID1500PluginClass : Caching files
[DEBUG][Python] 18.12.2020 22:44:20 [Python] (C:\Users\mohaas01\AppData\Roaming\NA-MIC\Extensions-28257\QuantitativeReporting\lib\Slicer-4.10\qt-scripted-modules\base\DICOMPluginBase.py:52) - DICOMTID1500PluginClass : Caching files
[DEBUG][Python] 18.12.2020 22:44:20 [Python] (C:\Users\mohaas01\AppData\Roaming\NA-MIC\Extensions-28257\QuantitativeReporting\lib\Slicer-4.10\qt-scripted-modules\base\DICOMPluginBase.py:49) - DICOMTID1500PluginClass : Using cached files
[DEBUG][Python] 18.12.2020 22:44:20 [Python] (C:\Users\mohaas01\AppData\Roaming\NA-MIC\Extensions-28257\QuantitativeReporting\lib\Slicer-4.10\qt-scripted-modules\base\DICOMPluginBase.py:49) - DICOMTID1500PluginClass : Using cached files
[DEBUG][Python] 18.12.2020 22:44:44 [Python] (C:/Users/mohaas01/AppData/Roaming/NA-MIC/Extensions-28257/QuantitativeReporting/lib/Slicer-4.10/qt-scripted-modules/DICOMSegmentationPlugin.py:81) - DICOM SEG load()
[DEBUG][Python] 18.12.2020 22:44:44 [Python] (C:/Users/mohaas01/AppData/Roaming/NA-MIC/Extensions-28257/QuantitativeReporting/lib/Slicer-4.10/qt-scripted-modules/DICOMSegmentationPlugin.py:84) - in load(): uid = 1.3.12.2.1107.5.4.5.164247.30000020072022243746900000399
[ERROR][Python] 18.12.2020 22:44:45 [Python] (C:/Users/mohaas01/AppData/Roaming/NA-MIC/Extensions-28257/QuantitativeReporting/lib/Slicer-4.10/qt-scripted-modules/DICOMSegmentationPlugin.py:117) - SEG2NRRD did not complete successfully, unable to load DICOM Segmentation
[DEBUG][Python] 18.12.2020 22:44:45 [Python] (C:\Users\mohaas01\AppData\Roaming\NA-MIC\Extensions-28257\QuantitativeReporting\lib\Slicer-4.10\qt-scripted-modules\base\DICOMPluginBase.py:34) - Cleaning up temporarily created directory C:/Users/mohaas01/AppData/Local/Temp/Slicer\QIICR\SEG\2020-12-18_224444\1.3.12.2.1107.5.4.5.164247.30000020072022243746900000399
[DEBUG][Qt] 18.12.2020 22:44:44 [] (unknown:0) - Found CommandLine Module, target is C:/Users/mohaas01/AppData/Roaming/NA-MIC/Extensions-28257/DCMQI/lib/Slicer-4.10/cli-modules/segimage2itkimage.exe
[DEBUG][Qt] 18.12.2020 22:44:44 [] (unknown:0) - ModuleType: CommandLineModule
[DEBUG][Qt] 18.12.2020 22:44:44 [] (unknown:0) - Convert DICOM Segmentation Image into ITK image(s) command line:
C:/Users/mohaas01/AppData/Roaming/NA-MIC/Extensions-28257/DCMQI/lib/Slicer-4.10/cli-modules/segimage2itkimage.exe --inputDICOM D:/MyData/JikeiTumorSegmentation/Test/CASE3_MRI_PRE_1.SEG.0016.0002.2020_20200730_103640831_003331.IMA --outputDirectory C:/Users/mohaas01/AppData/Local/Temp/Slicer\QIICR\SEG\2020-12-18_224444\1.3.12.2.1107.5.4.5.164247.30000020072022243746900000399 --outputType nrrd
[DEBUG][Qt] 18.12.2020 22:44:45 [] (unknown:0) - Convert DICOM Segmentation Image into ITK image(s) standard output:
dcmqi repository URL: git://github.com/QIICR/dcmqi.git revision: a33fa9e tag: v1.2.2
[ERROR][VTK] 18.12.2020 22:44:45 [vtkSlicerCLIModuleLogic (000002595ED33990)] (D:\D\S\Slicer-4102\Base\QTCLI\vtkSlicerCLIModuleLogic.cxx:2056) - Convert DICOM Segmentation Image into ITK image(s) standard error:
W: CodingSchemeDesignator (0008,0102) absent in CodeSequenceMacro (type 1)
W: CodeMeaning (0008,0104) absent in CodeSequenceMacro (type 1)
W: FrameOfReferenceUID (0020,0052) absent in FrameOfReferenceModule (type 1)
W: DeviceSerialNumber (0018,1000) absent in EnhancedGeneralEquipmentModule (type 1)
Plane Orientation (Patient) is missing, cannot parse input
ERROR: Failed to get image directions!
Fatal error encountered.
[ERROR][VTK] 18.12.2020 22:44:45 [vtkSlicerCLIModuleLogic (000002595ED33990)] (D:\D\S\Slicer-4102\Base\QTCLI\vtkSlicerCLIModuleLogic.cxx:2087) - Convert DICOM Segmentation Image into ITK image(s) completed with errors
[CRITICAL][Stream] 18.12.2020 22:44:45 [] (unknown:0) - SEG2NRRD did not complete successfully, unable to load DICOM Segmentation
[DEBUG][Python] 18.12.2020 22:44:45 [Python] (C:/Users/mohaas01/AppData/Roaming/NA-MIC/Extensions-28257/QuantitativeReporting/lib/Slicer-4.10/qt-scripted-modules/DICOMSegmentationPlugin.py:81) - DICOM SEG load()
[DEBUG][Python] 18.12.2020 22:44:45 [Python] (C:/Users/mohaas01/AppData/Roaming/NA-MIC/Extensions-28257/QuantitativeReporting/lib/Slicer-4.10/qt-scripted-modules/DICOMSegmentationPlugin.py:84) - in load(): uid = 1.3.12.2.1107.5.4.5.164247.30000020072022243746900000398
[ERROR][Python] 18.12.2020 22:44:45 [Python] (C:/Users/mohaas01/AppData/Roaming/NA-MIC/Extensions-28257/QuantitativeReporting/lib/Slicer-4.10/qt-scripted-modules/DICOMSegmentationPlugin.py:117) - SEG2NRRD did not complete successfully, unable to load DICOM Segmentation
[DEBUG][Python] 18.12.2020 22:44:45 [Python] (C:\Users\mohaas01\AppData\Roaming\NA-MIC\Extensions-28257\QuantitativeReporting\lib\Slicer-4.10\qt-scripted-modules\base\DICOMPluginBase.py:34) - Cleaning up temporarily created directory C:/Users/mohaas01/AppData/Local/Temp/Slicer\QIICR\SEG\2020-12-18_224444\1.3.12.2.1107.5.4.5.164247.30000020072022243746900000398
[DEBUG][Qt] 18.12.2020 22:44:45 [] (unknown:0) - Found CommandLine Module, target is C:/Users/mohaas01/AppData/Roaming/NA-MIC/Extensions-28257/DCMQI/lib/Slicer-4.10/cli-modules/segimage2itkimage.exe
[DEBUG][Qt] 18.12.2020 22:44:45 [] (unknown:0) - ModuleType: CommandLineModule
[DEBUG][Qt] 18.12.2020 22:44:45 [] (unknown:0) - Convert DICOM Segmentation Image into ITK image(s) command line:
C:/Users/mohaas01/AppData/Roaming/NA-MIC/Extensions-28257/DCMQI/lib/Slicer-4.10/cli-modules/segimage2itkimage.exe --outputDirectory C:/Users/mohaas01/AppData/Local/Temp/Slicer\QIICR\SEG\2020-12-18_224444\1.3.12.2.1107.5.4.5.164247.30000020072022243746900000398 --outputType nrrd
[DEBUG][Qt] 18.12.2020 22:44:45 [] (unknown:0) - Convert DICOM Segmentation Image into ITK image(s) standard output:
dcmqi repository URL: git://github.com/QIICR/dcmqi.git revision: a33fa9e tag: v1.2.2
[ERROR][VTK] 18.12.2020 22:44:45 [vtkSlicerCLIModuleLogic (000002595ED33990)] (D:\D\S\Slicer-4102\Base\QTCLI\vtkSlicerCLIModuleLogic.cxx:2056) - Convert DICOM Segmentation Image into ITK image(s) standard error:
Error: Input DICOM file must be specified!
[ERROR][VTK] 18.12.2020 22:44:45 [vtkSlicerCLIModuleLogic (000002595ED33990)] (D:\D\S\Slicer-4102\Base\QTCLI\vtkSlicerCLIModuleLogic.cxx:2087) - Convert DICOM Segmentation Image into ITK image(s) completed with errors
[CRITICAL][Stream] 18.12.2020 22:44:45 [] (unknown:0) - SEG2NRRD did not complete successfully, unable to load DICOM Segmentation
[INFO][Python] 18.12.2020 22:44:45 [Python] (C:/Program Files/Slicer 4.10.2/bin/…/lib/Slicer-4.10/qt-scripted-modules/DICOMScalarVolumePlugin.py:303) - Loading with imageIOName: GDCM
[INFO][Python] 18.12.2020 22:44:52 [Python] (C:/Program Files/Slicer 4.10.2/bin/…/lib/Slicer-4.10/qt-scripted-modules/DICOMScalarVolumePlugin.py:375) - Window/level found in DICOM tags (center=33.0, width=88.0) has been applied to volume Unnamed Series
[WARNING][Python] 18.12.2020 22:44:53 [Python] (C:/Program Files/Slicer 4.10.2/bin/…/lib/Slicer-4.10/qt-scripted-modules/DICOMScalarVolumePlugin.py:697) - Irregular volume geometry detected (maximum error of 0.00133695 mm is above tolerance threshold of 0.001 mm). Adding acquisition transform to regularize geometry.
[WARNING][Python] 18.12.2020 22:44:53 [Python] (C:\Program Files\Slicer 4.10.2\bin\Python\slicer\util.py:1110) -
Could not load: Unknown as a DICOMSegmentation
Could not load: Unknown as a DICOMSegmentation