Returning to the original topic of this post, I have been trying to export the segmentations made in Slicer as a DICOM dataset. What I would like to do is burn in my segmentation as an outline over the original CT dataset and then export that as a new uneditable DICOM dataset.
Orignal CT ------> Segmentation ------> New CT with Segmentation burned in
From the above discussion, it seems that based on the program that the end user will be viewing the file in, I need to export my segmentation as a DICOM RTSTRUCT file. I tried to replicate this tutorial (Create DICOM files from CT volume and segmentation - YouTube) but I keep receiving an error on the export.
Below is the error log corresponding to the screenshot:
Application log
[DEBUG][Qt] 28.12.2018 10:40:01 (unknown:0) - Session start time …: 2018-12-28 10:40:01
[DEBUG][Qt] 28.12.2018 10:40:01 (unknown:0) - Slicer version …: 4.11.0-2018-12-16 (revision 27662) macosx-amd64 - installed release
[DEBUG][Qt] 28.12.2018 10:40:01 (unknown:0) - Operating system …: Mac OS X / 10.13.6 / 17G65 - 64-bit
[DEBUG][Qt] 28.12.2018 10:40:01 (unknown:0) - Memory …: 8192 MB physical, 3072 MB virtual
[DEBUG][Qt] 28.12.2018 10:40:01 (unknown:0) - CPU …: GenuineIntel Intel(R) Core™ i5-7500 CPU @ 3.40GHz, 4 cores, 4 logical processors
[DEBUG][Qt] 28.12.2018 10:40:01 (unknown:0) - VTK configuration …: OpenGL2 rendering, Sequential threading
[DEBUG][Qt] 28.12.2018 10:40:01 (unknown:0) - Developer mode enabled …: no
[DEBUG][Qt] 28.12.2018 10:40:01 (unknown:0) - Prefer executable CLI …: yes
[DEBUG][Qt] 28.12.2018 10:40:01 (unknown:0) - Additional module paths …: /Applications/Slicer Nightly.app/Contents/Extensions-27662/QuantitativeReporting/lib/Slicer-4.11/qt-scripted-modules, /Applications/Slicer Nightly.app/Contents/Extensions-27662/SlicerDevelopmentToolbox/lib/Slicer-4.11/qt-scripted-modules, /Applications/Slicer Nightly.app/Contents/Extensions-27662/PETDICOMExtension/lib/Slicer-4.11/cli-modules, /Applications/Slicer Nightly.app/Contents/Extensions-27662/PETDICOMExtension/lib/Slicer-4.11/qt-scripted-modules, /Applications/Slicer Nightly.app/Contents/Extensions-27662/DCMQI/lib/Slicer-4.11/cli-modules, /Applications/Slicer Nightly.app/Contents/Extensions-27662/AnglePlanesExtension/lib/Slicer-4.11/qt-scripted-modules, /Applications/Slicer Nightly.app/Contents/Extensions-27662/EasyClip/lib/Slicer-4.11/qt-scripted-modules, /Applications/Slicer Nightly.app/Contents/Extensions-27662/MarkupsToModel/lib/Slicer-4.11/qt-loadable-modules, /Applications/Slicer Nightly.app/Contents/Extensions-27662/MatlabBridge/lib/Slicer-4.11/cli-modules, /Applications/Slicer Nightly.app/Contents/Extensions-27662/MatlabBridge/lib/Slicer-4.11/qt-loadable-modules, /Applications/Slicer Nightly.app/Contents/Extensions-27662/SlicerOpenIGTLink/lib/Slicer-4.11/qt-loadable-modules, /Applications/Slicer Nightly.app/Contents/Extensions-27662/SlicerOpenIGTLink/lib/Slicer-4.11/qt-scripted-modules, /Applications/Slicer Nightly.app/Contents/Extensions-27662/MeshToLabelMap/lib/Slicer-4.11/cli-modules, /Applications/Slicer Nightly.app/Contents/Extensions-27662/ModelToModelDistance/lib/Slicer-4.11/cli-modules, /Applications/Slicer Nightly.app/Contents/Extensions-27662/PedicleScrewSimulator/lib/Slicer-4.11/qt-scripted-modules, /Applications/Slicer Nightly.app/Contents/Extensions-27662/SegmentEditorExtraEffects/lib/Slicer-4.11/qt-scripted-modules, /Applications/Slicer Nightly.app/Contents/Extensions-27662/SegmentRegistration/lib/Slicer-4.11/qt-scripted-modules, /Applications/Slicer Nightly.app/Contents/Extensions-27662/MeshStatisticsExtension/lib/Slicer-4.11/qt-scripted-modules, /Applications/Slicer Nightly.app/Contents/Extensions-27662/SlicerProstate/lib/Slicer-4.11/cli-modules, /Applications/Slicer Nightly.app/Contents/Extensions-27662/SlicerProstate/lib/Slicer-4.11/qt-scripted-modules, /Applications/Slicer Nightly.app/Contents/Extensions-27662/SlicerFab/lib/Slicer-4.11/qt-scripted-modules, /Applications/Slicer Nightly.app/Contents/Extensions-27662/Sequences/lib/Slicer-4.11/qt-loadable-modules, /Applications/Slicer Nightly.app/Contents/Extensions-27662/Sequences/lib/Slicer-4.11/qt-scripted-modules, /Applications/Slicer Nightly.app/Contents/Extensions-27662/SlicerIGT/lib/Slicer-4.11/qt-loadable-modules, /Applications/Slicer Nightly.app/Contents/Extensions-27662/SlicerIGT/lib/Slicer-4.11/qt-scripted-modules, /Applications/Slicer Nightly.app/Contents/Extensions-27662/SlicerVMTK/lib/Slicer-4.11/qt-loadable-modules, /Applications/Slicer Nightly.app/Contents/Extensions-27662/SlicerVMTK/lib/Slicer-4.11/qt-scripted-modules, /Applications/Slicer Nightly.app/Contents/Extensions-27662/TCIABrowser/lib/Slicer-4.11/qt-scripted-modules, /Applications/Slicer Nightly.app/Contents/Extensions-27662/VolumeClip/lib/Slicer-4.11/qt-scripted-modules, /Applications/Slicer Nightly.app/Contents/Extensions-27662/SlicerHeart/lib/Slicer-4.11/qt-loadable-modules, /Applications/Slicer Nightly.app/Contents/Extensions-27662/SlicerHeart/lib/Slicer-4.11/qt-scripted-modules, /Applications/Slicer Nightly.app/Contents/Extensions-27662/SlicerRT/lib/Slicer-4.11/cli-modules, /Applications/Slicer Nightly.app/Contents/Extensions-27662/SlicerRT/lib/Slicer-4.11/qt-loadable-modules, /Applications/Slicer Nightly.app/Contents/Extensions-27662/SlicerRT/lib/Slicer-4.11/qt-scripted-modules
[DEBUG][Python] 28.12.2018 10:40:09 [Python] (/Applications/Slicer Nightly.app/Contents/lib/Slicer-4.11/qt-scripted-modules/SubjectHierarchyPlugins/AbstractScriptedSubjectHierarchyPlugin.py:36) - Scripted subject hierarchy plugin registered: Annotations
[DEBUG][Qt] 28.12.2018 10:40:14 (unknown:0) - MatlabExecutablePath not found, default path used: /Applications/MATLAB_XXXXX.app/bin/matlab
[DEBUG][Python] 28.12.2018 10:40:16 [Python] (/Applications/Slicer Nightly.app/Contents/lib/Slicer-4.11/qt-scripted-modules/SubjectHierarchyPlugins/AbstractScriptedSubjectHierarchyPlugin.py:36) - Scripted subject hierarchy plugin registered: SegmentEditor
[DEBUG][Python] 28.12.2018 10:40:16 [Python] (/Applications/Slicer Nightly.app/Contents/lib/Slicer-4.11/qt-scripted-modules/SubjectHierarchyPlugins/AbstractScriptedSubjectHierarchyPlugin.py:36) - Scripted subject hierarchy plugin registered: SegmentStatistics
[DEBUG][Qt] 28.12.2018 10:40:17 (unknown:0) - Switch to module: “Welcome”
[INFO][VTK] 28.12.2018 10:40:19 [vtkMRMLVolumeArchetypeStorageNode (0x7fed52b43f10)] (/Volumes/Dashboards/Preview/Slicer-0/Libs/MRML/Core/vtkMRMLVolumeArchetypeStorageNode.cxx:465) - Loaded volume from file: /Applications/Slicer Nightly.app/Contents/Extensions-27662/SlicerVMTK/lib/Slicer-4.11/qt-scripted-modules/Resources/Vesselness.png. Dimensions: 65x50x1. Number of components: 3. Pixel type: unsigned char.
[INFO][Stream] 28.12.2018 10:40:20 (unknown:0) - Loading Slicer RC file [/Users/AVarghese11/.slicerrc.py]
[INFO][VTK] 28.12.2018 10:40:31 [vtkMRMLVolumeArchetypeStorageNode (0x7fed529ad4a0)] (/Volumes/Dashboards/Preview/Slicer-0/Libs/MRML/Core/vtkMRMLVolumeArchetypeStorageNode.cxx:465) - Loaded volume from file: /Users/AVarghese11/Documents/3D Slicer Segmentation Practice/AAA2/Panoramix-cropped.nrrd. Dimensions: 441x321x215. Number of components: 1. Pixel type: short.
[INFO][VTK] 28.12.2018 10:40:32 [vtkMRMLVolumeArchetypeStorageNode (0x7fed529aa490)] (/Volumes/Dashboards/Preview/Slicer-0/Libs/MRML/Core/vtkMRMLVolumeArchetypeStorageNode.cxx:465) - Loaded volume from file: /Users/AVarghese11/Documents/3D Slicer Segmentation Practice/AAA2/Segmentation-label.nrrd. Dimensions: 441x321x215. Number of components: 1. Pixel type: short.
[DEBUG][Qt] 28.12.2018 10:40:32 (unknown:0) - “MRML Scene” Reader has successfully read the file “/Users/AVarghese11/Documents/3D Slicer Segmentation Practice/AAA2/2018-12-26-Scene.mrml” “[1.76s]”
[DEBUG][Qt] 28.12.2018 10:40:44 (unknown:0) - Switch to module: “Data”
[CRITICAL][Stream] 28.12.2018 10:41:13 (unknown:0) - Traceback (most recent call last):
[CRITICAL][Stream] 28.12.2018 10:41:13 (unknown:0) - File “<string>”, line 1, in <module>
[CRITICAL][Stream] 28.12.2018 10:41:13 (unknown:0) - KeyError: ‘DicomRtImportExportPlugin’
Please let me know if you have any suggestions