Dental Segmentator was working on Slicer 5.7 May or June 2024 build but on the latest 12.31.2024 build, it stalls. Any help would be appreciated.
Could some one also direct me to where I can download the old versions of the nightly build as a backup?
Please copy the complete log here (menu: Help / Report a bug). I can see in the screnshot that there were some error messages, but the log entry you selected was just some informational message.
Since I’m new, it won’t let me post with more than 3 links and the error log has multiple links
I took out the links. Hope this works.
Here’s the log:
[DEBUG][Qt] 02.01.2025 12:29:13 (unknown:0) - Session start time …: 20250102_122913
[DEBUG][Qt] 02.01.2025 12:29:13 (unknown:0) - Slicer version …: 5.7.0-2024-12-31 (revision 33176 / e18fac6) macosx-amd64 - installed release
[DEBUG][Qt] 02.01.2025 12:29:13 (unknown:0) - Operating system …: macOS / 15.1.1 / 24B91 / UTF-8 - 64-bit
[DEBUG][Qt] 02.01.2025 12:29:13 (unknown:0) - Memory …: 32768 MB physical, 0 MB virtual
[DEBUG][Qt] 02.01.2025 12:29:13 (unknown:0) - CPU …: Apple M1 Max, 10 cores, 10 logical processors
[DEBUG][Qt] 02.01.2025 12:29:13 (unknown:0) - VTK configuration …: OpenGL2 rendering, TBB threading
[DEBUG][Qt] 02.01.2025 12:29:13 (unknown:0) - Qt configuration …: version 5.15.8, with SSL, requested OpenGL 3.2 (core profile)
[DEBUG][Qt] 02.01.2025 12:29:13 (unknown:0) - DCMTK configuration …: version 3.6.8, no SSL
[DEBUG][Qt] 02.01.2025 12:29:13 (unknown:0) - Internationalization …: disabled, language=
[DEBUG][Qt] 02.01.2025 12:29:13 (unknown:0) - Developer mode …: disabled
[DEBUG][Qt] 02.01.2025 12:29:13 (unknown:0) - Application path …: /Applications/Slicer.app/Contents/MacOS
[DEBUG][Qt] 02.01.2025 12:29:13 (unknown:0) - Additional module paths …: Extensions-33176/AnglePlanesExtension/lib/Slicer-5.7/qt-scripted-modules, Extensions-33176/CMFreg/lib/Slicer-5.7/cli-modules, Extensions-33176/CMFreg/lib/Slicer-5.7/qt-scripted-modules, Extensions-33176/DatabaseInteractor/lib/Slicer-5.7/qt-scripted-modules, Extensions-33176/EasyClip/lib/Slicer-5.7/qt-scripted-modules, Extensions-33176/MeshStatisticsExtension/lib/Slicer-5.7/qt-scripted-modules, Extensions-33176/BoneTextureExtension/lib/Slicer-5.7/cli-modules, Extensions-33176/BoneTextureExtension/lib/Slicer-5.7/qt-scripted-modules, Extensions-33176/MeshToLabelMap/lib/Slicer-5.7/cli-modules, Extensions-33176/MeshToLabelMap/lib/Slicer-5.7/qt-scripted-modules, Extensions-33176/ModelToModelDistance/lib/Slicer-5.7/cli-modules, Extensions-33176/PickAndPaintExtension/lib/Slicer-5.7/qt-scripted-modules, Extensions-33176/Q3DC/lib/Slicer-5.7/qt-scripted-modules, Extensions-33176/ShapePopulationViewer/lib/Slicer-5.7/qt-loadable-modules, Extensions-33176/SlicerMarkupConstraints/lib/Slicer-5.7/qt-scripted-modules, Extensions-33176/SlicerCMF/lib/Slicer-5.7/qt-scripted-modules, Extensions-33176/ShapeVariationAnalyzer/lib/Slicer-5.7/cli-modules, Extensions-33176/ShapeVariationAnalyzer/lib/Slicer-5.7/qt-scripted-modules, Extensions-33176/NNUNet/lib/Slicer-5.7/qt-scripted-modules, Extensions-33176/PyTorch/lib/Slicer-5.7/qt-scripted-modules, Extensions-33176/DentalSegmentator/lib/Slicer-5.7/qt-scripted-modules, Extensions-33176/SlicerPythonTestRunner/lib/Slicer-5.7/qt-scripted-modules
[CRITICAL][FD] 02.01.2025 12:29:13 (unknown:0) - 2025-01-02 12:29:13.907 Slicer[44098:1058598] +[IMKClient subclass]: chose IMKClient_Modern
[CRITICAL][FD] 02.01.2025 12:29:13 (unknown:0) - 2025-01-02 12:29:13.907 Slicer[44098:1058598] +[IMKInputSession subclass]: chose IMKInputSession_Modern
[WARNING][Qt] 02.01.2025 12:29:17 (unknown:0) - libpng warning: iCCP: known incorrect sRGB profile
[DEBUG][Python] 02.01.2025 12:29:17 [Python] (/Applications/Slicer.app/Contents/lib/Slicer-5.7/qt-scripted-modules/SubjectHierarchyPlugins/AbstractScriptedSubjectHierarchyPlugin.py:40) - Scripted subject hierarchy plugin registered: SegmentEditor
[DEBUG][Python] 02.01.2025 12:29:17 [Python] (/Applications/Slicer.app/Contents/lib/Slicer-5.7/qt-scripted-modules/SubjectHierarchyPlugins/AbstractScriptedSubjectHierarchyPlugin.py:40) - Scripted subject hierarchy plugin registered: SegmentStatistics
[DEBUG][Qt] 02.01.2025 12:29:17 (unknown:0) - Switch to module: “Welcome”
[WARNING][Qt] 02.01.2025 12:29:18 (unknown:0) - Populating font family aliases took 139 ms. Replace uses of missing font family “.AppleSystemUIFont” with one that exists to avoid this cost.
[DEBUG][Qt] 02.01.2025 12:30:08 (unknown:0) - “Volume” Reader has successfully read the file “/Volumes/TTN/_Herbst Project/_Herbst/1 Chapman/Segmentations/V1 Chapman FH.nii.gz” “[0.51s]”
[DEBUG][Qt] 02.01.2025 12:30:13 (unknown:0) - Switch to module: “DentalSegmentator”
[CRITICAL][Qt] 02.01.2025 12:30:13 (unknown:0) - void qMRMLSegmentEditorWidget::setSourceVolumeNode(vtkMRMLNode *) failed: need to set segment editor and segmentation nodes first
[INFO][Python] 02.01.2025 12:30:17 [Python] (/Applications/Slicer.app/Contents/Extensions-33176/NNUNet/lib/Slicer-5.7/qt-scripted-modules/SlicerNNUNetLib/InstallLogic.py:56) - nnUNet is already installed (2.5.1) and compatible with requested version (nnunetv2).
[DEBUG][Python] 02.01.2025 12:30:17 [Python] (/Applications/Slicer.app/Contents/lib/Python/lib/python3.9/site-packages/urllib3/connectionpool.py:1055) - Starting new HTTPS connection (1):
[DEBUG][Python] 02.01.2025 12:30:17 [Python] (/Applications/Slicer.app/Contents/lib/Python/lib/python3.9/site-packages/urllib3/connectionpool.py:549) –
“GET / HTTP/1.1” 200 None
[DEBUG][Python] 02.01.2025 12:30:17 [Python] (/Applications/Slicer.app/Contents/lib/Python/lib/python3.9/site-packages/urllib3/connectionpool.py:1055) - Starting new HTTPS connection (1): api.github.com:443
[DEBUG][Python] 02.01.2025 12:30:17 [Python] (/Applications/Slicer.app/Contents/lib/Python/lib/python3.9/site-packages/urllib3/connectionpool.py:549)
“GET /repos/gaudot/SlicerDentalSegmentator HTTP/1.1” 200 1466
[DEBUG][Python] 02.01.2025 12:30:18 [Python] (/Applications/Slicer.app/Contents/lib/Python/lib/python3.9/site-packages/urllib3/connectionpool.py:549)
“GET /repos/gaudot/SlicerDentalSegmentator/releases HTTP/1.1” 200 810
[DEBUG][Python] 02.01.2025 12:30:18 [Python] (/Applications/Slicer.app/Contents/lib/Python/lib/python3.9/site-packages/urllib3/connectionpool.py:549)
“GET /repos/gaudot/SlicerDentalSegmentator/releases/147040025/assets HTTP/1.1” 200 598
[CRITICAL][Stream] 02.01.2025 12:30:18 (unknown:0) - Traceback (most recent call last):
[CRITICAL][Stream] 02.01.2025 12:30:18 (unknown:0) - File “/Applications/Slicer.app/Contents/Extensions-33176/DentalSegmentator/lib/Slicer-5.7/qt-scripted-modules/DentalSegmentatorLib/SegmentationWidget.py”, line 238, in onApplyClicked
[CRITICAL][Stream] 02.01.2025 12:30:18 (unknown:0) - self._runSegmentation()
[CRITICAL][Stream] 02.01.2025 12:30:18 (unknown:0) - File “/Applications/Slicer.app/Contents/Extensions-33176/DentalSegmentator/lib/Slicer-5.7/qt-scripted-modules/DentalSegmentatorLib/SegmentationWidget.py”, line 257, in _runSegmentation
[CRITICAL][Stream] 02.01.2025 12:30:18 (unknown:0) - if not parameter.isSelectedDeviceAvailable():
[CRITICAL][Stream] 02.01.2025 12:30:18 (unknown:0) - File “/Applications/Slicer.app/Contents/Extensions-33176/NNUNet/lib/Slicer-5.7/qt-scripted-modules/SlicerNNUNetLib/Parameter.py”, line 66, in isSelectedDeviceAvailable
[CRITICAL][Stream] 02.01.2025 12:30:18 (unknown:0) - import torch
[CRITICAL][Stream] 02.01.2025 12:30:18 (unknown:0) - ModuleNotFoundError: No module named ‘torch’
@nguyetun I fixed some things with the SlicerNNUNet extension used by DentalSegmentator. This would only be available in the latest Slicer preview from the past day or so. Can you install the latest macOS Slicer preview and try your installation again?
I do know see that DentalSegmenatot has a selection for CUDA which you won’t have being on Apple Silicon but it should pull the CPU only version of torch for macOS.
Thanks, the latest version 1.3.25 of Slicer works with Dental Segmentator.
Tung
