Issues with DentalSegmentator

jamesobutler · December 30, 2024, 4:18pm

There is a known issue in a dependency of Dental Segmentator that has been problematic for about a month. The issue hasn’t been fixed as it is a third party developer that has been unresponsive to the reported bugs.

References to the dependency issue:

github.com/gaudot/SlicerDentalSegmentator

DentalSegmentator doesnt work

opened 05:49PM - 26 Nov 24 UTC

okoratum

I was using 3D Slicer 5.7 2024-04-25 because it is the recommended version to wo…rk with blenderfordental software. Today i tried to use dentalsegmentator and i get error of inference folder and doesnt segment. So i uninstall the 3D Slicer completely and tried same version and lastest version and i get this error everytime, here is the log: 2024/11/26 19:41:35.182 :: Start nnUNet install with requirements : nnunetv2 2024/11/26 19:41:35.187 :: - Installing pandas... 2024/11/26 19:41:42.688 :: - Installing pillow<10.1... 2024/11/26 19:41:47.118 :: - Installing nnunetv2 --no-deps... 2024/11/26 19:41:48.244 :: - Installing acvl-utils<0.3,>=0.2 --no-deps... 2024/11/26 19:41:48.964 :: - Installing batchgenerators --no-deps... 2024/11/26 19:41:49.915 :: - Installing scikit-image --no-deps... 2024/11/26 19:41:51.590 :: - Installing networkx>=2.8 --no-deps... 2024/11/26 19:41:53.860 :: - Installing imageio>=2.33 --no-deps... 2024/11/26 19:41:54.776 :: - Installing tifffile>=2022.8.12 --no-deps... 2024/11/26 19:41:55.791 :: - Installing lazy-loader>=0.4 --no-deps... 2024/11/26 19:41:56.504 :: - Installing scikit-learn --no-deps... 2024/11/26 19:41:59.316 :: - Installing joblib>=1.2.0 --no-deps... 2024/11/26 19:42:00.224 :: - Installing threadpoolctl>=3.1.0 --no-deps... 2024/11/26 19:42:01.059 :: - Installing future --no-deps... 2024/11/26 19:42:02.205 :: - Installing unittest2 --no-deps... 2024/11/26 19:42:03.207 :: - Installing argparse --no-deps... 2024/11/26 19:42:04.062 :: - Installing traceback2 --no-deps... 2024/11/26 19:42:04.816 :: - Installing linecache2 --no-deps... 2024/11/26 19:42:05.546 :: - Installing connected-components-3d --no-deps... 2024/11/26 19:42:06.328 :: - Installing blosc2>=3.0.0b4 --no-deps... 2024/11/26 19:42:07.080 :: Install returned non-zero exit status : Command '['C:/Users/PC/AppData/Local/slicer.org/Slicer 5.7.0-2024-11-25/bin/../bin\\PythonSlicer.EXE', '-m', 'pip', 'install', 'blosc2>=3.0.0b4', '--no-deps']' returned non-zero exit status 1.. Attempting to continue... 2024/11/26 19:42:07.085 :: Error occurred during install : blosc2 I pressed apply again in hope it will fix itself and i am stuck at download model weights for a while. I restarted the app and installed pytorch compatible with my gpu in pytorchutils extension and run the extension again and then i got different error, here is the log: 2024/11/26 20:01:45.238 :: nnUNet is already installed (2.5.1) and compatible with requested version (nnunetv2). 2024/11/26 20:01:48.296 :: Transferring volume to nnUNet in C:/Users/PC/AppData/Local/Temp/Slicer-RuOTvc 2024/11/26 20:02:06.380 :: Starting nnUNet with the following parameters: 2024/11/26 20:02:06.380 :: 2024/11/26 20:02:06.380 :: C:\Users\PC\AppData\Local\slicer.org\Slicer 5.7.0-2024-11-25\lib\Python\Scripts\nnUNetv2_predict.exe -i C:/Users/PC/AppData/Local/Temp/Slicer-RuOTvc/input -o C:/Users/PC/AppData/Local/Temp/Slicer-RuOTvc/output -d Dataset111_453CT -tr nnUNetTrainer -p nnUNetPlans -c 3d_fullres -f 0 -npp 1 -nps 1 -step_size 0.5 -device cuda -chk checkpoint_final.pth --disable_tta 2024/11/26 20:02:06.380 :: 2024/11/26 20:02:06.380 :: JSON parameters : 2024/11/26 20:02:06.380 :: { 2024/11/26 20:02:06.380 :: "folds": "0", 2024/11/26 20:02:06.380 :: "device": "cuda", 2024/11/26 20:02:06.380 :: "stepSize": 0.5, 2024/11/26 20:02:06.380 :: "disableTta": true, 2024/11/26 20:02:06.380 :: "nProcessPreprocessing": 1, 2024/11/26 20:02:06.380 :: "nProcessSegmentationExport": 1, 2024/11/26 20:02:06.380 :: "checkPointName": "", 2024/11/26 20:02:06.380 :: "modelPath": { 2024/11/26 20:02:06.380 :: "_path": "C:\\Users\\PC\\AppData\\Local\\slicer.org\\Slicer 5.7.0-2024-11-25\\slicer.org\\Extensions-33123\\DentalSegmentator\\lib\\Slicer-5.7\\qt-scripted-modules\\Resources\\ML" 2024/11/26 20:02:06.380 :: } 2024/11/26 20:02:06.380 :: } 2024/11/26 20:02:06.405 :: nnUNet preprocessing... 2024/11/26 20:02:08.233 :: Traceback (most recent call last): 2024/11/26 20:02:08.233 :: File "C:\Users\PC\AppData\Local\slicer.org\Slicer 5.7.0-2024-11-25\lib\Python\Lib\runpy.py", line 197, in _run_module_as_main 2024/11/26 20:02:08.234 :: return _run_code(code, main_globals, None, 2024/11/26 20:02:08.234 :: File "C:\Users\PC\AppData\Local\slicer.org\Slicer 5.7.0-2024-11-25\lib\Python\Lib\runpy.py", line 87, in _run_code 2024/11/26 20:02:08.234 :: exec(code, run_globals) 2024/11/26 20:02:08.234 :: File "C:\Users\PC\AppData\Local\slicer.org\Slicer 5.7.0-2024-11-25\lib\Python\Scripts\nnUNetv2_predict.exe\__main__.py", line 4, in <module> 2024/11/26 20:02:08.234 :: File "C:\Users\PC\AppData\Local\slicer.org\Slicer 5.7.0-2024-11-25\lib\Python\Lib\site-packages\nnunetv2\inference\predict_from_raw_data.py", line 18, in <module> 2024/11/26 20:02:08.234 :: from tqdm import tqdm 2024/11/26 20:02:08.234 :: ModuleNotFoundError: No module named 'tqdm' 2024/11/26 20:02:08.469 :: Loading inference results... 2024/11/26 20:02:10.316 :: Error loading results : 2024/11/26 20:02:10.316 :: Failed to load the segmentation. 2024/11/26 20:02:10.316 :: Something went wrong during the nnUNet processing. 2024/11/26 20:02:10.316 :: Please check the logs for potential errors and contact the library maintainers. My PC Specs: Windows 11 Ryzen 7 7700X 32GB Ram RTX 4070

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Issues with DentalSegmentator

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