JuMaLe
(Juan Lenardi)
December 30, 2024, 2:37pm
1
Hello to everybody! I tried to use DentalSegmentator but when I click on “Apply” the process get stock at the very beginning.
what I’m missing here?
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:
Problem report for Slicer 5.7.0-2024-12-16 win-amd64: [please describe expected and actual behavior]
[DEBUG][Qt] 18.12.2024 10:51:23 (unknown:0) - Session start time …: 20241218_105123 [DEBUG][Qt] 18.12.2024 10:51:23 (unknown:0) - Slicer version …: 5.7.0-2024-12-16 (revision 33157 / f711b40) win-amd64 - installed release [DEBUG][Qt]
I am trying the dental segmentator with the sample CBCT. During the package installation I got this error message. This is with the R33134 on Linux:
Installing collected packages: connected-components-3d
Successfully installed connected-components-3d-3.21.0
ERROR: Ignored the following versions that require a different python version: 2.6.0 Requires-Python <4,>=3.10; 2.6.1 Requires-Python <4,>=3.10; 2.6.2 Requires-Python <4,>=3.10; 2.7.0 Requires-Python <4,>=3.10; 2.7.1 Requires-Python <4,>=3.1…
opened 05:49PM - 26 Nov 24 UTC
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