i installed cuda on mu PC and still whenever i run detalsegmentaror it says cuda not available on your system .
any idea what to do ?
thanks
correction
i installed cuda on PC and still whenever i run dentalsegmentor but it says cuda not available on your system
Hi @mohammed_alshakhas ,
Thank you for your interest in our extension.
For CUDA related problems, please have a look at this doc : GitHub - gaudot/SlicerDentalSegmentator: 3D Slicer extension for fully-automatic segmentation of CT and CBCT dental volumes.
To summarize, you can use the PyTorch slicer extension to manually set the pytorch + CUDA version which best suits your system.
Let me know if that helps.
Best,
Thibault
1 Like
let me take the chance to congratulate you and thank you for the amazing work. this extension is mindblowing.
2024/06/14 11:20:00.892 :: nnUNet is already installed (2.4.2) and compatible with requested version (nnunetv2).
2024/06/14 11:20:09.816 :: Transferring volume to nnUNet in C:/Users/DELL/AppData/Local/Temp/Slicer-bFASSs
2024/06/14 11:20:20.152 :: Starting nnUNet with the following parameters:
2024/06/14 11:20:20.152 ::
2024/06/14 11:20:20.152 :: C:\Users\DELL\AppData\Local\slicer.org\Slicer 5.7.0-2024-06-01\lib\Python\Scripts\nnUNetv2_predict.exe -i C:/Users/DELL/AppData/Local/Temp/Slicer-bFASSs/input -o C:/Users/DELL/AppData/Local/Temp/Slicer-bFASSs/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
2024/06/14 11:20:20.152 ::
2024/06/14 11:20:20.152 :: JSON parameters :
2024/06/14 11:20:20.152 :: {
2024/06/14 11:20:20.152 :: “folds”: “0”,
2024/06/14 11:20:20.152 :: “device”: “cuda”,
2024/06/14 11:20:20.152 :: “stepSize”: 0.5,
2024/06/14 11:20:20.152 :: “disableTta”: true,
2024/06/14 11:20:20.152 :: “nProcessPreprocessing”: 1,
2024/06/14 11:20:20.152 :: “nProcessSegmentationExport”: 1,
2024/06/14 11:20:20.152 :: “checkPointName”: “”,
2024/06/14 11:20:20.152 :: “modelPath”: {
2024/06/14 11:20:20.152 :: “_path”: “C:\Users\DELL\AppData\Local\slicer.org\Slicer 5.7.0-2024-06-01\slicer.org\Extensions-32886\DentalSegmentator\lib\Slicer-5.7\qt-scripted-modules\Resources\ML”
2024/06/14 11:20:20.152 :: }
2024/06/14 11:20:20.152 :: }
2024/06/14 11:20:20.159 :: nnUNet preprocessing…
2024/06/14 11:20:21.429 :: Traceback (most recent call last):
2024/06/14 11:20:21.429 :: File “C:\Users\DELL\AppData\Local\slicer.org\Slicer 5.7.0-2024-06-01\lib\Python\Lib\runpy.py”, line 197, in _run_module_as_main
2024/06/14 11:20:21.430 :: return _run_code(code, main_globals, None,
2024/06/14 11:20:21.430 :: File “C:\Users\DELL\AppData\Local\slicer.org\Slicer 5.7.0-2024-06-01\lib\Python\Lib\runpy.py”, line 87, in run_code
2024/06/14 11:20:21.430 :: exec(code, run_globals)
2024/06/14 11:20:21.430 :: File "C:\Users\DELL\AppData\Local\slicer.org\Slicer 5.7.0-2024-06-01\lib\Python\Scripts\nnUNetv2_predict.exe_main.py", line 4, in
2024/06/14 11:20:21.430 :: File “C:\Users\DELL\AppData\Local\slicer.org\Slicer 5.7.0-2024-06-01\lib\Python\Lib\site-packages\nnunetv2\inference\predict_from_raw_data.py”, line 12, in
2024/06/14 11:20:21.430 :: from batchgenerators.dataloading.multi_threaded_augmenter import MultiThreadedAugmenter
2024/06/14 11:20:21.430 :: File “C:\Users\DELL\AppData\Local\slicer.org\Slicer 5.7.0-2024-06-01\lib\Python\Lib\site-packages\batchgenerators\dataloading\multi_threaded_augmenter.py”, line 26, in
2024/06/14 11:20:21.435 :: from threadpoolctl import threadpool_limits
2024/06/14 11:20:21.435 :: ModuleNotFoundError: No module named ‘threadpoolctl’
2024/06/14 11:20:21.613 :: Loading inference results…
2024/06/14 11:20:25.688 :: Error loading results :
2024/06/14 11:20:25.688 :: Failed to load the segmentation.
2024/06/14 11:20:25.688 :: Check the inference folder content C:\Users\DELL\AppData\Local\Temp\Slicer-bFASSs\output
Dear developer, I am a newcomer from China, please can you tell me the way to solve the problem, the detailed process, thank you, thank you
2024/06/14 11:20:00.892 :: nnUNet is already installed (2.4.2) and compatible with requested version (nnunetv2).
2024/06/14 11:20:09.816 :: Transferring volume to nnUNet in C:/Users/DELL/AppData/Local/Temp/Slicer-bFASSs
2024/06/14 11:20:20.152 :: Starting nnUNet with the following parameters:
2024/06/14 11:20:20.152 ::
2024/06/14 11:20:20.152 :: C:\Users\DELL\AppData\Local\slicer.org\Slicer 5.7.0-2024-06-01\lib\Python\Scripts\nnUNetv2_predict.exe -i C:/Users/DELL/AppData/Local/Temp/Slicer-bFASSs/input -o C:/Users/DELL/AppData/Local/Temp/Slicer-bFASSs/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
2024/06/14 11:20:20.152 ::
2024/06/14 11:20:20.152 :: JSON parameters :
2024/06/14 11:20:20.152 :: {
2024/06/14 11:20:20.152 :: “folds”: “0”,
2024/06/14 11:20:20.152 :: “device”: “cuda”,
2024/06/14 11:20:20.152 :: “stepSize”: 0.5,
2024/06/14 11:20:20.152 :: “disableTta”: true,
2024/06/14 11:20:20.152 :: “nProcessPreprocessing”: 1,
2024/06/14 11:20:20.152 :: “nProcessSegmentationExport”: 1,
2024/06/14 11:20:20.152 :: “checkPointName”: “”,
2024/06/14 11:20:20.152 :: “modelPath”: {
2024/06/14 11:20:20.152 :: “_path”: “C:\Users\DELL\AppData\Local\slicer.org\Slicer 5.7.0-2024-06-01\slicer.org\Extensions-32886\DentalSegmentator\lib\Slicer-5.7\qt-scripted-modules\Resources\ML”
2024/06/14 11:20:20.152 :: }
2024/06/14 11:20:20.152 :: }
2024/06/14 11:20:20.159 :: nnUNet preprocessing…
2024/06/14 11:20:21.429 :: Traceback (most recent call last):
2024/06/14 11:20:21.429 :: File “C:\Users\DELL\AppData\Local\slicer.org\Slicer 5.7.0-2024-06-01\lib\Python\Lib\runpy.py”, line 197, in _run_module_as_main
2024/06/14 11:20:21.430 :: return _run_code(code, main_globals, None,
2024/06/14 11:20:21.430 :: File “C:\Users\DELL\AppData\Local\slicer.org\Slicer 5.7.0-2024-06-01\lib\Python\Lib\runpy.py”, line 87, in run_code
2024/06/14 11:20:21.430 :: exec(code, run_globals)
2024/06/14 11:20:21.430 :: File "C:\Users\DELL\AppData\Local\slicer.org\Slicer 5.7.0-2024-06-01\lib\Python\Scripts\nnUNetv2_predict.exe_main.py", line 4, in
2024/06/14 11:20:21.430 :: File “C:\Users\DELL\AppData\Local\slicer.org\Slicer 5.7.0-2024-06-01\lib\Python\Lib\site-packages\nnunetv2\inference\predict_from_raw_data.py”, line 12, in
2024/06/14 11:20:21.430 :: from batchgenerators.dataloading.multi_threaded_augmenter import MultiThreadedAugmenter
2024/06/14 11:20:21.430 :: File “C:\Users\DELL\AppData\Local\slicer.org\Slicer 5.7.0-2024-06-01\lib\Python\Lib\site-packages\batchgenerators\dataloading\multi_threaded_augmenter.py”, line 26, in
2024/06/14 11:20:21.435 :: from threadpoolctl import threadpool_limits
2024/06/14 11:20:21.435 :: ModuleNotFoundError: No module named ‘threadpoolctl’
2024/06/14 11:20:21.613 :: Loading inference results…
2024/06/14 11:20:25.688 :: Error loading results :
2024/06/14 11:20:25.688 :: Failed to load the segmentation.
2024/06/14 11:20:25.688 :: Check the inference folder content C:\Users\DELL\AppData\Local\Temp\Slicer-bFASSs\output
Dear developer, I am a newcomer from China, please can you tell me the solution, the detailed process so that we can recommend you in the Chinese market, thank you, thank you
Hello, dowload:
https://slicer-packages.kitware.com/api/v1/item/665d6717c8a295ea328461ef/download
This is slicer package “Slicer-5.7.0-2024-06-01-win-amd64”. this work.
Downloading and installing still doesn’t work
@1546161 Thank you for your interest in our extension.
The error you are providing seems to indicate something went wrong when installing the nnUNet python dependencies.
When first launching the Dental Segmentator, you should have multiple logs with printed “Installing …”, you also have console logs in the Python console.
Could you try checking if you have any errors at this step so we can investigate further? (you will have to install a clean 3D Slicer version / remove the 3D Slicer directory).
If you want to manually solve this problem, you can also try installing the dependency manually using slicer.util.pip_install("threadpoolctl") in the python console.