# Cuda issue with dentalsegmentator

**URL:** <https://discourse.slicer.org/t/cuda-issue-with-dentalsegmentator/36549>\
**Category:** Support\
**Created:** [June 2, 2024, 10:05am UTC](https://discourse.slicer.org/t/cuda-issue-with-dentalsegmentator/36549 "2024-06-02T10:05:12Z")\
**Posts on this page:** 9\
**Page:** 1

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**Author:** ![mohammed\_alshakhas](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/mohammed_alshakhas/32/10025_2.png) [@mohammed\_alshakhas](https://discourse.slicer.org/u/mohammed_alshakhas)\
**Post date:** [June 2, 2024, 10:05am UTC](https://discourse.slicer.org/t/cuda-issue-with-dentalsegmentator/36549/1 "2024-06-02T10:05:12Z")

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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

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**Author:** ![mohammed\_alshakhas](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/mohammed_alshakhas/32/10025_2.png) [@mohammed\_alshakhas](https://discourse.slicer.org/u/mohammed_alshakhas)\
**Post date:** [June 2, 2024, 12:48pm UTC](https://discourse.slicer.org/t/cuda-issue-with-dentalsegmentator/36549/2 "2024-06-02T12:48:38Z")

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correction  
i installed cuda on PC and still whenever i run dentalsegmentor but it says cuda not available on your system

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**Author:** ![Thibault\_Pelletier](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/thibault_pelletier/32/4767_2.png) [@Thibault\_Pelletier](https://discourse.slicer.org/u/Thibault_Pelletier)\
**Post date:** [June 3, 2024, 7:27am UTC](https://discourse.slicer.org/t/cuda-issue-with-dentalsegmentator/36549/3 "2024-06-03T07:27:15Z")

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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.](https://github.com/gaudot/SlicerDentalSegmentator?tab=readme-ov-file#torch-cuda-not-properly-installed)

To summarize, you can use the [PyTorch slicer extension](https://github.com/fepegar/SlicerPyTorch) to manually set the pytorch + CUDA version which best suits your system.

Let me know if that helps.  
Best,  
Thibault

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**Author:** ![mohammed\_alshakhas](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/mohammed_alshakhas/32/10025_2.png) [@mohammed\_alshakhas](https://discourse.slicer.org/u/mohammed_alshakhas)\
**Post date:** [June 3, 2024, 9:48am UTC](https://discourse.slicer.org/t/cuda-issue-with-dentalsegmentator/36549/4 "2024-06-03T09:48:45Z")

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let me take the chance to congratulate you and thank you for the amazing work. this extension is mindblowing.

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**Author:** ![1546161](https://avatars.discourse-cdn.com/v4/letter/1/d07c76/32.png) [@1546161](https://discourse.slicer.org/u/1546161)\
**Post date:** [June 14, 2024, 4:47am UTC](https://discourse.slicer.org/t/cuda-issue-with-dentalsegmentator/36549/5 "2024-06-14T04:47:28Z")

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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

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<div class="post-metadata">

**Author:** ![1546161](https://avatars.discourse-cdn.com/v4/letter/1/d07c76/32.png) [@1546161](https://discourse.slicer.org/u/1546161)\
**Post date:** [June 14, 2024, 4:53am UTC](https://discourse.slicer.org/t/cuda-issue-with-dentalsegmentator/36549/6 "2024-06-14T04:53:03Z")

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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

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<div class="post-metadata">

**Author:** ![Marce](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/marce/32/76822_2.png) [@Marce](https://discourse.slicer.org/u/Marce)\
**Post date:** [June 14, 2024, 7:31am UTC](https://discourse.slicer.org/t/cuda-issue-with-dentalsegmentator/36549/7 "2024-06-14T07:31:42Z")

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> [@1546161](#):
>
> ModuleNotFoundError: Ningún módulo llamado ‘threadpoolctl’  
> 2024 /06/14 11:20:21.613 :: Cargando resultados de inferencia…

Hello, dowload:  
[https://slicer-packages.kitware.com/api/v1/item/665d6717c8a295ea328461ef/download](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.

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<div class="post-metadata">

**Author:** ![1546161](https://avatars.discourse-cdn.com/v4/letter/1/d07c76/32.png) [@1546161](https://discourse.slicer.org/u/1546161)\
**Post date:** [June 14, 2024, 7:56am UTC](https://discourse.slicer.org/t/cuda-issue-with-dentalsegmentator/36549/8 "2024-06-14T07:56:46Z")

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Downloading and installing still doesn’t work

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<div class="post-metadata">

**Author:** ![Thibault\_Pelletier](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/thibault_pelletier/32/4767_2.png) [@Thibault\_Pelletier](https://discourse.slicer.org/u/Thibault_Pelletier)\
**Post date:** [June 14, 2024, 8:24am UTC](https://discourse.slicer.org/t/cuda-issue-with-dentalsegmentator/36549/9 "2024-06-14T08:24:26Z")

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@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.