# Issues with DentalSegmentator

**URL:** <https://discourse.slicer.org/t/issues-with-dentalsegmentator/40905>\
**Category:** Support\
**Tags:** segmentation, dental\
**Created:** [December 30, 2024, 2:37pm UTC](https://discourse.slicer.org/t/issues-with-dentalsegmentator/40905 "2024-12-30T14:37:41Z")\
**Posts on this page:** 1\
**Showing post:** 2

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**Author:** ![jamesobutler](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jamesobutler/32/7511_2.png) [@jamesobutler](https://discourse.slicer.org/u/jamesobutler)\
**Post date:** [December 30, 2024, 4:18pm UTC](https://discourse.slicer.org/t/issues-with-dentalsegmentator/40905/2 "2024-12-30T16:18:04Z")

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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:

> [@DentalSegmentator does not complete on Slicer 5.7.0](https://discourse.slicer.org/t/dentalsegmentator-does-not-complete-on-slicer-5-7-0/40793):
>
> 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]

> [@Dental segmantator](https://discourse.slicer.org/t/dental-segmantator/40519):
>
> 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…

> <https://github.com/gaudot/SlicerDentalSegmentator/issues/21>
>
> 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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