New extension: DentalSegmentator for automatic dental CT & CBCT segmentation

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Dear All,

We are glad to announce the availability of DentalSegmentator, a new 3D Slicer extension for automatic segmentation of dental CT and CBCT scans. It is now available in the latest Slicer 5.7.0 preview release.

Fig4
Fig41920×1202 160 KB

This tool is based on a nnU-Net model trained and evaluated on more than 700 CT and CBCT scans. It has been shown to be robust in most situations, even in the presence of metallic artefacts or varying field of views.

It generates the following segmentations :

  • Maxilla & Upper Skull
  • Mandible
  • Upper Teeth
  • Lower Teeth
  • Mandibular canal

dentalsegmentator_example
dentalsegmentator_example850×615 55.7 KB

Segment editor tools and model export features are directly available in the module. The extension does not require a GPU, but a CUDA-capable GPU is needed for fast results (around 1-2 minutes).

Install tutorial and demonstration video:

If you use DentalSegmentator for your work, please cite our paper and nnU-Net:

Dot G, Chaurasia A, Dubois G, et al. DentalSegmentator: robust deep learning-based CBCT image segmentation. Published online March 18, 2024:2024.03.18.24304458. doi:10.1101/2024.03.18.24304458

Isensee F, Jaeger PF, Kohl SAA, Petersen J, Maier-Hein KH. nnU-Net: a self-configuring method for deep learning-based biomedical image segmentation. Nat Methods. 2021;18(2):203-211. doi:10.1038/s41592-020-01008-z

The module was developed by T. Pelletier and R. Fenioux (Kitware SAS); financed by the FFO (FĂ©dĂ©ration Française d’Orthodontie) and the Fondation des Gueules CassĂ©es.

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5 posts were split to a new topic: DentalSegmentator extension is not working

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3 posts were split to a new topic: DentalSegmentator version of 2024-04-22 fails to load segmentation result

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A post was merged into an existing topic: DentalSegmentator fails with “RuntimeError: Invalid nnUNet configuration. Model folder is missing the following folds”

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2 posts were split to a new topic: DentalSegmentator inaccuracies separating cortical bone and teeth

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A post was split to a new topic: UnicodeDecodeError when running DentalSegmentator

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3 posts were merged into an existing topic: Cuda issue with dentalsegmentator

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3 posts were split to a new topic: DentalSegmentator for condyle segmentation?

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3 posts were split to a new topic: DentalSegmentator result mesh is inverted

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2 posts were split to a new topic: Dental segmentation for dogs and cats

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Thank you very much for creating the module, but it doesn’t work. I have the latest version of the program installed, as well as all the required plugins. However, when I click ‘apply,’ it just keeps loading and doesn’t do anything. I’ve left it running for up to an hour, but nothing happens.

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Awesome work. Congrats!
I would like to know if it is possible to set parameters so we can run it on a 2gb NVIDIA laptop GPU.
I run it on CPU just fine (it takes several minutes). But I ran out of memory when tried to run on CUDA.

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A GPU with 2GB RAM is only sufficient for some very lightweight visualization tasks, it is too small to be useful for 3D segmentation.

You can either upgrade to a stronger GPU (I would recommend minimum 12GB GPU RAM, but 24GB would be safer if you want to use it for a few years) or use your CPU.

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Thank you very much for the clarification! I understood perfectly. My laptop’s GPU is not suitable for the task.

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A post was split to a new topic: Install DentalSegmentator from behind restrictive firewall