# MONAI AutoSeg3D for CBCT (CMF)
**URL:** https://discourse.slicer.org/t/monai-autoseg3d-for-cbct-cmf/37175
**Category:** Support
**Tags:** segmentation
**Created:** [July 3, 2024, 12:27pm UTC](https://discourse.slicer.org/t/monai-autoseg3d-for-cbct-cmf/37175 "2024-07-03T12:27:47Z")
**Posts on this page:** 11
**Page:** 1
### Author:  [@ssingh](https://discourse.slicer.org/u/ssingh)
#### Post date: [July 3, 2024, 12:27pm UTC](https://discourse.slicer.org/t/monai-autoseg3d-for-cbct-cmf/37175/1 "2024-07-03T12:27:47Z")
I tried MONAI AutoSeg3D auto-segmentation on CMF scan (CBCT).
I see that the segmentation results appear like as if it was done on a downsampled image.
Please see the snapshot here:
I have used Whole Body segmentation TS2. I think TS2 implies Total Segmentator V2. I Observed a similar result when I used the Total Segmentator extension.
I also see the following log in the AutoSeg3d:
```auto
Using orientation_ras
Using crop_foreground
Using resample with resample_resolution [1.5, 1.5, 1.5]
Running Inference ...
```
So it appears it resamples the image to 1.5x1.5x1.5
Is it possible to run the AutoSeg3D to get a better(finer) segmentation mask result? The extension currently does not provide such a control.
Thanks
---
### Author:  [@Gauthier](https://discourse.slicer.org/u/Gauthier)
#### Post date: [July 4, 2024, 8:26am UTC](https://discourse.slicer.org/t/monai-autoseg3d-for-cbct-cmf/37175/2 "2024-07-04T08:26:45Z")
Hello,
To my knowledge Monain Auto3DSeg has not been trained on those kind of data for now. You could give a try to DentalSegmentator : [https://discourse.slicer.org/t/new-extension-dentalsegmentator-for-automatic-dental-ct-cbct-segmentation](https://discourse.slicer.org/t/new-extension-dentalsegmentator-for-automatic-dental-ct-cbct-segmentation)
Best,
Gauthier
---
### Author:  [@ssingh](https://discourse.slicer.org/u/ssingh)
#### Post date: [July 4, 2024, 8:35am UTC](https://discourse.slicer.org/t/monai-autoseg3d-for-cbct-cmf/37175/3 "2024-07-04T08:35:18Z")
@Gauthier thanks for your reply.
Yes, I have used DentalSegmentator and AMASSS. They perform better. I wanted to see the performance of this tool as well. Basically, then use the best one.
On Dental Segmentator: Only the extension code is open source, however I could not find the implementation on auto segmentation model training. Is that also available, say if someone wants to extend work on Dental Segmentator?
Regards,
Sukhraj
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### Author:  [@Gauthier](https://discourse.slicer.org/u/Gauthier)
#### Post date: [July 4, 2024, 8:41am UTC](https://discourse.slicer.org/t/monai-autoseg3d-for-cbct-cmf/37175/4 "2024-07-04T08:41:33Z")
Hello,
Thanks for your reply.
The pretrained nnU-Net model for DentalSegmentator is shared here : [DentalSegmentator nnU-Net pretrained model for CBCT image segmentation](https://zenodo.org/doi/10.5281/zenodo.10829674)
Best regards,
Gauthier
---
### Author:  [@ssingh](https://discourse.slicer.org/u/ssingh)
#### Post date: [July 4, 2024, 8:48am UTC](https://discourse.slicer.org/t/monai-autoseg3d-for-cbct-cmf/37175/5 "2024-07-04T08:48:32Z")
So essentially, learn how to use and train further a pre-trained model in nn-Unet, is all that is needed to extend Dental Segmentator.
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### Author:  [@Gauthier](https://discourse.slicer.org/u/Gauthier)
#### Post date: [July 4, 2024, 8:57am UTC](https://discourse.slicer.org/t/monai-autoseg3d-for-cbct-cmf/37175/6 "2024-07-04T08:57:14Z")
Yes that would be the idea! nnU-Net offers a basic implementation of finetuning: [nnUNet/documentation/pretraining\_and\_finetuning.md at master · MIC-DKFZ/nnUNet · GitHub](https://github.com/MIC-DKFZ/nnUNet/blob/master/documentation/pretraining_and_finetuning.md)
We haven’t used it for now, so I could not tell you more about the performance bumps that coud be obtained. It will probably depend a lot on what is your objective!
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### Author:  [@philippepellerin](https://discourse.slicer.org/u/philippepellerin)
#### Post date: [July 6, 2024, 3:15pm UTC](https://discourse.slicer.org/t/monai-autoseg3d-for-cbct-cmf/37175/7 "2024-07-06T15:15:53Z")
Have you tried the whole head model in Monai AutoSeg3D? You will get the skull, the mandible, the rachis, eyeball, brain, and masticatory muscles.
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### Author:  [@ssingh](https://discourse.slicer.org/u/ssingh)
#### Post date: [July 7, 2024, 4:28pm UTC](https://discourse.slicer.org/t/monai-autoseg3d-for-cbct-cmf/37175/8 "2024-07-07T16:28:32Z")
@philippepellerin I can’t find the Head Model int the model list, please see the snapshot:
Am I missing something? I am using Slicer 5.7.x
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### Author:  [@ssingh](https://discourse.slicer.org/u/ssingh)
#### Post date: [July 7, 2024, 4:38pm UTC](https://discourse.slicer.org/t/monai-autoseg3d-for-cbct-cmf/37175/9 "2024-07-07T16:38:59Z")
@philippepellerin Thanks for noticing in detail.
I observed a head model “Whole Head Segmentation” is available in 5.6.2 version of slicer.
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### Author:  [@Camila\_Da\_Rocha\_Camp](https://discourse.slicer.org/u/Camila_Da_Rocha_Camp)
#### Post date: [December 29, 2024, 10:58pm UTC](https://discourse.slicer.org/t/monai-autoseg3d-for-cbct-cmf/37175/10 "2024-12-29T22:58:34Z")
It is not performing the “whole head segmentation on my software” function. Maybe you know what’s wrong with the software. I’m using 3D slicer version 5.6.2.
Can you help me?
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### Author:  [@ssingh](https://discourse.slicer.org/u/ssingh)
#### Post date: [March 31, 2025, 7:34am UTC](https://discourse.slicer.org/t/monai-autoseg3d-for-cbct-cmf/37175/11 "2025-03-31T07:34:04Z")
Hello,
Sorry for the late reply.
Please download the latest Slicer 5.8.x and install the MONAI Auto3Dseg extension. You should be able to see the model:
