MONAI AutoSeg3D for CBCT (CMF)

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1

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:

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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:


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

2

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

Best,
Gauthier

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3

@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

4

Hello,

Thanks for your reply.

The pretrained nnU-Net model for DentalSegmentator is shared here : DentalSegmentator nnU-Net pretrained model for CBCT image segmentation

Best regards,
Gauthier

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5

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.

6

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

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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7

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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8

@philippepellerin I can’t find the Head Model int the model list, please see the snapshot:
image

Am I missing something? I am using Slicer 5.7.x

9

@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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