# Segmentating bone in Total Segmentator
**URL:** https://discourse.slicer.org/t/segmentating-bone-in-total-segmentator/29399
**Category:** Support
**Tags:** segmentation
**Created:** [May 10, 2023, 12:14pm UTC](https://discourse.slicer.org/t/segmentating-bone-in-total-segmentator/29399 "2023-05-10T12:14:24Z")
**Posts on this page:** 11
**Page:** 1
### Author:  [@KEF](https://discourse.slicer.org/u/KEF)
#### Post date: [May 10, 2023, 12:14pm UTC](https://discourse.slicer.org/t/segmentating-bone-in-total-segmentator/29399/1 "2023-05-10T12:14:24Z")
Hello
I am new to 3D slicer and I am currently testing it to segment bone. I just downloaded the Total segmentator extention and tried to apply it to a CT of two legs. When the prosess finished it curiously only chose the femur, but I also need the tibia, fibia and the foot. Does anyone know why this happen? What do I need to do for it to also segment the rest?
I am using slicer version 5.2.2
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### Author:  [@lassoan](https://discourse.slicer.org/u/lassoan)
#### Post date: [May 10, 2023, 12:15pm UTC](https://discourse.slicer.org/t/segmentating-bone-in-total-segmentator/29399/2 "2023-05-10T12:15:10Z")
Unofrtunately, lower extremitties are only [available in the paying version of TotalSegmentator](https://github.com/wasserth/TotalSegmentator#subtasks).
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### Author:  [@KEF](https://discourse.slicer.org/u/KEF)
#### Post date: [May 10, 2023, 12:25pm UTC](https://discourse.slicer.org/t/segmentating-bone-in-total-segmentator/29399/3 "2023-05-10T12:25:48Z")
Ok, thank you.
Where would I find the prices for these applications?
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### Author:  [@rbumm](https://discourse.slicer.org/u/rbumm)
#### Post date: [May 10, 2023, 3:42pm UTC](https://discourse.slicer.org/t/segmentating-bone-in-total-segmentator/29399/4 "2023-05-10T15:42:11Z")
Please contact Jakob Wasserthal, as far as we know there are academic licenses available too.
[His email is in this text](https://github.com/wasserth/TotalSegmentator#subtasks).
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### Author:  [@diazandr3s](https://discourse.slicer.org/u/diazandr3s)
#### Post date: [May 13, 2023, 7:26pm UTC](https://discourse.slicer.org/t/segmentating-bone-in-total-segmentator/29399/5 "2023-05-13T19:26:16Z")
Hi @KEF,
You may also consider retraining the whole-body CT segmentation model freely available in the MONAI model zoo: [model-zoo/models/wholeBody\_ct\_segmentation at dev · Project-MONAI/model-zoo · GitHub](https://github.com/Project-MONAI/model-zoo/tree/dev/models/wholeBody_ct_segmentation)
You could take advantage of the active learning capabilities of the MONAI Label library to get a model for the lower extremities segmentation.
We could consider presenting this as a Slicer project: [NA-MIC Project Weeks | Website for NA-MIC Project Weeks](https://projectweek.na-mic.org/PW39_2023_Montreal/)
Happy to help. Let me know.
Andres
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### Author:  [@zariliusra](https://discourse.slicer.org/u/zariliusra)
#### Post date: [October 1, 2023, 3:48am UTC](https://discourse.slicer.org/t/segmentating-bone-in-total-segmentator/29399/6 "2023-10-01T03:48:58Z")
Is there any tutorial on how to use it?
Or if i already have TotalSegmentator bone weigth , how to use it with monailabel?
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### Author:  [@diazandr3s](https://discourse.slicer.org/u/diazandr3s)
#### Post date: [October 3, 2023, 7:39pm UTC](https://discourse.slicer.org/t/segmentating-bone-in-total-segmentator/29399/7 "2023-10-03T19:39:45Z")
Hi @zariliusra,
Have you tried the whole-body CT segmentation model? [https://github.com/Project-MONAI/model-zoo/tree/dev/models/wholeBody\_ct\_segmentation](https://github.com/Project-MONAI/model-zoo/tree/dev/models/wholeBody_ct_segmentation)
You can use this model in MONAI Label like any other MONAI Bundle. Here is more information: [https://github.com/Project-MONAI/MONAILabel/tree/main/sample-apps/monaibundle](https://github.com/Project-MONAI/MONAILabel/tree/main/sample-apps/monaibundle)
Another option is to create the label files from the TotalSegmentator dataset with only bones (or the labels you wish) and train the segmentation model from the [radiology app](https://github.com/Project-MONAI/MONAILabel/tree/main/sample-apps/radiology#segmentation) in MONAI Label.
Once you create the label files, please these steps: [https://youtu.be/KtPE8m0LvcQ?si=Ol2AMebXCdjRLgQ\_&t=456](https://youtu.be/KtPE8m0LvcQ?si=Ol2AMebXCdjRLgQ_&t=456)
Hope this helps
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### Author:  [@diazandr3s](https://discourse.slicer.org/u/diazandr3s)
#### Post date: [October 9, 2023, 11:11am UTC](https://discourse.slicer.org/t/segmentating-bone-in-total-segmentator/29399/8 "2023-10-09T11:11:25Z")
Hi @zariliusra,
I’ve trained a MONAI Label model to segment only bone: [radiology\_bone - Google Drive](https://drive.google.com/drive/folders/1yQ3Yy89uwPPmm3zr3ekV5jg37Y7_hF0j?usp=sharing)
It uses the TotalSegmentatorV1 dataset. The model isn’t perfect but it works decently.
Download those files, place them in a folder (i.e. radiology\_bone) and start a MONAI Label server using this command:
> monailabel start\_server --app /PATH\_TO\_FOLDER\_radiology\_bone --studies /PATH\_TO\_YOUR\_NIFTI\_OR\_NRRD\_IMAGES --conf models segmentation
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### Author:  [@mau\_igna\_06](https://discourse.slicer.org/u/mau_igna_06)
#### Post date: [October 9, 2023, 1:48pm UTC](https://discourse.slicer.org/t/segmentating-bone-in-total-segmentator/29399/9 "2023-10-09T13:48:48Z")
Hi
> [@diazandr3s](#):
>
> I’ve trained a MONAI Label model to segment only bone: [radiology\_bone - Google Drive](https://drive.google.com/drive/folders/1yQ3Yy89uwPPmm3zr3ekV5jg37Y7_hF0j?usp=sharing)
May be it would be of the interest of the community to have such training command/script 🙂
Could you share it? 🙂
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### Author:  [@diazandr3s](https://discourse.slicer.org/u/diazandr3s)
#### Post date: [October 9, 2023, 2:19pm UTC](https://discourse.slicer.org/t/segmentating-bone-in-total-segmentator/29399/10 "2023-10-09T14:19:45Z")
Hi @mau_igna_06,
The folder I’ve shared is a MONAI Label app (radiology app) that works for bone segmentation.
With this app, you can do both inference and training - as with any other MONAI Label app.
In the _lib/configs/segmentation.py_ file you can see the labels this model can segment and the network used.
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### Author:  [@zariliusra](https://discourse.slicer.org/u/zariliusra)
#### Post date: [October 9, 2023, 2:43pm UTC](https://discourse.slicer.org/t/segmentating-bone-in-total-segmentator/29399/11 "2023-10-09T14:43:23Z")
Thank you very much. It is really amazing how the experts are helping newbie researchers in this forum. 😳