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
Unofrtunately, lower extremitties are only available in the paying version of TotalSegmentator.
Ok, thank you.
Where would I find the prices for these applications?
Please contact Jakob Wasserthal, as far as we know there are academic licenses available too.
His email is in this text.
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
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
Happy to help. Let me know.
Is there any tutorial on how to use it?
Or if i already have TotalSegmentator bone weigth , how to use it with monailabel?
Have you tried the whole-body CT segmentation model? 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
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 in MONAI Label.
Once you create the label files, please these steps: https://youtu.be/KtPE8m0LvcQ?si=Ol2AMebXCdjRLgQ_&t=456
Hope this helps
I’ve trained a MONAI Label model to segment only bone: radiology_bone - Google Drive
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
May be it would be of the interest of the community to have such training command/script
Could you share it?
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.
Thank you very much. It is really amazing how the experts are helping newbie researchers in this forum.