New extension: Fully automatic whole-body CT segmentation in 2 minutes using TotalSegmentator

A post was merged into an existing topic: TotalSegmentator failed to compute results - file not found

3 posts were split to a new topic: Convert TotalSegmentator results to RT structure set

2 posts were split to a new topic: TotalSegmentator results computed in fast mode are rough

Hello, I have problems to install totalsegmentator, already I have read the document several times where, and I have made several attempts to install it without results. Can someone explain to me how to install it? a tutorial video?

Please describe what you did, what you expected to happen, and what happened instead. Include screenshots and copy here all messages displayed in the log window of the TotalSegmentator module.

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5 posts were split to a new topic: Segment the body surface using sTotalSegmentator

A post was split to a new topic: Export TotalSegmentator results to DICOM

Will this plugin use our local weights to compute(refined or trained by my local dataset), and the weights uploaded to googledrive for users to download

2 posts were split to a new topic: TotalSegmentator indicates that GTX 1060 GPU has not enough memory

2 posts were split to a new topic: Can TotalSegmentator capture deformities such as Can TotalSegmentator heterotopic ossification?

A post was split to a new topic: Run TotalSegmentator on MultiVolume

Congratulation for implementing TotalSegmentator to Slicer. I use Slicer to segment bones of the lower extremities and wondered, if you are planning on implementing the v2.0 of TotalSegmentator as well? I would greatly appreciate this work as the segmentation of the lower extremity is enabled in this version.

Thank you very much
Julius

Yes, it is planned to implement TotalSegmentator v2 as soon as possible.

We have a functional prototype in this pull request of TotalSegmentator v2 in Slicer. We need to tune a few small things before we release it, probably in a week or so. If you don’t want to wait for that then you can get the updated TotalSegmentator.py and .ui files from github and overwrite the files in your Slicer installation folder.

That’s great thank you!

A post was split to a new topic: Segmenting fractured bones

Is there any chance to use “total segmentator” with cone beam CT acquired with angiography systems in the body (liver)? Thanks

Yes, it works on CBCT images as well. However, if the image quality is very bad (which is not uncommon, especially for low-dose acquisitions) then the accuracy will suffer.

Hi,
I am trying to make it run and when I look in pytorch utils it said torch version 1.8.1
However, when i run the totalsegmentator it says that it needs to install a higher version of torch (1.12.1) and restart. And then it restarts but nothing happens.
Does anyone have any idea what I am doing wrong?

You have some old pytorch 1.x version in your pip cache that gets installed by default.

You can go to Pytorch Utils module, uninstall this old version, restart Slicer, go to Pytorch Utils module again, and before you click to install Pytorch, write >=2 in the version requirement textbox.

These uninstall and install steps should be performed automatically if you use the latest Slicer Stable Release or latest Slicer Preview Release.

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