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

Wow, this is really amazing! Excellent work. As Pellerin said, great Xmas present!!


Wow that is awesome!


Hmm. Does the module require any special CUDA drivers, or it must work on standard Game-ready Nvidia drivers?

I tried module, and it ignored my 2080ti. :smiling_face_with_tear:

You must use one of the CUDA versions listed on pytorch website as “Compute platform” for your system, which is currently CUDA 11.6 or 11.7 for Windows and Linux. All other CUDA versions are ignored. Gaming cards (GeForce RTX) are fine. See documentation for some more details.


This is extremely beautifull!!! Cant wait to try it out! Im amazed!!! <3


3 posts were split to a new topic: Use TotalSegmentator with atlasess

Hei, thank you so much, this looks amazing, but not able to find it in extensions manager. Using 5.0.3 ?

Please use the extension from Slicer 5.2.1 stable, it is not compatible with previous Slicer versions.

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haha, let us know if it works! :dog2:

Needs a little refining for canine data sets :grinning:

. What is the lights extension, I have tried to find that but can’t?

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The “Lights” module is in the “Sandbox” extension.

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I’ve been following and using Slicer for a while. Today I’m giving a try to this magnific new tool. It really works well with the Sample data, but I get a wrong segmentation when working with my own DICOM file.

I add the file, then open TotalSegmentator with the configs you can see there. What can be happening? Thanks again for you huge contribution for this field.

That result looks reasonable. There’s a big segment called ‘face’ at the front of the head. My understanding is that this can be used to remove features that might otherwise identify the individual subject. Removing these features makes it easier to share 3D data.


Thanks for your reply, Pieper!

I guess that CMF structures can’t be segmented due to data protection on the training process. I’m right?
After reading your comment I have loaded different body CT scans and the result was good.

Hats off to the development team.

Right now there are no CMF-specific substructures included in the TotalSegmentator model. There are dedicated models in development to subdivide the head into relevant anatomical regions. Some of that work will be discussed during the upcoming Project Week.


Truly amazing! Thanks for sharing this!

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6 posts were split to a new topic: Error while installing pytorch

After installing the totalsegmentor and trying to run it by pressing apply, i got a message that pytorch will be installed in several minutes. However, after one hour it is still not proceeding. Does anyone have a suggestion what might go wrong?

It works for some of my CT data, for other i get this error:
Traceback (most recent call last):
File “E:\apps\Slicer 5.2.1\bin\Python\slicer\”, line 2961, in tryWithErrorDisplay
File “E:/apps/Slicer 5.2.1/NA-MIC/Extensions-31317/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/”, line 258, in onApplyButton
self.logic.process(self.ui.inputVolumeSelector.currentNode(), self.ui.outputSegmentationSelector.currentNode(),
File “E:/apps/Slicer 5.2.1/NA-MIC/Extensions-31317/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/”, line 715, in process
File “E:/apps/Slicer 5.2.1/NA-MIC/Extensions-31317/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/”, line 624, in logProcessOutput
raise CalledProcessError(retcode, proc.args, output=proc.stdout, stderr=proc.stderr)
subprocess.CalledProcessError: Command ‘[‘E:/apps/Slicer 5.2.1/bin/…/bin\PythonSlicer.EXE’, ‘E:\apps\Slicer 5.2.1\lib\Python\Scripts\TotalSegmentator’, ‘-i’, ‘C:/Users/ar38/AppData/Local/Temp/Slicer/__SlicerTemp__2022-12-28_14+33+20.804/total-segmentator-input.nii’, ‘-o’, ‘C:/Users/ar38/AppData/Local/Temp/Slicer/__SlicerTemp__2022-12-28_14+33+20.804/segmentation’, ‘–ml’, ‘–task’, ‘total’, ‘–fast’]’ returned non-zero exit status 120.

Do you know what is the reason for this? Thanks in advance

Amazing work, thanks for sharing such a powerful tool.
Any plan to add the shoulder rotator cuff muscles one day?