TotalSegmentator error at first run: "Command ‘pip’, ‘install’, ‘git+https://github.com/wasserth/TotalSegmentator.git’, ‘–no-deps’]’ returned non-zero exit status"

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Please start all over again.

It would be great if you could read the troubleshooting section of the TotalSegmentator extension in the beginning.

  • Uninstall 3D Slicer and delete the installation directory.
  • Install 3D Slicer stable in a new directory.
  • Install the Pytorch extension.
  • In the Pytorch extension, select CPU support just for a test.

image

  • Install Pytorch.
  • Restart 3D Slicer.
  • Install the Totalsegmentator extension.
  • Load the CT Chest dataset
  • Run TotalSegmentator (will take longer because of using CPU).

If not working, please post the results of the log and/or complete content of progress window here.
We will handle GPU support later, probably by someone who has an M2 Macbook at hand. Not sure GPU support works in this case.