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TotalSegmentator (Python) issues
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Task to record any issues faced from the TotalSegmentator (Python) side

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a178n created this task.
  1. Output segmentation nifti file comes without any label-pixel metadata eg. in json format , eventhough its known until the last moment before writing it out. Ref. T29461
  1. The installation and run command documentation is not working exactly as per documentation on Windows.

The run command TotalSegmentator -i ct.nii.gz -o segmentations doesn't seem to work because the install instruction pip install TotalSegmentator is not creating TotalSegmentator.exe file inside the ~\venv\Scirpts\ location.
Instead, the pip installation merely keeps a python file. Hence, the correct invocation command would then be python ~\venv\Scirpts\TotalSegmentator -i ct.nii.gz -o segmentations.

  1. No explicit CPU only inferencing possible. Currently, whether or not the inferencing would run on cpu or gpu is decided by the installation of pytorch in the virtual environment. This might not be enough for MITK tool stability guarantee across all user machines.
  1. The install instruction pip install TotalSegmentator installed Pytorch CPU version on Windows eventhough there is Nvidia GPU and Cuda drivers available. Not sure this is problem of TotalSegmentator dependency specification or a general pip on Windows issue. Anyway, I had to manually uninstall pytorch cpu version and install again with the cuda supported package.