Slicer 5.8.0 totalsegmentator erro

Support
1

I installed slicer 5.8.0 and extension of total segmentator .But total segmentator did not work successfully. And total segmentator run successfully in slicer 5.6.2.
I reinstalled slicer 5.8.0 and extension of total segmentator several times, but problem is still not resolved.
Could you give me some suggestion to resolve this problem?

error window pops up：

Failed to compute results.

Command '['/Applications/Slicer 2.app/Contents/bin/../bin/PythonSlicer', '/Applications/Slicer 2.app/Contents/lib/Python/bin/TotalSegmentator', '-i', '/private/var/folders/xm/g5xx81wd55b1rvslqnrdgwv80000gn/T/Slicer-cy/__SlicerTemp__2025-02-24_19+49+25.194/total-segmentator-input.nii', '-o', '/private/var/folders/xm/g5xx81wd55b1rvslqnrdgwv80000gn/T/Slicer-cy/__SlicerTemp__2025-02-24_19+49+25.194/segmentation', '--ml', '--task', 'total', '--fast']' returned non-zero exit status 1.

Traceback (most recent call last):
  File "/Applications/Slicer 2.app/Contents/bin/Python/slicer/util.py", line 3303, in tryWithErrorDisplay
    yield
  File "/Applications/Slicer 2.app/Contents/Extensions-33216/TotalSegmentator/lib/Slicer-5.8/qt-scripted-modules/TotalSegmentator.py", line 307, in onApplyButton
    self.logic.process(self.ui.inputVolumeSelector.currentNode(), self.ui.outputSegmentationSelector.currentNode(),
  File "/Applications/Slicer 2.app/Contents/Extensions-33216/TotalSegmentator/lib/Slicer-5.8/qt-scripted-modules/TotalSegmentator.py", line 1037, in process
    self.processVolume(inputFile, inputVolume,
  File "/Applications/Slicer 2.app/Contents/Extensions-33216/TotalSegmentator/lib/Slicer-5.8/qt-scripted-modules/TotalSegmentator.py", line 1104, in processVolume
    self.logProcessOutput(proc)
  File "/Applications/Slicer 2.app/Contents/Extensions-33216/TotalSegmentator/lib/Slicer-5.8/qt-scripted-modules/TotalSegmentator.py", line 883, in logProcessOutput
    raise CalledProcessError(retcode, proc.args, output=proc.stdout, stderr=proc.stderr)
subprocess.CalledProcessError: Command '['/Applications/Slicer 2.app/Contents/bin/../bin/PythonSlicer', '/Applications/Slicer 2.app/Contents/lib/Python/bin/TotalSegmentator', '-i', '/private/var/folders/xm/g5xx81wd55b1rvslqnrdgwv80000gn/T/Slicer-cy/__SlicerTemp__2025-02-24_19+49+25.194/total-segmentator-input.nii', '-o', '/private/var/folders/xm/g5xx81wd55b1rvslqnrdgwv80000gn/T/Slicer-cy/__SlicerTemp__2025-02-24_19+49+25.194/segmentation', '--ml', '--task', 'total', '--fast']' returned non-zero exit status 1.
2

Are you using a GPU?
If so, could it be that GPU memory is not being released properly or is occupied by another process?

I had a similar issue before, and in my case, an “out of memory” error didn’t appear, which made it difficult to figure out the cause. You might want to check if GPU memory is still in use by running:

sh

nvidia-smi

If some process is occupying the memory, try terminating it and then running TotalSegmentator again.

3

thanks for your reply！
I use MacBook Air m1,which gpu not available.
And total segmentation work well in 5.6.2 version of slicer installed in my Macbook for long time.

4

Since you’re using a CPU, this topic might be relevant to your issue:

How to solve PyTorch version error in TotalSegmentator using CPU

It seems that there could be a PyTorch version compatibility issue when running TotalSegmentator on CPU. You might want to check if updating or downgrading PyTorch helps resolve the problem.

5

I check PyTorch module. and PyTorch 2.2.2 already installed ,using cpu.