TotalSegmentator

Support
1

When I use the Total Segmentator module for total segmentation, if I select full resolution, the following error will appear, but if I select fast, the following error will not appear.

Failed to compute results.

Command ‘[‘C:/Users/hooray/AppData/Local/slicer.org/Slicer 5.4.0/bin/…/bin\PythonSlicer.EXE’, ‘C:\Users\hooray\AppData\Local\slicer.org\Slicer 5.4.0\lib\Python\Scripts\TotalSegmentator’, ‘-i’, ‘C:/Windows/Temp/Slicer/__SlicerTemp__2023-11-09_10+57+56.252/total-segmentator-input.nii’, ‘-o’, ‘C:/Windows/Temp/Slicer/__SlicerTemp__2023-11-09_10+57+56.252/segmentation’, ‘–ml’, ‘–task’, ‘total’]’ returned non-zero exit status 1.

2

It is probably a GPU memory issue. What is your GPU (model, brand?)

3

I don’t have a GPU with more than 7G of video memory, so I am using CPU computing. Can’t CPU computing use full resolution?

4

Yes, you can configure Pytorch to use the CPU only. Uninstall Pytorch, then select “cpu”, then install Pytorch again.

image

1 Like
5

I changed my computer to a 4060laptop gpu, and now I get the following error

WARNING: Ignoring invalid distribution -illow (e:\soft\slicer 5.5.0-2023-11-14\lib\python\lib\site-packages)
Requirement already satisfied: pillow<10.1 in e:\soft\slicer 5.5.0-2023-11-14\lib\python\lib\site-packages (10.0.1)
WARNING: Ignoring invalid distribution -illow (e:\soft\slicer 5.5.0-2023-11-14\lib\python\lib\site-packages)
WARNING: There was an error checking the latest version of pip.
E:/Soft/Slicer 5.5.0-2023-11-14/slicer.org/Extensions-32325/TotalSegmentator/lib/Slicer-5.5/qt-scripted-modules/TotalSegmentator.py:880: UserWarning: ‘has_cuda’ is deprecated, please use ‘torch.backends.cuda.is_built()’
cuda = torch.cuda if torch.has_cuda and torch.cuda.is_available() else None
[Python] Failed to compute results.
[Python] Command ‘[‘E:/Soft/Slicer 5.5.0-2023-11-14/bin/…/bin\PythonSlicer.EXE’, ‘E:\Soft\Slicer 5.5.0-2023-11-14\lib\Python\Scripts\TotalSegmentator.exe’, ‘-i’, ‘C:/Users/13790/AppData/Local/Temp/Slicer/__SlicerTemp__2023-11-17_09+51+55.923/total-segmentator-input.nii’, ‘-o’, ‘C:/Users/13790/AppData/Local/Temp/Slicer/__SlicerTemp__2023-11-17_09+51+55.923/segmentation’, ‘–ml’, ‘–task’, ‘total’]’ returned non-zero exit status 1.
Traceback (most recent call last):
File “E:/Soft/Slicer 5.5.0-2023-11-14/slicer.org/Extensions-32325/TotalSegmentator/lib/Slicer-5.5/qt-scripted-modules/TotalSegmentator.py”, line 292, in onApplyButton
self.logic.process(self.ui.inputVolumeSelector.currentNode(), self.ui.outputSegmentationSelector.currentNode(),
File “E:/Soft/Slicer 5.5.0-2023-11-14/slicer.org/Extensions-32325/TotalSegmentator/lib/Slicer-5.5/qt-scripted-modules/TotalSegmentator.py”, line 967, in process
self.logProcessOutput(proc)
File “E:/Soft/Slicer 5.5.0-2023-11-14/slicer.org/Extensions-32325/TotalSegmentator/lib/Slicer-5.5/qt-scripted-modules/TotalSegmentator.py”, line 787, in logProcessOutput
raise CalledProcessError(retcode, proc.args, output=proc.stdout, stderr=proc.stderr)
subprocess.CalledProcessError: Command ‘[‘E:/Soft/Slicer 5.5.0-2023-11-14/bin/…/bin\PythonSlicer.EXE’, ‘E:\Soft\Slicer 5.5.0-2023-11-14\lib\Python\Scripts\TotalSegmentator.exe’, ‘-i’, ‘C:/Users/13790/AppData/Local/Temp/Slicer/__SlicerTemp__2023-11-17_09+51+55.923/total-segmentator-input.nii’, ‘-o’, ‘C:/Users/13790/AppData/Local/Temp/Slicer/__SlicerTemp__2023-11-17_09+51+55.923/segmentation’, ‘–ml’, ‘–task’, ‘total’]’ returned non-zero exit status 1.