TotalSegmentator "Failed to compute results." , "returned non-zero exit status 120"

Support
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Operating system: Windows 11 Home
Slicer version: 5.6.2
CPU: Intel(R) Core™ i5-9300H CPU @ 2.40GHz 2.40 GHz
RAM: 8.00 GB (7.81 GB usable)
Free disc space: 51.8 GB (SSD Windows C:)
PyTorch version:
image

I have come across a relatively common problem (as I can see from the support forum).
Specifically when I tried running TotalSegmentator (fast) on several CT scans (one at a time) i got the error “Failed to compute results”. The exact error text:

Summary

Failed to compute results.

Command ‘[‘C:/Users/jimly/AppData/Local/slicer.org/Slicer 5.6.2/bin/…/bin\PythonSlicer.EXE’, ‘C:\Users\jimly\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Scripts\TotalSegmentator.exe’, ‘-i’, ‘C:/Users/jimly/AppData/Local/Temp/Slicer/__SlicerTemp__2024-05-07_08+54+49.068/total-segmentator-input.nii’, ‘-o’, ‘C:/Users/jimly/AppData/Local/Temp/Slicer/__SlicerTemp__2024-05-07_08+54+49.068/segmentation’, ‘–ml’, ‘–task’, ‘total’, ‘–fast’]’ returned non-zero exit status 120.

Traceback (most recent call last):
File “C:\Users\jimly\AppData\Local\slicer.org\Slicer 5.6.2\bin\Python\slicer\util.py”, line 3255, in tryWithErrorDisplay
yield
File “C:/Users/jimly/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py”, line 298, in onApplyButton
self.logic.process(self.ui.inputVolumeSelector.currentNode(), self.ui.outputSegmentationSelector.currentNode(),
File “C:/Users/jimly/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py”, line 961, in process
self.processVolume(inputFile, inputVolume,
File “C:/Users/jimly/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py”, line 1035, in processVolume
self.logProcessOutput(proc)
File “C:/Users/jimly/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py”, line 807, in logProcessOutput
raise CalledProcessError(retcode, proc.args, output=proc.stdout, stderr=proc.stderr)
subprocess.CalledProcessError: Command ‘[‘C:/Users/jimly/AppData/Local/slicer.org/Slicer 5.6.2/bin/…/bin\PythonSlicer.EXE’, ‘C:\Users\jimly\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Scripts\TotalSegmentator.exe’, ‘-i’, ‘C:/Users/jimly/AppData/Local/Temp/Slicer/__SlicerTemp__2024-05-07_08+54+49.068/total-segmentator-input.nii’, ‘-o’, ‘C:/Users/jimly/AppData/Local/Temp/Slicer/__SlicerTemp__2024-05-07_08+54+49.068/segmentation’, ‘–ml’, ‘–task’, ‘total’, ‘–fast’]’ returned non-zero exit status 120.

After reading the advice available on this topic, I did the following:

  1. Uninstalled PyTorch Util
  2. Restarted 3D Slicer
  3. Re-installed PyTorch Util with the requirement: >=2
  4. Restarted Slicer once more
  5. Run TotalSegmentator again

I got the same error.

I then did the following:

  1. Unistalled 3D Slicer
  2. Entirely deleted the folders:
    C:\Users\jimly.totalsegmentator
    C:\Users\jimly\AppData\Local\slicer.org\Slicer 5.6.2
    C:\Users\jimly\AppData\Local\slicer.org\Slicer
  3. Reinstalled 3D Slicer
  4. Uninstalled PyTorch Util - Restarted 3D Slicer - Re-installed PyTorch Util with the requirement: >=2 - Restarted Slicer once more
  5. Forced TotalSegmentator Python Package to Reinstall
  6. Run TotalSegmentator

I got the exact same error.

I should also quote the system dialogue that occured while running TotalSegmentator:

Summary

Processing started
Writing input file to C:/Users/jimly/AppData/Local/Temp/Slicer/__SlicerTemp__2024-05-07_15+40+18.698/total-segmentator-input.nii
Creating segmentations with TotalSegmentator AI…
Total Segmentator arguments: [‘-i’, ‘C:/Users/jimly/AppData/Local/Temp/Slicer/__SlicerTemp__2024-05-07_15+40+18.698/total-segmentator-input.nii’, ‘-o’, ‘C:/Users/jimly/AppData/Local/Temp/Slicer/__SlicerTemp__2024-05-07_15+40+18.698/segmentation’, ‘–ml’, ‘–task’, ‘total’, ‘–fast’]

If you use this tool please cite: https://pubs.rsna.org/doi/10.1148/ryai.230024

TotalSegmentator sends anonymous usage statistics. If you want to disable it check the documentation.
Using ‘fast’ option: resampling to lower resolution (3mm)
Downloading model for Task 297 …

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multiprocessing.pool.RemoteTraceback:
“”"
Traceback (most recent call last):
File “C:\Users\jimly\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\multiprocessing\pool.py”, line 125, in worker
result = (True, func(*args, **kwds))
File “C:\Users\jimly\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\multiprocessing\pool.py”, line 51, in starmapstar
return list(itertools.starmap(args[0], args[1]))
File “C:\Users\jimly\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\nnunetv2\inference\export_prediction.py”, line 39, in export_prediction_from_softmax
segmentation = label_manager.convert_logits_to_segmentation(predicted_array_or_file)
File “C:\Users\jimly\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\nnunetv2\utilities\label_handling\label_handling.py”, line 181, in convert_logits_to_segmentation
probabilities = self.apply_inference_nonlin(predicted_logits)
File “C:\Users\jimly\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\nnunetv2\utilities\label_handling\label_handling.py”, line 140, in apply_inference_nonlin
probabilities = self.inference_nonlin(logits_torch)
File “C:\Users\jimly\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\nnunetv2\utilities\helpers.py”, line 5, in softmax_helper_dim0
return torch.softmax(x, 0)
RuntimeError: [enforce fail at alloc_cpu.cpp:114] data. DefaultCPUAllocator: not enough memory: you tried to allocate 1889976736 bytes.
“”"

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File “C:\Users\jimly\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\runpy.py”, line 197, in _run_module_as_main
return _run_code(code, main_globals, None,
File “C:\Users\jimly\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\runpy.py”, line 87, in run_code
exec(code, run_globals)
File "C:\Users\jimly\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Scripts\TotalSegmentator.exe_main.py", line 7, in
File “C:\Users\jimly\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\totalsegmentator\bin\TotalSegmentator.py”, line 127, in main
totalsegmentator(args.input, args.output, args.ml, args.nr_thr_resamp, args.nr_thr_saving,
File “C:\Users\jimly\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\totalsegmentator\python_api.py”, line 293, in totalsegmentator
seg_img, ct_img = nnUNet_predict_image(input, output, task_id, model=model, folds=folds,
File “C:\Users\jimly\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\totalsegmentator\nnunet.py”, line 395, in nnUNet_predict_image
nnUNetv2_predict(tmp_dir, tmp_dir, task_id, model, folds, trainer, tta,
File “C:\Users\jimly\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\totalsegmentator\nnunet.py”, line 178, in nnUNetv2_predict
predict_from_raw_data(dir_in,
File “C:\Users\jimly\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\nnunetv2\inference\predict_from_raw_data.py”, line 347, in predict_from_raw_data
[i.get() for i in r]
File “C:\Users\jimly\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\nnunetv2\inference\predict_from_raw_data.py”, line 347, in
[i.get() for i in r]
File “C:\Users\jimly\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\multiprocessing\pool.py”, line 771, in get
raise self._value
RuntimeError: [enforce fail at alloc_cpu.cpp:114] data. DefaultCPUAllocator: not enough memory: you tried to allocate 1889976736 bytes.
Exception in thread Thread-5:
Traceback (most recent call last):
File “C:\Users\jimly\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\threading.py”, line 973, in _bootstrap_inner
Exception ignored in: <totalsegmentator.libs.DummyFile object at 0x000001CF5434B130>
AttributeError: ‘DummyFile’ object has no attribute ‘flush’
Download finished. Extracting…
Resampling…
Resampled in 63.89s
Predicting…

Please help me.

2

Hello,
Are running totalSegmentator on the sample data or on some of your data?
Maybe try on the sample data to make sure that the error is still there

3

Thanks for the feedback!

I have tried it on some sample data and it works.
What can I do to apply totalSegmentator on my data?

4

Thanks @Matteboo, very good intuition.

As the error message described, your computer does not have enough memory to process your image:

RuntimeError: [enforce fail at alloc_cpu.cpp:114] data. DefaultCPUAllocator: not enough memory: you tried to allocate 1889976736 bytes.

You can use Crop volume module to crop the your image to the relevant region and/or resample (with using a scaling factor >1) until the memory usage drops low enough so that your computer can handle it.

Alternatively, you can add more physical RAM to your computer (you need to buy additional hardware component and put it into your computer) or adjust your Windows system settings to increase the amount of virtual memory (you can add as much virtual memory as you have free disk space, but processing can be many times slower).

5

Thanks a lot for the prompt response!
I will try physically upgrading my RAM and I will return with some feedback.

How much RAM would you suggest I add?

I read that I should have 10-fold memory than the ammount of data I am trying to load. If that holds true and I tried to load 1889976736 bytes (~2 gb), then I should have at least 20 gb RAM.

6

I would say nowadays 16GB would be a minimum, but if you work with larger images then 32GB may be useful, too.

For AI image segmentation the biggest difference in computation time would be if you could get a good NVIDIA GPU. If you only use pre-trained models then I would recommend one with at least 16GB RAM, if you want to do training as well then I would recommend at least 24GB GPU RAM.

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