Totalsegmentator failing with error 120

Support
1

Hi all,

I am having issues with the Totalsegmentator module. I have tried the steps that I have seen here:TotalSegmentator fails with error 120 - #4 by lassoan and here:TotalSegmentator error at first run: Command ...Python\Scripts\TotalSegmentator... returned non-zero exit status 120 to resolve the issue with no solution yet.

I am running on Windows 11 with Slicer 5.6.1 and an RTX 3080. Additionally, I have downloaded and installed both versions of CUDA listed on the Pytorch website, thinking that there was an issue with one of them. As for data I am using the sample CTLiver data.

Here is a screenshot of my Pytorch Utils

image

And here is my error output:

Traceback (most recent call last):
  File "C:\Users\Logan\AppData\Local\slicer.org\Slicer 5.6.1\bin\Python\slicer\util.py", line 3255, in tryWithErrorDisplay
    yield
  File "C:/Users/Logan/AppData/Local/slicer.org/Slicer 5.6.1/slicer.org/Extensions-32438/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py", line 292, in onApplyButton
    self.logic.process(self.ui.inputVolumeSelector.currentNode(), self.ui.outputSegmentationSelector.currentNode(),
  File "C:/Users/Logan/AppData/Local/slicer.org/Slicer 5.6.1/slicer.org/Extensions-32438/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py", line 967, in process
    self.logProcessOutput(proc)
  File "C:/Users/Logan/AppData/Local/slicer.org/Slicer 5.6.1/slicer.org/Extensions-32438/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py", line 787, in logProcessOutput
    raise CalledProcessError(retcode, proc.args, output=proc.stdout, stderr=proc.stderr)
subprocess.CalledProcessError: Command '['C:/Users/Logan/AppData/Local/slicer.org/Slicer 5.6.1/bin/../bin\\PythonSlicer.EXE', 'C:\\Users\\Logan\\AppData\\Local\\slicer.org\\Slicer 5.6.1\\lib\\Python\\Scripts\\TotalSegmentator.exe', '-i', 'C:/Users/Logan/AppData/Local/Temp/Slicer/__SlicerTemp__2024-02-20_12+51+51.753/total-segmentator-input.nii', '-o', 'C:/Users/Logan/AppData/Local/Temp/Slicer/__SlicerTemp__2024-02-20_12+51+51.753/segmentation', '--ml', '--task', 'total']' returned non-zero exit status 120.
2

Does this happen on a laptop? If yes, have you set up SlicerApp-real.exe to use the NVIDIA GPU?

How much free disk space do you have?

I would recommend to reinstall Slicer from scratch into an empty folder. Also remove the downloaded TotalSegmentator model from your user profile folder. When installing TotalSegmentator and its dependencies make sure to have at least 20GB of free disk space.

3

Hi @lassoan this is happening on my desktop workstation. I still have over 800 gigabytes of free space on my main C drive.

Do I still need the SlicerApp-real.exe for my desktop?

I will begin removing slicer and the old dependencies and check back in shortly.

4

On desktop systems the NVIDIA GPU is used for all applications (if you have some low-performance Intel integrated graphics system then it is usually disabled). So, there is no need to specify SlicerApp-real to be used for the high-performance GPU.

With 800GB free disk space, installation is not corrupted by running out of disk space.

Reinstalling Slicer into a new empty folder and deleting all downloaded TotalSegmentator files (in %USERPROFILE%\.totalsegmentator) may still make sense, as you may have installed various Python package versions and/or you may have some failed installations due to temporary network issues.

5

Ok, I did a completely clean install of Slicer and removed every single dependency that I could find related to the program in my C drive and in Appdata (including .totalsegmentator). Additionally, I updated my graphics driver, but I am still getting the 120 error. I’ve pasted the log again below. I have also included the full log where it is installing everything on a first run in case something is not happening that should be. Should I delete slicer, pytorch, and python for a truly clean install and try again?

Logs 
Traceback (most recent call last):
  File "C:\Slicer\Slicer 5.6.1\bin\Python\slicer\util.py", line 3255, in tryWithErrorDisplay
    yield
  File "C:/Slicer/Slicer 5.6.1/slicer.org/Extensions-32438/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py", line 292, in onApplyButton
    self.logic.process(self.ui.inputVolumeSelector.currentNode(), self.ui.outputSegmentationSelector.currentNode(),
  File "C:/Slicer/Slicer 5.6.1/slicer.org/Extensions-32438/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py", line 967, in process
    self.logProcessOutput(proc)
  File "C:/Slicer/Slicer 5.6.1/slicer.org/Extensions-32438/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py", line 787, in logProcessOutput
    raise CalledProcessError(retcode, proc.args, output=proc.stdout, stderr=proc.stderr)
subprocess.CalledProcessError: Command '['C:/Slicer/Slicer 5.6.1/bin/../bin\\PythonSlicer.EXE', 'C:\\Slicer\\Slicer 5.6.1\\lib\\Python\\Scripts\\TotalSegmentator.exe', '-i', 'C:/Users/Logan/AppData/Local/Temp/Slicer/__SlicerTemp__2024-02-20_14+01+32.822/total-segmentator-input.nii', '-o', 'C:/Users/Logan/AppData/Local/Temp/Slicer/__SlicerTemp__2024-02-20_14+01+32.822/segmentation', '--ml', '--task', 'total']' returned non-zero exit status 120.

TotalSegmentator Python package is required. Installing it from https://github.com/wasserth/TotalSegmentator/archive/bbc1e7b3df64339e67acbebe2cf3c739098aabf4.zip... (it may take several minutes)
- Installing numpy...
- Installing psutil...
- Installing nibabel>=2.3.0...
- Installing tqdm>=4.45.0...
- Installing p-tqdm...
- Installing xvfbwrapper...
- Installing fury...
- Installing rt-utils...
- Installing dicom2nifti...
nnunetv2 Python package is required. Installing nnunetv2==2.1
 ...
- Installing acvl-utils>=0.2...
- Installing dynamic-network-architectures>=0.2...
- Installing tqdm...
- Installing dicom2nifti...
- Installing scikit-image>=0.14...
- Installing medpy...
- Installing scipy...
- Installing batchgenerators>=0.25...
- Installing numpy...
- Installing scikit-learn...
- Installing scikit-image>=0.19.3...
- Installing pandas...
- Installing graphviz...
- Installing tifffile...
- Installing nibabel...
- Installing matplotlib...
- Installing seaborn...
- Installing imagecodecs...
- Installing yacs...
TotalSegmentator installation is completed successfully.
Processing started
Writing input file to C:/Users/Logan/AppData/Local/Temp/Slicer/__SlicerTemp__2024-02-20_14+01+32.822/total-segmentator-input.nii
Creating segmentations with TotalSegmentator AI...
Total Segmentator arguments: ['-i', 'C:/Users/Logan/AppData/Local/Temp/Slicer/__SlicerTemp__2024-02-20_14+01+32.822/total-segmentator-input.nii', '-o', 'C:/Users/Logan/AppData/Local/Temp/Slicer/__SlicerTemp__2024-02-20_14+01+32.822/segmentation', '--ml', '--task', 'total']

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.
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Traceback (most recent call last):
  File "C:\Slicer\Slicer 5.6.1\lib\Python\Lib\runpy.py", line 197, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "C:\Slicer\Slicer 5.6.1\lib\Python\Lib\runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "C:\Slicer\Slicer 5.6.1\lib\Python\Scripts\TotalSegmentator.exe\__main__.py", line 7, in <module>
  File "C:\Slicer\Slicer 5.6.1\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:\Slicer\Slicer 5.6.1\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:\Slicer\Slicer 5.6.1\lib\Python\Lib\site-packages\totalsegmentator\nnunet.py", line 375, in nnUNet_predict_image
    nnUNetv2_predict(tmp_dir, tmp_dir, tid, model, folds, trainer, tta,
  File "C:\Slicer\Slicer 5.6.1\lib\Python\Lib\site-packages\totalsegmentator\nnunet.py", line 178, in nnUNetv2_predict
    predict_from_raw_data(dir_in,
  File "C:\Slicer\Slicer 5.6.1\lib\Python\Lib\site-packages\nnunetv2\inference\predict_from_raw_data.py", line 159, in predict_from_raw_data
    load_what_we_need(model_training_output_dir, use_folds, checkpoint_name)
  File "C:\Slicer\Slicer 5.6.1\lib\Python\Lib\site-packages\nnunetv2\inference\predict_from_raw_data.py", line 96, in load_what_we_need
    trainer_class = recursive_find_python_class(join(nnunetv2.__path__[0], "training", "nnUNetTrainer"),
  File "C:\Slicer\Slicer 5.6.1\lib\Python\Lib\site-packages\nnunetv2\utilities\find_class_by_name.py", line 12, in recursive_find_python_class
    m = importlib.import_module(current_module + "." + modname)
  File "C:\Slicer\Slicer 5.6.1\lib\Python\Lib\importlib\__init__.py", line 127, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 1030, in _gcd_import
  File "<frozen importlib._bootstrap>", line 1007, in _find_and_load
  File "<frozen importlib._bootstrap>", line 986, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 680, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 850, in exec_module
  File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed
  File "C:\Slicer\Slicer 5.6.1\lib\Python\Lib\site-packages\nnunetv2\training\nnUNetTrainer\nnUNetTrainer.py", line 51, in <module>
    from nnunetv2.utilities.get_network_from_plans import get_network_from_plans
  File "C:\Slicer\Slicer 5.6.1\lib\Python\Lib\site-packages\nnunetv2\utilities\get_network_from_plans.py", line 1, in <module>
    from dynamic_network_architectures.architectures.unet import PlainConvUNet, ResidualEncoderUNet
ImportError: cannot import name 'ResidualEncoderUNet' from 'dynamic_network_architectures.architectures.unet' (C:\Slicer\Slicer 5.6.1\lib\Python\Lib\site-packages\dynamic_network_architectures\architectures\unet.py)
Exception ignored in: <totalsegmentator.libs.DummyFile object at 0x000001AB451E5700>
AttributeError: 'DummyFile' object has no attribute 'flush'
Download finished. Extracting...
Resampling...
  Resampled in 6.01s
Predicting part 1 of 5 ...
6

This error indicates that your nnunet installation is corrupted. Wipe out the entire C:\Slicer\Slicer 5.6.1 folder and install Slicer and TotalSegmentator extension from scratch.

7

Sadly, I got the same result. I posted the outputs below. As you suggested, I wiped out the entire C:\Slicer\Slicer 5.6.1 folder and installed Slicer and TotalSegmentator extension from scratch. Prior to this, I even removed Python (it had multiple versions for some reason) and grabbed the most recent version. I made a timeline for troubleshooting. Unsure how to further chase the nnunet error from here. If it would be helpful, I can stream myself doing this and then post the VOD here for enhanced clarification.

Clean slicer, removed all extension folders.

image
image951×595 53.6 KB

grabbed Totalsegmentator

image
image2549×214 31.2 KB

grabbed Pytorch. I noted that when I grabbed Totalsegmentator it said it downloaded Pytorch but there was nothing there after a restart.
image

imported CTLiver data

image
image1920×1045 105 KB

Running Totalsegmentator for the first time (it asked me to restart here so I did)

image
image390×700 7.19 KB

Logs 
Traceback (most recent call last):
  File "C:\Users\Logan\AppData\Local\slicer.org\Slicer 5.6.1\bin\Python\slicer\util.py", line 3255, in tryWithErrorDisplay
    yield
  File "C:/Users/Logan/AppData/Local/slicer.org/Slicer 5.6.1/slicer.org/Extensions-32438/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py", line 292, in onApplyButton
    self.logic.process(self.ui.inputVolumeSelector.currentNode(), self.ui.outputSegmentationSelector.currentNode(),
  File "C:/Users/Logan/AppData/Local/slicer.org/Slicer 5.6.1/slicer.org/Extensions-32438/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py", line 967, in process
    self.logProcessOutput(proc)
  File "C:/Users/Logan/AppData/Local/slicer.org/Slicer 5.6.1/slicer.org/Extensions-32438/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py", line 787, in logProcessOutput
    raise CalledProcessError(retcode, proc.args, output=proc.stdout, stderr=proc.stderr)
subprocess.CalledProcessError: Command '['C:/Users/Logan/AppData/Local/slicer.org/Slicer 5.6.1/bin/../bin\\PythonSlicer.EXE', 'C:\\Users\\Logan\\AppData\\Local\\slicer.org\\Slicer 5.6.1\\lib\\Python\\Scripts\\TotalSegmentator.exe', '-i', 'C:/Users/Logan/AppData/Local/Temp/Slicer/__SlicerTemp__2024-02-20_14+56+35.190/total-segmentator-input.nii', '-o', 'C:/Users/Logan/AppData/Local/Temp/Slicer/__SlicerTemp__2024-02-20_14+56+35.190/segmentation', '--ml', '--task', 'total']' returned non-zero exit status 120.

TotalSegmentator Python package is required. Installing it from https://github.com/wasserth/TotalSegmentator/archive/bbc1e7b3df64339e67acbebe2cf3c739098aabf4.zip... (it may take several minutes)
- Installing numpy...
- Installing psutil...
- Installing nibabel>=2.3.0...
- Installing tqdm>=4.45.0...
- Installing p-tqdm...
- Installing xvfbwrapper...
- Installing fury...
- Installing rt-utils...
- Installing dicom2nifti...
nnunetv2 Python package is required. Installing nnunetv2==2.1
 ...
- Installing acvl-utils>=0.2...
- Installing dynamic-network-architectures>=0.2...
- Installing tqdm...
- Installing dicom2nifti...
- Installing scikit-image>=0.14...
- Installing medpy...
- Installing scipy...
- Installing batchgenerators>=0.25...
- Installing numpy...
- Installing scikit-learn...
- Installing scikit-image>=0.19.3...
- Installing pandas...
- Installing graphviz...
- Installing tifffile...
- Installing nibabel...
- Installing matplotlib...
- Installing seaborn...
- Installing imagecodecs...
- Installing yacs...
TotalSegmentator installation is completed successfully.
Processing started
Writing input file to C:/Users/Logan/AppData/Local/Temp/Slicer/__SlicerTemp__2024-02-20_14+56+35.190/total-segmentator-input.nii
Creating segmentations with TotalSegmentator AI...
Total Segmentator arguments: ['-i', 'C:/Users/Logan/AppData/Local/Temp/Slicer/__SlicerTemp__2024-02-20_14+56+35.190/total-segmentator-input.nii', '-o', 'C:/Users/Logan/AppData/Local/Temp/Slicer/__SlicerTemp__2024-02-20_14+56+35.190/segmentation', '--ml', '--task', 'total']

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.
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Traceback (most recent call last):
  File "C:\Users\Logan\AppData\Local\slicer.org\Slicer 5.6.1\lib\Python\Lib\runpy.py", line 197, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "C:\Users\Logan\AppData\Local\slicer.org\Slicer 5.6.1\lib\Python\Lib\runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "C:\Users\Logan\AppData\Local\slicer.org\Slicer 5.6.1\lib\Python\Scripts\TotalSegmentator.exe\__main__.py", line 7, in <module>
  File "C:\Users\Logan\AppData\Local\slicer.org\Slicer 5.6.1\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\Logan\AppData\Local\slicer.org\Slicer 5.6.1\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\Logan\AppData\Local\slicer.org\Slicer 5.6.1\lib\Python\Lib\site-packages\totalsegmentator\nnunet.py", line 375, in nnUNet_predict_image
    nnUNetv2_predict(tmp_dir, tmp_dir, tid, model, folds, trainer, tta,
  File "C:\Users\Logan\AppData\Local\slicer.org\Slicer 5.6.1\lib\Python\Lib\site-packages\totalsegmentator\nnunet.py", line 178, in nnUNetv2_predict
    predict_from_raw_data(dir_in,
  File "C:\Users\Logan\AppData\Local\slicer.org\Slicer 5.6.1\lib\Python\Lib\site-packages\nnunetv2\inference\predict_from_raw_data.py", line 159, in predict_from_raw_data
    load_what_we_need(model_training_output_dir, use_folds, checkpoint_name)
  File "C:\Users\Logan\AppData\Local\slicer.org\Slicer 5.6.1\lib\Python\Lib\site-packages\nnunetv2\inference\predict_from_raw_data.py", line 96, in load_what_we_need
    trainer_class = recursive_find_python_class(join(nnunetv2.__path__[0], "training", "nnUNetTrainer"),
  File "C:\Users\Logan\AppData\Local\slicer.org\Slicer 5.6.1\lib\Python\Lib\site-packages\nnunetv2\utilities\find_class_by_name.py", line 12, in recursive_find_python_class
    m = importlib.import_module(current_module + "." + modname)
  File "C:\Users\Logan\AppData\Local\slicer.org\Slicer 5.6.1\lib\Python\Lib\importlib\__init__.py", line 127, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 1030, in _gcd_import
  File "<frozen importlib._bootstrap>", line 1007, in _find_and_load
  File "<frozen importlib._bootstrap>", line 986, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 680, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 850, in exec_module
  File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed
  File "C:\Users\Logan\AppData\Local\slicer.org\Slicer 5.6.1\lib\Python\Lib\site-packages\nnunetv2\training\nnUNetTrainer\nnUNetTrainer.py", line 51, in <module>
    from nnunetv2.utilities.get_network_from_plans import get_network_from_plans
  File "C:\Users\Logan\AppData\Local\slicer.org\Slicer 5.6.1\lib\Python\Lib\site-packages\nnunetv2\utilities\get_network_from_plans.py", line 1, in <module>
    from dynamic_network_architectures.architectures.unet import PlainConvUNet, ResidualEncoderUNet
ImportError: cannot import name 'ResidualEncoderUNet' from 'dynamic_network_architectures.architectures.unet' (C:\Users\Logan\AppData\Local\slicer.org\Slicer 5.6.1\lib\Python\Lib\site-packages\dynamic_network_architectures\architectures\unet.py)
Exception ignored in: <totalsegmentator.libs.DummyFile object at 0x000001F770F8C760>
AttributeError: 'DummyFile' object has no attribute 'flush'
Download finished. Extracting...
Resampling...
  Resampled in 5.88s
Predicting part 1 of 5 ...
8

One thing that just came to mind would be that this isn’t a cpu issue, is it? I am running an AMD 7950X. The days where certain applications only run on certain chips are fairly gone but I suppose it is one thing to check.

9

Most likely the issue is that the dynamic-network-architectures is somehow corrupted. Maybe you have some old corrupted copy in the pip cache.

First of all, check its version:

from importlib.metadata import version
print(version("dynamic_network_architectures"))

Then check if you can import dynamic_network_architectures and its path is within the Slicer build tree:

import dynamic_network_architectures
import inspect
print(inspect.getabsfile(dynamic_network_architectures))

Then check if you can load ResidualEncoderUNet and it is in the correct location:

from dynamic_network_architectures.architectures.unet import ResidualEncoderUNet
print(inspect.getabsfile(ResidualEncoderUNet))

If this fails check if the content of your dynamic_network_architectures file folder matches the content of the folder on my computer (from a working TotalSegmentator installation): site-packages.zip

10

I ran into the same issue as @Logan_Moore when I tried on my machine.

@lassoan It appears that your dynamic_network_architectures is version 0.2, while mine is version 0.4.

Checking for ResidualEncoderUNet I get:

Traceback (most recent call last):
  File "<string>", line 1, in <module>
ImportError: cannot import name 'ResidualEncoderUNet' from 'dynamic_network_architectures.architectures.unet' (C:\Users\butlej30383\AppData\Local\slicer.org\Slicer 5.7.0-2024-02-17\lib\Python\Lib\site-packages\dynamic_network_architectures\architectures\unet.py)
1 Like
11

Aha! So, it is not a too old package, but a too recent package.

Unfortunately, developer of dynamic_network_architectures broke backward compatibility with a recent update. ResidualEncoderUNet package must be imported as from dynamic_network_architectures.architectures.residual_unet import ResidualEncoderUNet now, but since this change was snuck into a minor version update (0.2 to 0.4) developer of TotalSegmentator did not suspect anything bad would happen.

As a workaround, you can downgrade dynamic_network_architectures package by running this command in the Python console (that I’ll also add to the TotalSegmentator Slicer module):

pip_install('dynamic_network_architectures==0.2.0')

I’ve filed a bug report to TotalSegmentator to make sure the incompatibility is fixed properly:

3 Likes
12

And we have success! Thank you, @lassoan and @jamesobutler, for your work and patience with this. I am glad the issue could be identified and flagged for a future fix

image
image756×828 153 KB

1 Like
13

Awesome, it is good that with some shared effort we figured this all out.

14

FYI, maintainer of dynamic-network-architectures yanked the incompatible releases and published a new release that is backward compatible, so this issue should not come up again.

1 Like