# Error running TotalSegmentator - returned non-zero exit status 120

**URL:** <https://discourse.slicer.org/t/error-running-totalsegmentator-returned-non-zero-exit-status-120/28587>\
**Category:** Support\
**Tags:** segmentation, totalsegmentator\
**Created:** [March 27, 2023, 1:42am UTC](https://discourse.slicer.org/t/error-running-totalsegmentator-returned-non-zero-exit-status-120/28587 "2023-03-27T01:42:05Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![yf025](https://avatars.discourse-cdn.com/v4/letter/y/7ab992/32.png) [@yf025](https://discourse.slicer.org/u/yf025)\
**Post date:** [March 27, 2023, 1:42am UTC](https://discourse.slicer.org/t/error-running-totalsegmentator-returned-non-zero-exit-status-120/28587/1 "2023-03-27T01:42:05Z")

</div>

I installed pytorch module and totalsegmentator in extensions manager then nii was imported ，but after I clicking “apply” and waiting for the process“TotalSegmentator Python package is required. Installing… (it may take several minutes)”，then the error info poped out。Need help to solve this，thx！  
Here are the error infos。  
Failed to compute results.  
Command '[‘C:/ProgramData/NA-MIC/Slicer 5.2.2/bin/…/bin\PythonSlicer.EXE’, ‘-m’, ‘pip’, ‘install’, '[https://github.com/wasserth/TotalSegmentator/archive/b38eb449ad8652a987878a925203cbfa354e9b85.zip’]’](https://github.com/wasserth/TotalSegmentator/archive/b38eb449ad8652a987878a925203cbfa354e9b85.zip'%5D') returned non-zero exit status 1.

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<div class="post-metadata">

**Author:** ![jamesobutler](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jamesobutler/32/7511_2.png) [@jamesobutler](https://discourse.slicer.org/u/jamesobutler)\
**Post date:** [March 27, 2023, 1:58am UTC](https://discourse.slicer.org/t/error-running-totalsegmentator-returned-non-zero-exit-status-120/28587/2 "2023-03-27T01:58:21Z")

</div>

Based on the provided information I believe this is the following issue linked below. The current workaround is to restart Slicer after the TotalSegmentor python package is installed and it should proceed successfully.

> <https://github.com/lassoan/SlicerTotalSegmentator/issues/17>
>
> I'm currently using Slicer 5.2.2, have SlicerPyTorch installed and pointing to S…licerTotalSegmentor as of https://github.com/lassoan/SlicerTotalSegmentator/commit/493fa5bcbb75267e21ec086f95d0eb01ec1562a5.
> 
> I start Slicer fresh, and when I go into TotalSegmentor and press apply, it appropriate warns that PyTorch needs to be downloaded and installed and then it installs the TotalSegmentor package. However I observe that the install process uninstall \`scipy\` 1.9.2 that is included as part of Slicer 5.2.2 and it installs \`scipy\` 1.9.1. This produces an exit code that results in TotalSegmentor not running. Is it expected for the uninstall/install of \`scipy\` to be successful in Slicer? If I close Slicer, reopen and then press "Apply" in TotalSegmentor then it is successful.
> 
> Is access denied because the \`scipy\` package is in-use as it has been \[imported in Slicer on startup\](https://github.com/Slicer/Slicer/blob/fb46bd16846dc7c7a69c398aef0fc3baf533905e/Base/Python/slicer/\_\_init\_\_.py#L68-L69)? 
> \`\`\`
> ERROR: Could not install packages due to an OSError: \[WinError 5\] Access is denied: 'C:\\\\Users\\\\butlej30383\\\\AppData\\\\Local\\\\NA-MIC\\\\Slicer 5.2.2\\\\lib\\\\Python\\\\Lib\\\\site-packages\\\\~cipy\\\\\_lib\\\\\_ccallback\_c.cp39-win\_amd64.pyd'
> Consider using the \`--user\` option or check the permissions.
> \`\`\`
> 
> !\[image\](https://user-images.githubusercontent.com/15837524/225063222-ddf680f7-0caf-4d1e-bf2d-2e652e463fc6.png)
> 
> Additional FYI: The latest \`torch 2.0.0\` was downloaded and installed here.
> \<details\>
> \<summary\>See full pip output here\</summary\>
> Python 3.9.10 (main, Feb 22 2023, 01:07:37) \[MSC v.1930 64 bit (AMD64)\] on win32
> \>\>\> 
> Collecting light-the-torch\>=0.5
> Downloading light\_the\_torch-0.7.1-py3-none-any.whl (14 kB)
> Requirement already satisfied: pip\<23.1,\>=22.3 in c:\\users\\butlej30383\\appdata\\local\\na-mic\\slicer 5.2.2\\lib\\python\\lib\\site-packages (from light-the-torch\>=0.5) (23.0)
> Installing collected packages: light-the-torch
> WARNING: The script ltt.exe is installed in 'C:\\Users\\butlej30383\\AppData\\Local\\NA-MIC\\Slicer 5.2.2\\lib\\Python\\Scripts' which is not on PATH.
> Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
> Successfully installed light-the-torch-0.7.1
> 
> \[notice\] A new release of pip is available: 23.0 -\> 23.0.1
> \[notice\] To update, run: python-real.exe -m pip install --upgrade pip
> Collecting torch
> Downloading https://download.pytorch.org/whl/cu118/torch-2.0.0%2Bcu118-cp39-cp39-win\_amd64.whl (2611.4 MB)
> ---------------------------------------- 2.6/2.6 GB 1.7 MB/s eta 0:00:00
> Collecting jinja2
> Downloading Jinja2-3.1.2-py3-none-any.whl (133 kB)
> -------------------------------------- 133.1/133.1 kB 1.6 MB/s eta 0:00:00
> Collecting typing-extensions
> Downloading typing\_extensions-4.5.0-py3-none-any.whl (27 kB)
> Collecting filelock
> Downloading filelock-3.9.1-py3-none-any.whl (9.7 kB)
> Collecting networkx
> Downloading networkx-3.0-py3-none-any.whl (2.0 MB)
> ---------------------------------------- 2.0/2.0 MB 10.0 MB/s eta 0:00:00
> Collecting sympy
> Downloading sympy-1.11.1-py3-none-any.whl (6.5 MB)
> ---------------------------------------- 6.5/6.5 MB 29.5 MB/s eta 0:00:00
> Collecting MarkupSafe\>=2.0
> Downloading MarkupSafe-2.1.2-cp39-cp39-win\_amd64.whl (16 kB)
> Collecting mpmath\>=0.19
> Downloading mpmath-1.3.0-py3-none-any.whl (536 kB)
> ------------------------------------- 536.2/536.2 kB 32.9 MB/s eta 0:00:00
> Installing collected packages: mpmath, typing-extensions, sympy, networkx, MarkupSafe, filelock, jinja2, torch
> WARNING: The script isympy.exe is installed in 'C:\\Users\\butlej30383\\AppData\\Local\\NA-MIC\\Slicer 5.2.2\\lib\\Python\\Scripts' which is not on PATH.
> Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
> WARNING: The scripts convert-caffe2-to-onnx.exe, convert-onnx-to-caffe2.exe and torchrun.exe are installed in 'C:\\Users\\butlej30383\\AppData\\Local\\NA-MIC\\Slicer 5.2.2\\lib\\Python\\Scripts' which is not on PATH.
> Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
> Successfully installed MarkupSafe-2.1.2 filelock-3.9.1 jinja2-3.1.2 mpmath-1.3.0 networkx-3.0 sympy-1.11.1 torch-2.0.0+cu118 typing-extensions-4.5.0
> 
> \[notice\] A new release of pip is available: 23.0 -\> 23.0.1
> \[notice\] To update, run: python-real.exe -m pip install --upgrade pip
> Collecting matplotlib
> Downloading matplotlib-3.7.1-cp39-cp39-win\_amd64.whl (7.6 MB)
> ---------------------------------------- 7.6/7.6 MB 18.8 MB/s eta 0:00:00
> Collecting python-dateutil\>=2.7
> Downloading python\_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
> -------------------------------------- 247.7/247.7 kB 7.7 MB/s eta 0:00:00
> Collecting kiwisolver\>=1.0.1
> Downloading kiwisolver-1.4.4-cp39-cp39-win\_amd64.whl (55 kB)
> ---------------------------------------- 55.4/55.4 kB 1.5 MB/s eta 0:00:00
> Collecting fonttools\>=4.22.0
> Downloading fonttools-4.39.0-py3-none-any.whl (1.0 MB)
> ---------------------------------------- 1.0/1.0 MB 12.7 MB/s eta 0:00:00
> Collecting cycler\>=0.10
> Downloading cycler-0.11.0-py3-none-any.whl (6.4 kB)
> Requirement already satisfied: pillow\>=6.2.0 in c:\\users\\butlej30383\\appdata\\local\\na-mic\\slicer 5.2.2\\lib\\python\\lib\\site-packages (from matplotlib) (9.4.0)
> Requirement already satisfied: pyparsing\>=2.3.1 in c:\\users\\butlej30383\\appdata\\local\\na-mic\\slicer 5.2.2\\lib\\python\\lib\\site-packages (from matplotlib) (3.0.9)
> Requirement already satisfied: packaging\>=20.0 in c:\\users\\butlej30383\\appdata\\local\\na-mic\\slicer 5.2.2\\lib\\python\\lib\\site-packages (from matplotlib) (23.0)
> Collecting importlib-resources\>=3.2.0
> Downloading importlib\_resources-5.12.0-py3-none-any.whl (36 kB)
> Requirement already satisfied: numpy\>=1.20 in c:\\users\\butlej30383\\appdata\\local\\na-mic\\slicer 5.2.2\\lib\\python\\lib\\site-packages (from matplotlib) (1.23.4)
> Collecting contourpy\>=1.0.1
> Downloading contourpy-1.0.7-cp39-cp39-win\_amd64.whl (160 kB)
> -------------------------------------- 160.2/160.2 kB 3.2 MB/s eta 0:00:00
> Collecting zipp\>=3.1.0
> Downloading zipp-3.15.0-py3-none-any.whl (6.8 kB)
> Requirement already satisfied: six\>=1.5 in c:\\users\\butlej30383\\appdata\\local\\na-mic\\slicer 5.2.2\\lib\\python\\lib\\site-packages (from python-dateutil\>=2.7-\>matplotlib) (1.16.0)
> Installing collected packages: zipp, python-dateutil, kiwisolver, fonttools, cycler, contourpy, importlib-resources, matplotlib
> WARNING: The scripts fonttools.exe, pyftmerge.exe, pyftsubset.exe and ttx.exe are installed in 'C:\\Users\\butlej30383\\AppData\\Local\\NA-MIC\\Slicer 5.2.2\\lib\\Python\\Scripts' which is not on PATH.
> Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
> Successfully installed contourpy-1.0.7 cycler-0.11.0 fonttools-4.39.0 importlib-resources-5.12.0 kiwisolver-1.4.4 matplotlib-3.7.1 python-dateutil-2.8.2 zipp-3.15.0
> 
> \[notice\] A new release of pip is available: 23.0 -\> 23.0.1
> \[notice\] To update, run: python-real.exe -m pip install --upgrade pip
> Collecting https://github.com/wasserth/TotalSegmentator/archive/b38eb449ad8652a987878a925203cbfa354e9b85.zip
> Downloading https://github.com/wasserth/TotalSegmentator/archive/b38eb449ad8652a987878a925203cbfa354e9b85.zip
> - 5.5 MB 16.0 MB/s 0:00:00
> Preparing metadata (setup.py): started
> Preparing metadata (setup.py): finished with status 'done'
> Requirement already satisfied: numpy in c:\\users\\butlej30383\\appdata\\local\\na-mic\\slicer 5.2.2\\lib\\python\\lib\\site-packages (from TotalSegmentator==1.5.3) (1.23.4)
> Collecting psutil
> Downloading psutil-5.9.4-cp36-abi3-win\_amd64.whl (252 kB)
> -------------------------------------- 252.5/252.5 kB 2.6 MB/s eta 0:00:00
> Requirement already satisfied: SimpleITK in c:\\users\\butlej30383\\appdata\\local\\na-mic\\slicer 5.2.2\\lib\\python\\lib\\site-packages (from TotalSegmentator==1.5.3) (2.2.0rc2.dev368)
> Collecting nibabel\>=2.3.0
> Downloading nibabel-5.0.1-py3-none-any.whl (3.3 MB)
> ---------------------------------------- 3.3/3.3 MB 17.4 MB/s eta 0:00:00
> Collecting tqdm\>=4.45.0
> Downloading tqdm-4.65.0-py3-none-any.whl (77 kB)
> ---------------------------------------- 77.1/77.1 kB ? eta 0:00:00
> Collecting p\_tqdm
> Downloading p\_tqdm-1.4.0.tar.gz (5.2 kB)
> Preparing metadata (setup.py): started
> Preparing metadata (setup.py): finished with status 'done'
> Collecting xvfbwrapper
> Downloading xvfbwrapper-0.2.9.tar.gz (5.6 kB)
> Preparing metadata (setup.py): started
> Preparing metadata (setup.py): finished with status 'done'
> Collecting fury
> Downloading fury-0.8.0-py3-none-any.whl (349 kB)
> ------------------------------------- 349.2/349.2 kB 22.6 MB/s eta 0:00:00
> Collecting batchgenerators==0.21
> Downloading batchgenerators-0.21-py3-none-any.whl (74 kB)
> ---------------------------------------- 74.7/74.7 kB ? eta 0:00:00
> Collecting nnunet-customized==1.2
> Downloading nnunet\_customized-1.2-py3-none-any.whl (474 kB)
> ------------------------------------- 474.0/474.0 kB 29.0 MB/s eta 0:00:00
> Requirement already satisfied: requests in c:\\users\\butlej30383\\appdata\\local\\na-mic\\slicer 5.2.2\\lib\\python\\lib\\site-packages (from TotalSegmentator==1.5.3) (2.28.2)
> Requirement already satisfied: scipy in c:\\users\\butlej30383\\appdata\\local\\na-mic\\slicer 5.2.2\\lib\\python\\lib\\site-packages (from batchgenerators==0.21-\>TotalSegmentator==1.5.3) (1.9.2)
> Collecting future
> Downloading future-0.18.3.tar.gz (840 kB)
> ------------------------------------- 840.9/840.9 kB 51.9 MB/s eta 0:00:00
> Preparing metadata (setup.py): started
> Preparing metadata (setup.py): finished with status 'done'
> Collecting scikit-learn
> Downloading scikit\_learn-1.2.2-cp39-cp39-win\_amd64.whl (8.4 MB)
> ---------------------------------------- 8.4/8.4 MB 38.2 MB/s eta 0:00:00
> Collecting scikit-image
> Downloading scikit\_image-0.20.0-cp39-cp39-win\_amd64.whl (23.9 MB)
> --------------------------------------- 23.9/23.9 MB 28.4 MB/s eta 0:00:00
> Collecting threadpoolctl
> Downloading threadpoolctl-3.1.0-py3-none-any.whl (14 kB)
> Requirement already satisfied: pillow\>=7.1.2 in c:\\users\\butlej30383\\appdata\\local\\na-mic\\slicer 5.2.2\\lib\\python\\lib\\site-packages (from batchgenerators==0.21-\>TotalSegmentator==1.5.3) (9.4.0)
> Collecting unittest2
> Downloading unittest2-1.1.0-py2.py3-none-any.whl (96 kB)
> ---------------------------------------- 96.4/96.4 kB ? eta 0:00:00
> Collecting dicom2nifti
> Downloading dicom2nifti-2.4.8-py3-none-any.whl (43 kB)
> ---------------------------------------- 43.6/43.6 kB ? eta 0:00:00
> Collecting pandas
> Downloading pandas-1.5.3-cp39-cp39-win\_amd64.whl (10.9 MB)
> --------------------------------------- 10.9/10.9 MB 54.4 MB/s eta 0:00:00
> Collecting tifffile
> Downloading tifffile-2023.2.28-py3-none-any.whl (216 kB)
> ------------------------------------- 216.4/216.4 kB 12.9 MB/s eta 0:00:00
> Collecting medpy
> Downloading MedPy-0.4.0.tar.gz (151 kB)
> ---------------------------------------- 151.8/151.8 kB ? eta 0:00:00
> Preparing metadata (setup.py): started
> Preparing metadata (setup.py): finished with status 'done'
> Requirement already satisfied: torch\>=1.6.0a in c:\\users\\butlej30383\\appdata\\local\\na-mic\\slicer 5.2.2\\lib\\python\\lib\\site-packages (from nnunet-customized==1.2-\>TotalSegmentator==1.5.3) (2.0.0+cu118)
> Requirement already satisfied: packaging\>=17 in c:\\users\\butlej30383\\appdata\\local\\na-mic\\slicer 5.2.2\\lib\\python\\lib\\site-packages (from nibabel\>=2.3.0-\>TotalSegmentator==1.5.3) (23.0)
> Requirement already satisfied: setuptools in c:\\users\\butlej30383\\appdata\\local\\na-mic\\slicer 5.2.2\\lib\\python\\lib\\site-packages (from nibabel\>=2.3.0-\>TotalSegmentator==1.5.3) (67.0.0)
> Collecting colorama
> Downloading colorama-0.4.6-py2.py3-none-any.whl (25 kB)
> Requirement already satisfied: vtk\>=9.1.0 in c:\\users\\butlej30383\\appdata\\local\\na-mic\\slicer 5.2.2\\lib\\python\\lib\\site-packages (from fury-\>TotalSegmentator==1.5.3) (9.1.20220125)
> Collecting pathos\>=0.2.5
> Downloading pathos-0.3.0-py3-none-any.whl (79 kB)
> ---------------------------------------- 79.8/79.8 kB ? eta 0:00:00
> Requirement already satisfied: six\>=1.13.0 in c:\\users\\butlej30383\\appdata\\local\\na-mic\\slicer 5.2.2\\lib\\python\\lib\\site-packages (from p\_tqdm-\>TotalSegmentator==1.5.3) (1.16.0)
> Requirement already satisfied: idna\<4,\>=2.5 in c:\\users\\butlej30383\\appdata\\local\\na-mic\\slicer 5.2.2\\lib\\python\\lib\\site-packages (from requests-\>TotalSegmentator==1.5.3) (3.4)
> Requirement already satisfied: certifi\>=2017.4.17 in c:\\users\\butlej30383\\appdata\\local\\na-mic\\slicer 5.2.2\\lib\\python\\lib\\site-packages (from requests-\>TotalSegmentator==1.5.3) (2022.12.7)
> Requirement already satisfied: charset-normalizer\<4,\>=2 in c:\\users\\butlej30383\\appdata\\local\\na-mic\\slicer 5.2.2\\lib\\python\\lib\\site-packages (from requests-\>TotalSegmentator==1.5.3) (3.0.1)
> Requirement already satisfied: urllib3\<1.27,\>=1.21.1 in c:\\users\\butlej30383\\appdata\\local\\na-mic\\slicer 5.2.2\\lib\\python\\lib\\site-packages (from requests-\>TotalSegmentator==1.5.3) (1.26.14)
> Collecting multiprocess\>=0.70.14
> Downloading multiprocess-0.70.14-py39-none-any.whl (132 kB)
> ---------------------------------------- 132.9/132.9 kB ? eta 0:00:00
> Collecting ppft\>=1.7.6.6
> Downloading ppft-1.7.6.6-py3-none-any.whl (52 kB)
> ---------------------------------------- 52.8/52.8 kB ? eta 0:00:00
> Collecting dill\>=0.3.6
> Downloading dill-0.3.6-py3-none-any.whl (110 kB)
> ---------------------------------------- 110.5/110.5 kB ? eta 0:00:00
> Collecting pox\>=0.3.2
> Downloading pox-0.3.2-py3-none-any.whl (29 kB)
> Collecting lazy\_loader\>=0.1
> Downloading lazy\_loader-0.1-py3-none-any.whl (8.6 kB)
> Collecting PyWavelets\>=1.1.1
> Downloading PyWavelets-1.4.1-cp39-cp39-win\_amd64.whl (4.2 MB)
> ---------------------------------------- 4.2/4.2 MB 38.2 MB/s eta 0:00:00
> Requirement already satisfied: networkx\>=2.8 in c:\\users\\butlej30383\\appdata\\local\\na-mic\\slicer 5.2.2\\lib\\python\\lib\\site-packages (from scikit-image-\>batchgenerators==0.21-\>TotalSegmentator==1.5.3) (3.0)
> Collecting scipy
> Downloading scipy-1.9.1-cp39-cp39-win\_amd64.whl (38.6 MB)
> --------------------------------------- 38.6/38.6 MB 40.9 MB/s eta 0:00:00
> Collecting imageio\>=2.4.1
> Downloading imageio-2.26.0-py3-none-any.whl (3.4 MB)
> ---------------------------------------- 3.4/3.4 MB 30.8 MB/s eta 0:00:00
> Requirement already satisfied: typing-extensions in c:\\users\\butlej30383\\appdata\\local\\na-mic\\slicer 5.2.2\\lib\\python\\lib\\site-packages (from torch\>=1.6.0a-\>nnunet-customized==1.2-\>TotalSegmentator==1.5.3) (4.5.0)
> Requirement already satisfied: sympy in c:\\users\\butlej30383\\appdata\\local\\na-mic\\slicer 5.2.2\\lib\\python\\lib\\site-packages (from torch\>=1.6.0a-\>nnunet-customized==1.2-\>TotalSegmentator==1.5.3) (1.11.1)
> Requirement already satisfied: jinja2 in c:\\users\\butlej30383\\appdata\\local\\na-mic\\slicer 5.2.2\\lib\\python\\lib\\site-packages (from torch\>=1.6.0a-\>nnunet-customized==1.2-\>TotalSegmentator==1.5.3) (3.1.2)
> Requirement already satisfied: filelock in c:\\users\\butlej30383\\appdata\\local\\na-mic\\slicer 5.2.2\\lib\\python\\lib\\site-packages (from torch\>=1.6.0a-\>nnunet-customized==1.2-\>TotalSegmentator==1.5.3) (3.9.1)
> Collecting python-gdcm
> Downloading python\_gdcm-3.0.21-cp39-cp39-win\_amd64.whl (27.2 MB)
> --------------------------------------- 27.2/27.2 MB 36.4 MB/s eta 0:00:00
> Requirement already satisfied: pydicom\>=2.2.0 in c:\\users\\butlej30383\\appdata\\local\\na-mic\\slicer 5.2.2\\lib\\python\\lib\\site-packages (from dicom2nifti-\>nnunet-customized==1.2-\>TotalSegmentator==1.5.3) (2.3.1)
> Requirement already satisfied: python-dateutil\>=2.8.1 in c:\\users\\butlej30383\\appdata\\local\\na-mic\\slicer 5.2.2\\lib\\python\\lib\\site-packages (from pandas-\>nnunet-customized==1.2-\>TotalSegmentator==1.5.3) (2.8.2)
> Collecting pytz\>=2020.1
> Downloading pytz-2022.7.1-py2.py3-none-any.whl (499 kB)
> ------------------------------------- 499.4/499.4 kB 15.8 MB/s eta 0:00:00
> Collecting joblib\>=1.1.1
> Downloading joblib-1.2.0-py3-none-any.whl (297 kB)
> ------------------------------------- 298.0/298.0 kB 18.0 MB/s eta 0:00:00
> Collecting argparse
> Downloading argparse-1.4.0-py2.py3-none-any.whl (23 kB)
> Collecting traceback2
> Downloading traceback2-1.4.0-py2.py3-none-any.whl (16 kB)
> Requirement already satisfied: MarkupSafe\>=2.0 in c:\\users\\butlej30383\\appdata\\local\\na-mic\\slicer 5.2.2\\lib\\python\\lib\\site-packages (from jinja2-\>torch\>=1.6.0a-\>nnunet-customized==1.2-\>TotalSegmentator==1.5.3) (2.1.2)
> Requirement already satisfied: mpmath\>=0.19 in c:\\users\\butlej30383\\appdata\\local\\na-mic\\slicer 5.2.2\\lib\\python\\lib\\site-packages (from sympy-\>torch\>=1.6.0a-\>nnunet-customized==1.2-\>TotalSegmentator==1.5.3) (1.3.0)
> Collecting linecache2
> Downloading linecache2-1.0.0-py2.py3-none-any.whl (12 kB)
> Building wheels for collected packages: TotalSegmentator, p\_tqdm, xvfbwrapper, future, medpy
> Building wheel for TotalSegmentator (setup.py): started
> Building wheel for TotalSegmentator (setup.py): finished with status 'done'
> Created wheel for TotalSegmentator: filename=TotalSegmentator-1.5.3-py3-none-any.whl size=40473 sha256=72631d27e92da70d44e97e4309a78d20e685ff9af743f96d7e69538a655f33f7
> Stored in directory: C:\\Users\\butlej30383\\AppData\\Local\\Temp\\pip-ephem-wheel-cache-98sqy9xm\\wheels\\9f\\4f\\c3\\aa92a6088ded23ae736534c7fd546ac5aec3409f87bbed6852
> Building wheel for p\_tqdm (setup.py): started
> Building wheel for p\_tqdm (setup.py): finished with status 'done'
> Created wheel for p\_tqdm: filename=p\_tqdm-1.4.0-py3-none-any.whl size=5411 sha256=fa28bb84f74c368e3ca9f728cac1ce3da2df3fb07f95dcf27cf8d23c317ab512
> Stored in directory: c:\\users\\butlej30383\\appdata\\local\\pip\\cache\\wheels\\53\\8b\\76\\19cce68cdb3253aee026a593ec9bc772607b85193cf65e1f53
> Building wheel for xvfbwrapper (setup.py): started
> Building wheel for xvfbwrapper (setup.py): finished with status 'done'
> Created wheel for xvfbwrapper: filename=xvfbwrapper-0.2.9-py3-none-any.whl size=5027 sha256=b15a6b7c25585d54d8fb6e75a0c52c862db0ca6335cbbb1f53a9fb4607d54d0d
> Stored in directory: c:\\users\\butlej30383\\appdata\\local\\pip\\cache\\wheels\\aa\\09\\0e\\c0fa4c721cfb0a003121597a24181add912b7488054d2311ad
> Building wheel for future (setup.py): started
> Building wheel for future (setup.py): finished with status 'done'
> Created wheel for future: filename=future-0.18.3-py3-none-any.whl size=492055 sha256=e5d845853ca1d4176cfadcbc5699dbe1277875648cb957ad91f9787813b5c77a
> Stored in directory: c:\\users\\butlej30383\\appdata\\local\\pip\\cache\\wheels\\bf\\5d\\6a\\2e53874f7ec4e2bede522385439531fafec8fafe005b5c3d1b
> Building wheel for medpy (setup.py): started
> Building wheel for medpy (setup.py): finished with status 'done'
> Created wheel for medpy: filename=MedPy-0.4.0-py3-none-any.whl size=215911 sha256=47f6a0c552cdc868104caf188bd34e85fbd5fd46a2882b6893bc782b1b948d8c
> Stored in directory: c:\\users\\butlej30383\\appdata\\local\\pip\\cache\\wheels\\41\\46\\a2\\7c585b78f216a3dd8723dbab5f439822fa5dfbff563757a49e
> Successfully built TotalSegmentator p\_tqdm xvfbwrapper future medpy
> Installing collected packages: xvfbwrapper, pytz, linecache2, argparse, traceback2, tifffile, threadpoolctl, scipy, PyWavelets, python-gdcm, psutil, ppft, pox, nibabel, lazy\_loader, joblib, imageio, future, dill, colorama, unittest2, tqdm, scikit-learn, scikit-image, pandas, multiprocess, medpy, fury, dicom2nifti, pathos, batchgenerators, p\_tqdm, nnunet-customized, TotalSegmentator
> WARNING: The scripts lsm2bin.exe, tiff2fsspec.exe, tiffcomment.exe and tifffile.exe are installed in 'C:\\Users\\butlej30383\\AppData\\Local\\NA-MIC\\Slicer 5.2.2\\lib\\Python\\Scripts' which is not on PATH.
> Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
> Attempting uninstall: scipy
> Found existing installation: scipy 1.9.2
> Uninstalling scipy-1.9.2:
> Successfully uninstalled scipy-1.9.2
> ERROR: Could not install packages due to an OSError: \[WinError 5\] Access is denied: 'C:\\\\Users\\\\butlej30383\\\\AppData\\\\Local\\\\NA-MIC\\\\Slicer 5.2.2\\\\lib\\\\Python\\\\Lib\\\\site-packages\\\\~cipy\\\\\_lib\\\\\_ccallback\_c.cp39-win\_amd64.pyd'
> Consider using the \`--user\` option or check the permissions.
> 
> 
> \[notice\] A new release of pip is available: 23.0 -\> 23.0.1
> \[notice\] To update, run: python-real.exe -m pip install --upgrade pip
> \[Python\] Failed to compute results.
> \[Python\] Command '\['C:/Users/butlej30383/AppData/Local/NA-MIC/Slicer 5.2.2/bin/../bin\\\\PythonSlicer.EXE', '-m', 'pip', 'install', 'https://github.com/wasserth/TotalSegmentator/archive/b38eb449ad8652a987878a925203cbfa354e9b85.zip'\]' returned non-zero exit status 1.
> Traceback (most recent call last):
> File "C:/GitHub/SlicerTotalSegmentator/TotalSegmentator/TotalSegmentator.py", line 255, in onApplyButton
> self.logic.setupPythonRequirements()
> File "C:/GitHub/SlicerTotalSegmentator/TotalSegmentator/TotalSegmentator.py", line 624, in setupPythonRequirements
> slicer.util.pip\_install(self.totalSegmentatorPythonPackageDownloadUrl)
> File "C:\\Users\\butlej30383\\AppData\\Local\\NA-MIC\\Slicer 5.2.2\\bin\\Python\\slicer\\util.py", line 3578, in pip\_install
> \_executePythonModule('pip', args)
> File "C:\\Users\\butlej30383\\AppData\\Local\\NA-MIC\\Slicer 5.2.2\\bin\\Python\\slicer\\util.py", line 3540, in \_executePythonModule
> logProcessOutput(proc)
> File "C:\\Users\\butlej30383\\AppData\\Local\\NA-MIC\\Slicer 5.2.2\\bin\\Python\\slicer\\util.py", line 3509, in logProcessOutput
> raise CalledProcessError(retcode, proc.args, output=proc.stdout, stderr=proc.stderr)
> subprocess.CalledProcessError: Command '\['C:/Users/butlej30383/AppData/Local/NA-MIC/Slicer 5.2.2/bin/../bin\\\\PythonSlicer.EXE', '-m', 'pip', 'install', 'https://github.com/wasserth/TotalSegmentator/archive/b38eb449ad8652a987878a925203cbfa354e9b85.zip'\]' returned non-zero exit status 1.
> \</details\>

---

<div class="post-metadata">

**Author:** ![drvarunagarwal](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/drvarunagarwal/32/8914_2.png) [@drvarunagarwal](https://discourse.slicer.org/u/drvarunagarwal)\
**Post date:** [December 17, 2023, 5:10pm UTC](https://discourse.slicer.org/t/error-running-totalsegmentator-returned-non-zero-exit-status-120/28587/3 "2023-12-17T17:10:44Z")

</div>

hi

I installed totalsegmentator and pytorch  
I loaded demo CT data

Getting the following error:

Command ‘[‘C:/Users/drvka/AppData/Local/slicer.org/Slicer 5.7.0-2023-12-11/bin/…/bin\PythonSlicer.EXE’, ‘C:\Users\drvka\AppData\Local\slicer.org\Slicer 5.7.0-2023-12-11\lib\Python\Scripts\TotalSegmentator.exe’, ‘-i’, ‘C:/Users/drvka/AppData/Local/Temp/Slicer/\_\_SlicerTemp\_\_2023-12-17\_22+28+40.501/total-segmentator-input.nii’, ‘-o’, ‘C:/Users/drvka/AppData/Local/Temp/Slicer/\_\_SlicerTemp\_\_2023-12-17\_22+28+40.501/segmentation’, ‘–ml’, ‘–task’, ‘total’, ‘–fast’]’ returned non-zero exit status 120.

ON CLICKING MORE DETAILS:

Traceback (most recent call last):  
File “C:\Users\drvka\AppData\Local\slicer.org\Slicer 5.7.0-2023-12-11\bin\Python\slicer\util.py”, line 3255, in tryWithErrorDisplay  
yield  
File “C:/Users/drvka/AppData/Local/slicer.org/Slicer 5.7.0-2023-12-11/slicer.org/Extensions-32642/TotalSegmentator/lib/Slicer-5.7/qt-scripted-modules/TotalSegmentator.py”, line 292, in onApplyButton  
self.logic.process(self.ui.inputVolumeSelector.currentNode(), self.ui.outputSegmentationSelector.currentNode(),  
File “C:/Users/drvka/AppData/Local/slicer.org/Slicer 5.7.0-2023-12-11/slicer.org/Extensions-32642/TotalSegmentator/lib/Slicer-5.7/qt-scripted-modules/TotalSegmentator.py”, line 967, in process  
self.logProcessOutput(proc)  
File “C:/Users/drvka/AppData/Local/slicer.org/Slicer 5.7.0-2023-12-11/slicer.org/Extensions-32642/TotalSegmentator/lib/Slicer-5.7/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/drvka/AppData/Local/slicer.org/Slicer 5.7.0-2023-12-11/bin/…/bin\PythonSlicer.EXE’, ‘C:\Users\drvka\AppData\Local\slicer.org\Slicer 5.7.0-2023-12-11\lib\Python\Scripts\TotalSegmentator.exe’, ‘-i’, ‘C:/Users/drvka/AppData/Local/Temp/Slicer/\_\_SlicerTemp\_\_2023-12-17\_22+28+40.501/total-segmentator-input.nii’, ‘-o’, ‘C:/Users/drvka/AppData/Local/Temp/Slicer/\_\_SlicerTemp\_\_2023-12-17\_22+28+40.501/segmentation’, ‘–ml’, ‘–task’, ‘total’, ‘–fast’]’ returned non-zero exit status 120.

---

<div class="post-metadata">

**Author:** ![drvarunagarwal](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/drvarunagarwal/32/8914_2.png) [@drvarunagarwal](https://discourse.slicer.org/u/drvarunagarwal)\
**Post date:** [December 17, 2023, 5:11pm UTC](https://discourse.slicer.org/t/error-running-totalsegmentator-returned-non-zero-exit-status-120/28587/4 "2023-12-17T17:11:33Z")

</div>

Processing started  
Writing input file to C:/Users/drvka/AppData/Local/Temp/Slicer/\_\_SlicerTemp\_\_2023-12-17\_22+28+40.501/total-segmentator-input.nii  
Creating segmentations with TotalSegmentator AI…  
Total Segmentator arguments: [‘-i’, ‘C:/Users/drvka/AppData/Local/Temp/Slicer/\_\_SlicerTemp\_\_2023-12-17\_22+28+40.501/total-segmentator-input.nii’, ‘-o’, ‘C:/Users/drvka/AppData/Local/Temp/Slicer/\_\_SlicerTemp\_\_2023-12-17\_22+28+40.501/segmentation’, ‘–ml’, ‘–task’, ‘total’, ‘–fast’]  
Traceback (most recent call last):  
File “C:\Users\drvka\AppData\Local\slicer.org\Slicer 5.7.0-2023-12-11\lib\Python\Lib\runpy.py”, line 197, in \_run\_module\_as\_main  
return _run\_code(code, main\_globals, None,  
File “C:\Users\drvka\AppData\Local\slicer.org\Slicer 5.7.0-2023-12-11\lib\Python\Lib\runpy.py”, line 87, in run\_code  
exec(code, run\_globals)  
File "C:\Users\drvka\AppData\Local\slicer.org\Slicer 5.7.0-2023-12-11\lib\Python\Scripts\TotalSegmentator.exe\_main.py", line 7, in   
File “C:\Users\drvka\AppData\Local\slicer.org\Slicer 5.7.0-2023-12-11\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\drvka\AppData\Local\slicer.org\Slicer 5.7.0-2023-12-11\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\drvka\AppData\Local\slicer.org\Slicer 5.7.0-2023-12-11\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\drvka\AppData\Local\slicer.org\Slicer 5.7.0-2023-12-11\lib\Python\Lib\site-packages\totalsegmentator\nnunet.py”, line 178, in nnUNetv2\_predict  
predict\_from\_raw\_data(dir\_in,  
File “C:\Users\drvka\AppData\Local\slicer.org\Slicer 5.7.0-2023-12-11\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\drvka\AppData\Local\slicer.org\Slicer 5.7.0-2023-12-11\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\drvka\AppData\Local\slicer.org\Slicer 5.7.0-2023-12-11\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\drvka\AppData\Local\slicer.org\Slicer 5.7.0-2023-12-11\lib\Python\Lib\importlib\_init_.py", line 127, in import\_module  
return \_bootstrap.\_gcd\_import(name[level:], package, level)  
File “”, line 1030, in \_gcd\_import  
File “”, line 1007, in \_find\_and\_load  
File “”, line 986, in \_find\_and\_load\_unlocked  
File “”, line 680, in \_load\_unlocked  
File “”, line 850, in exec\_module  
File “”, line 228, in \_call\_with\_frames\_removed  
File “C:\Users\drvka\AppData\Local\slicer.org\Slicer 5.7.0-2023-12-11\lib\Python\Lib\site-packages\nnunetv2\training\nnUNetTrainer\nnUNetTrainer.py”, line 43, in   
from nnunetv2.training.logging.nnunet\_logger import nnUNetLogger  
File “C:\Users\drvka\AppData\Local\slicer.org\Slicer 5.7.0-2023-12-11\lib\Python\Lib\site-packages\nnunetv2\training\logging\nnunet\_logger.py”, line 1, in   
import matplotlib  
ModuleNotFoundError: No module named ‘matplotlib’  
Exception ignored in: \<totalsegmentator.libs.DummyFile object at 0x000001C347AEC6A0\>  
AttributeError: ‘DummyFile’ object has no attribute ‘flush’

---

<div class="post-metadata">

**Author:** ![drvarunagarwal](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/drvarunagarwal/32/8914_2.png) [@drvarunagarwal](https://discourse.slicer.org/u/drvarunagarwal)\
**Post date:** [December 17, 2023, 5:12pm UTC](https://discourse.slicer.org/t/error-running-totalsegmentator-returned-non-zero-exit-status-120/28587/5 "2023-12-17T17:12:10Z")

</div>

please advise how to run totalsegmentator and solve the above issue

thanks

* * *

so I figured out

In the advanced option I forced reinstall python packages for total segmentor and it is working now

Leaving this here in case it helps others who might run into similar problems