# Problem with TotalSegmentator

**URL:** <https://discourse.slicer.org/t/problem-with-totalsegmentator/36418>\
**Category:** Support\
**Created:** [May 27, 2024, 1:25pm UTC](https://discourse.slicer.org/t/problem-with-totalsegmentator/36418 "2024-05-27T13:25:17Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![vieimar](https://avatars.discourse-cdn.com/v4/letter/v/ee7513/32.png) [@vieimar](https://discourse.slicer.org/u/vieimar)\
**Post date:** [May 27, 2024, 1:25pm UTC](https://discourse.slicer.org/t/problem-with-totalsegmentator/36418/1 "2024-05-27T13:25:17Z")

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I am trying to use TotalSegmentator but I have a problem : “Traceback (most recent call last):  
File “C:\Users\maria\AppData\Local\slicer.org\Slicer 5.6.2\bin\Python\slicer\util.py”, line 3255, in tryWithErrorDisplay  
yield  
File “C:/Users/maria/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/maria/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/maria/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/maria/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/maria/AppData/Local/slicer.org/Slicer 5.6.2/bin/…/bin\PythonSlicer.EXE’, ‘C:\Users\maria\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Scripts\TotalSegmentator.exe’, ‘-i’, ‘C:/Users/maria/AppData/Local/slicer.org/Slicer 5.6.2/\_\_SlicerTemp\_\_2024-05-27\_15+18+36.694/total-segmentator-input.nii’, ‘-o’, ‘C:/Users/maria/AppData/Local/slicer.org/Slicer 5.6.2/\_\_SlicerTemp\_\_2024-05-27\_15+18+36.694/segmentation’, ‘–ml’, ‘–task’, ‘total’, ‘–fast’]’ returned non-zero exit status 1.” I don’t undersantand where the problem comes from ? Thank you for your help.

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**Author:** ![Matteboo](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/matteboo/32/66548_2.png) [@Matteboo](https://discourse.slicer.org/u/Matteboo)\
**Post date:** [May 27, 2024, 1:37pm UTC](https://discourse.slicer.org/t/problem-with-totalsegmentator/36418/2 "2024-05-27T13:37:30Z")

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Hello,  
Could you give us the error message in this box please. It’s a more pertinent error message

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/e/c/ecd3278f326e0f5a17f9fedcd247bb1842503d73.jpeg)

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**Author:** ![vieimar](https://avatars.discourse-cdn.com/v4/letter/v/ee7513/32.png) [@vieimar](https://discourse.slicer.org/u/vieimar)\
**Post date:** [May 27, 2024, 1:45pm UTC](https://discourse.slicer.org/t/problem-with-totalsegmentator/36418/3 "2024-05-27T13:45:52Z")

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Yes: here is my problem : Processing started  
Writing input file to C:/Users/maria/AppData/Local/slicer.org/Slicer 5.6.2/\_\_SlicerTemp\_\_2024-05-27\_15+33+06.139/total-segmentator-input.nii  
Creating segmentations with TotalSegmentator AI…  
Total Segmentator arguments: [‘-i’, ‘C:/Users/maria/AppData/Local/slicer.org/Slicer 5.6.2/\_\_SlicerTemp\_\_2024-05-27\_15+33+06.139/total-segmentator-input.nii’, ‘-o’, ‘C:/Users/maria/AppData/Local/slicer.org/Slicer 5.6.2/\_\_SlicerTemp\_\_2024-05-27\_15+33+06.139/segmentation’, ‘–ml’, ‘–task’, ‘total’]  
Traceback (most recent call last):  
File “C:\Users\maria\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\maria\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\maria\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Scripts\TotalSegmentator.exe\_main.py", line 4, in   
File “C:\Users\maria\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\totalsegmentator\bin\TotalSegmentator.py”, line 8, in   
from totalsegmentator.python\_api import totalsegmentator  
File “C:\Users\maria\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\totalsegmentator\python\_api.py”, line 11, in   
from totalsegmentator.statistics import get\_basic\_statistics, get\_radiomics\_features\_for\_entire\_dir  
File “C:\Users\maria\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\totalsegmentator\statistics.py”, line 8, in   
import pandas as pd  
File "C:\Users\maria\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\pandas\_init_.py", line 77, in   
from pandas.core.api import (  
File “C:\Users\maria\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\pandas\core\api.py”, line 1, in   
from pandas._libs import (  
File "C:\Users\maria\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\pandas\_libs\_init_.py", line 16, in   
import pandas.\_libs.pandas\_parser # isort: skip # type: ignore[reportUnusedImport]  
ModuleNotFoundError: No module named ‘pandas.\_libs.pandas\_parser’

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<div class="post-metadata">

**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [June 19, 2024, 1:50pm UTC](https://discourse.slicer.org/t/problem-with-totalsegmentator/36418/4 "2024-06-19T13:50:04Z")

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It seems that some required Python libraries were not installed correctly (or an incompatible version was installed by some other extensions). “Force reinstall” in “Advanced” section in TotalSegmentator module should fix the issue. If not then you may need to install Slicer from scratch again.