# Erors regarding segmentation

**URL:** <https://discourse.slicer.org/t/erors-regarding-segmentation/33089>\
**Category:** Support\
**Tags:** segmentation\
**Created:** [November 28, 2023, 3:17pm UTC](https://discourse.slicer.org/t/erors-regarding-segmentation/33089 "2023-11-28T15:17:52Z")\
**Posts on this page:** 1\
**Page:** 1

<div class="post-metadata">

**Author:** ![segmentator](https://avatars.discourse-cdn.com/v4/letter/s/ad7895/32.png) [@segmentator](https://discourse.slicer.org/u/segmentator)\
**Post date:** [November 28, 2023, 3:17pm UTC](https://discourse.slicer.org/t/erors-regarding-segmentation/33089/1 "2023-11-28T15:17:52Z")

</div>

Hello,

My PC does the segmantation in about 75 seconds, but then I get multiple errors during extraction of features. Also, this error doesn’t happen in another PC that I tried.

Here is the log:

```auto
Requirement already satisfied: pillow<10.1 in c:\users\ali doruk\appdata\local\slicer.org\slicer 5.6.0\lib\python\lib\site-packages (10.0.1)
WARNING: There was an error checking the latest version of pip.
C:/Users/Ali Doruk/AppData/Local/slicer.org/Slicer 5.6.0/slicer.org/Extensions-32390/TotalSegmentator/lib/Slicer-5.6/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
.......[VTK] RadiomicsCLI standard error:
[VTK] [2023-11-28 10:45:04] I: radiomics.script: Starting PyRadiomics (version: v3.1.0)
[VTK] [2023-11-28 10:45:04] I: radiomics.script: Processing input...
[VTK] [2023-11-28 10:45:04] E: radiomics.script: Error extracting features!
[VTK] Traceback (most recent call last):
[VTK] File "C:\Users\Ali Doruk\AppData\Local\slicer.org\Slicer 5.6.0\slicer.org\Extensions-32390\SlicerRadiomics\Lib\site-packages\radiomics\scripts\ __init__.py", line 135, in run
[VTK] results = self._processCases(caseGenerator)
[VTK] File "C:\Users\Ali Doruk\AppData\Local\slicer.org\Slicer 5.6.0\slicer.org\Extensions-32390\SlicerRadiomics\Lib\site-packages\radiomics\scripts\ __init__.py", line 233, in _processCases
[VTK] setting_overrides = self._parseOverrides()
[VTK] File "C:\Users\Ali Doruk\AppData\Local\slicer.org\Slicer 5.6.0\slicer.org\Extensions-32390\SlicerRadiomics\Lib\site-packages\radiomics\scripts\ __init__.py", line 353, in _parseOverrides
[VTK] settingsSchema = yaml.safe_load(schema)['mapping']['setting']['mapping']
[VTK] File "C:\Users\Ali Doruk\AppData\Local\slicer.org\Slicer 5.6.0\slicer.org\Extensions-32390\SlicerRadiomics\Lib\site-packages\ruamel\yaml\main.py", line 1105, in safe_load
[VTK] error_deprecation('safe_load', 'load', arg="typ='safe', pure=True")
[VTK] File "C:\Users\Ali Doruk\AppData\Local\slicer.org\Slicer 5.6.0\slicer.org\Extensions-32390\SlicerRadiomics\Lib\site-packages\ruamel\yaml\main.py", line 1037, in error_deprecation
[VTK] raise AttributeError(s)
[VTK] AttributeError: 
[VTK] "safe_load()" has been removed, use
[VTK] 
[VTK] yaml = YAML(typ='safe', pure=True)
[VTK] yaml.load(...)
[VTK] 
[VTK] instead of file "C:\Users\Ali Doruk\AppData\Local\slicer.org\Slicer 5.6.0\slicer.org\Extensions-32390\SlicerRadiomics\Lib\site-packages\radiomics\scripts\ __init__.py", line 353
[VTK] 
[VTK] settingsSchema = yaml.safe_load(schema)['mapping']['setting']['mapping']
[VTK] 
[VTK] 
.Done
[2023-11-28 10:45:04] I: radiomics.script: Starting PyRadiomics (version: v3.1.0)
[2023-11-28 10:45:04] I: radiomics.script: Processing input...
[2023-11-28 10:45:04] E: radiomics.script: Error extracting features!
Traceback (most recent call last):
  File "C:\Users\Ali Doruk\AppData\Local\slicer.org\Slicer 5.6.0\slicer.org\Extensions-32390\SlicerRadiomics\Lib\site-packages\radiomics\scripts\ __init__.py", line 135, in run
    results = self._processCases(caseGenerator)
  File "C:\Users\Ali Doruk\AppData\Local\slicer.org\Slicer 5.6.0\slicer.org\Extensions-32390\SlicerRadiomics\Lib\site-packages\radiomics\scripts\ __init__.py", line 233, in _processCases
    setting_overrides = self._parseOverrides()
  File "C:\Users\Ali Doruk\AppData\Local\slicer.org\Slicer 5.6.0\slicer.org\Extensions-32390\SlicerRadiomics\Lib\site-packages\radiomics\scripts\ __init__.py", line 353, in _parseOverrides
    settingsSchema = yaml.safe_load(schema)['mapping']['setting']['mapping']
  File "C:\Users\Ali Doruk\AppData\Local\slicer.org\Slicer 5.6.0\slicer.org\Extensions-32390\SlicerRadiomics\Lib\site-packages\ruamel\yaml\main.py", line 1105, in safe_load
    error_deprecation('safe_load', 'load', arg="typ='safe', pure=True")
  File "C:\Users\Ali Doruk\AppData\Local\slicer.org\Slicer 5.6.0\slicer.org\Extensions-32390\SlicerRadiomics\Lib\site-packages\ruamel\yaml\main.py", line 1037, in error_deprecation
    raise AttributeError(s)
AttributeError: 
"safe_load()" has been removed, use

  yaml = YAML(typ='safe', pure=True)
  yaml.load(...)

instead of file "C:\Users\Ali Doruk\AppData\Local\slicer.org\Slicer 5.6.0\slicer.org\Extensions-32390\SlicerRadiomics\Lib\site-packages\radiomics\scripts\ __init__.py", line 353

      settingsSchema = yaml.safe_load(schema)['mapping']['setting']['mapping']

..[VTK] RadiomicsCLI standard error:
[VTK] [2023-11-28 10:45:07] I: radiomics.script: Starting PyRadiomics (version: v3.1.0)
[VTK] [2023-11-28 10:45:07] I: radiomics.script: Processing input...
[VTK] [2023-11-28 10:45:07] E: radiomics.script: Error extracting features!
[VTK] Traceback (most recent call last):
[VTK] File "C:\Users\Ali Doruk\AppData\Local\slicer.org\Slicer 5.6.0\slicer.org\Extensions-32390\SlicerRadiomics\Lib\site-packages\radiomics\scripts\ __init__.py", line 135, in run
[VTK] results = self._processCases(caseGenerator)
[VTK] File "C:\Users\Ali Doruk\AppData\Local\slicer.org\Slicer 5.6.0\slicer.org\Extensions-32390\SlicerRadiomics\Lib\site-packages\radiomics\scripts\ __init__.py", line 233, in _processCases
[VTK] setting_overrides = self._parseOverrides()
[VTK] File "C:\Users\Ali Doruk\AppData\Local\slicer.org\Slicer 5.6.0\slicer.org\Extensions-32390\SlicerRadiomics\Lib\site-packages\radiomics\scripts\ __init__.py", line 353, in _parseOverrides
[VTK] settingsSchema = yaml.safe_load(schema)['mapping']['setting']['mapping']
[VTK] File "C:\Users\Ali Doruk\AppData\Local\slicer.org\Slicer 5.6.0\slicer.org\Extensions-32390\SlicerRadiomics\Lib\site-packages\ruamel\yaml\main.py", line 1105, in safe_load
[VTK] error_deprecation('safe_load', 'load', arg="typ='safe', pure=True")
[VTK] File "C:\Users\Ali Doruk\AppData\Local\slicer.org\Slicer 5.6.0\slicer.org\Extensions-32390\SlicerRadiomics\Lib\site-packages\ruamel\yaml\main.py", line 1037, in error_deprecation
[VTK] raise AttributeError(s)
[VTK] AttributeError: 
[VTK] "safe_load()" has been removed, use
[VTK] 
[VTK] yaml = YAML(typ='safe', pure=True)
[VTK] yaml.load(...)
[VTK] 
[VTK] instead of file "C:\Users\Ali Doruk\AppData\Local\slicer.org\Slicer 5.6.0\slicer.org\Extensions-32390\SlicerRadiomics\Lib\site-packages\radiomics\scripts\ __init__.py", line 353
[VTK] 
[VTK] settingsSchema = yaml.safe_load(schema)['mapping']['setting']['mapping']
[VTK] 
[VTK] 
..Done
[2023-11-28 10:45:07] I: radiomics.script: Starting PyRadiomics (version: v3.1.0)
[2023-11-28 10:45:07] I: radiomics.script: Processing input...
[2023-11-28 10:45:07] E: radiomics.script: Error extracting features!
Traceback (most recent call last):
  File "C:\Users\Ali Doruk\AppData\Local\slicer.org\Slicer 5.6.0\slicer.org\Extensions-32390\SlicerRadiomics\Lib\site-packages\radiomics\scripts\ __init__.py", line 135, in run
    results = self._processCases(caseGenerator)
  File "C:\Users\Ali Doruk\AppData\Local\slicer.org\Slicer 5.6.0\slicer.org\Extensions-32390\SlicerRadiomics\Lib\site-packages\radiomics\scripts\ __init__.py", line 233, in _processCases
    setting_overrides = self._parseOverrides()
  File "C:\Users\Ali Doruk\AppData\Local\slicer.org\Slicer 5.6.0\slicer.org\Extensions-32390\SlicerRadiomics\Lib\site-packages\radiomics\scripts\ __init__.py", line 353, in _parseOverrides
    settingsSchema = yaml.safe_load(schema)['mapping']['setting']['mapping']
  File "C:\Users\Ali Doruk\AppData\Local\slicer.org\Slicer 5.6.0\slicer.org\Extensions-32390\SlicerRadiomics\Lib\site-packages\ruamel\yaml\main.py", line 1105, in safe_load
    error_deprecation('safe_load', 'load', arg="typ='safe', pure=True")
  File "C:\Users\Ali Doruk\AppData\Local\slicer.org\Slicer 5.6.0\slicer.org\Extensions-32390\SlicerRadiomics\Lib\site-packages\ruamel\yaml\main.py", line 1037, in error_deprecation
    raise AttributeError(s)
AttributeError: 
"safe_load()" has been removed, use

  yaml = YAML(typ='safe', pure=True)
  yaml.load(...)

instead of file "C:\Users\Ali Doruk\AppData\Local\slicer.org\Slicer 5.6.0\slicer.org\Extensions-32390\SlicerRadiomics\Lib\site-packages\radiomics\scripts\ __init__.py", line 353

      settingsSchema = yaml.safe_load(schema)['mapping']['setting']['mapping']

..[VTK] RadiomicsCLI standard error:
[VTK] [2023-11-28 10:45:10] I: radiomics.script: Starting PyRadiomics (version: v3.1.0)
[VTK] [2023-11-28 10:45:10] I: radiomics.script: Processing input...
[VTK] [2023-11-28 10:45:10] E: radiomics.script: Error extracting features!
[VTK] Traceback (most recent call last):
[VTK] File "C:\Users\Ali Doruk\AppData\Local\slicer.org\Slicer 5.6.0\slicer.org\Extensions-32390\SlicerRadiomics\Lib\site-packages\radiomics\scripts\ __init__.py", line 135, in run
[VTK] results = self._processCases(caseGenerator)
[VTK] File "C:\Users\Ali Doruk\AppData\Local\slicer.org\Slicer 5.6.0\slicer.org\Extensions-32390\SlicerRadiomics\Lib\site-packages\radiomics\scripts\ __init__.py", line 233, in _processCases
[VTK] setting_overrides = self._parseOverrides()
[VTK] File "C:\Users\Ali Doruk\AppData\Local\slicer.org\Slicer 5.6.0\slicer.org\Extensions-32390\SlicerRadiomics\Lib\site-packages\radiomics\scripts\ __init__.py", line 353, in _parseOverrides
[VTK] settingsSchema = yaml.safe_load(schema)['mapping']['setting']['mapping']
[VTK] File "C:\Users\Ali Doruk\AppData\Local\slicer.org\Slicer 5.6.0\slicer.org\Extensions-32390\SlicerRadiomics\Lib\site-packages\ruamel\yaml\main.py", line 1105, in safe_load
[VTK] error_deprecation('safe_load', 'load', arg="typ='safe', pure=True")
[VTK] File "C:\Users\Ali Doruk\AppData\Local\slicer.org\Slicer 5.6.0\slicer.org\Extensions-32390\SlicerRadiomics\Lib\site-packages\ruamel\yaml\main.py", line 1037, in error_deprecation
[VTK] raise AttributeError(s)
[VTK] AttributeError: 
[VTK] "safe_load()" has been removed, use
[VTK] 
[VTK] yaml = YAML(typ='safe', pure=True)
[VTK] yaml.load(...)
[VTK] 
[VTK] instead of file "C:\Users\Ali Doruk\AppData\Local\slicer.org\Slicer 5.6.0\slicer.org\Extensions-32390\SlicerRadiomics\Lib\site-packages\radiomics\scripts\ __init__.py", line 353
[VTK] 
[VTK] settingsSchema = yaml.safe_load(schema)['mapping']['setting']['mapping']
[VTK] 
[VTK] 
.Done
[2023-11-28 10:45:10] I: radiomics.script: Starting PyRadiomics (version: v3.1.0)
[2023-11-28 10:45:10] I: radiomics.script: Processing input...
[2023-11-28 10:45:10] E: radiomics.script: Error extracting features!
Traceback (most recent call last):
  File "C:\Users\Ali Doruk\AppData\Local\slicer.org\Slicer 5.6.0\slicer.org\Extensions-32390\SlicerRadiomics\Lib\site-packages\radiomics\scripts\ __init__.py", line 135, in run
    results = self._processCases(caseGenerator)
  File "C:\Users\Ali Doruk\AppData\Local\slicer.org\Slicer 5.6.0\slicer.org\Extensions-32390\SlicerRadiomics\Lib\site-packages\radiomics\scripts\ __init__.py", line 233, in _processCases
    setting_overrides = self._parseOverrides()
  File "C:\Users\Ali Doruk\AppData\Local\slicer.org\Slicer 5.6.0\slicer.org\Extensions-32390\SlicerRadiomics\Lib\site-packages\radiomics\scripts\ __init__.py", line 353, in _parseOverrides
    settingsSchema = yaml.safe_load(schema)['mapping']['setting']['mapping']
  File "C:\Users\Ali Doruk\AppData\Local\slicer.org\Slicer 5.6.0\slicer.org\Extensions-32390\SlicerRadiomics\Lib\site-packages\ruamel\yaml\main.py", line 1105, in safe_load
    error_deprecation('safe_load', 'load', arg="typ='safe', pure=True")
  File "C:\Users\Ali Doruk\AppData\Local\slicer.org\Slicer 5.6.0\slicer.org\Extensions-32390\SlicerRadiomics\Lib\site-packages\ruamel\yaml\main.py", line 1037, in error_deprecation
    raise AttributeError(s)
AttributeError: 
"safe_load()" has been removed, use

  yaml = YAML(typ='safe', pure=True)
  yaml.load(...)

instead of file "C:\Users\Ali Doruk\AppData\Local\slicer.org\Slicer 5.6.0\slicer.org\Extensions-32390\SlicerRadiomics\Lib\site-packages\radiomics\scripts\ __init__.py", line 353

      settingsSchema = yaml.safe_load(schema)['mapping']['setting']['mapping']

..[VTK] RadiomicsCLI standard error:
[VTK] [2023-11-28 10:45:12] I: radiomics.script: Starting PyRadiomics (version: v3.1.0)
[VTK] [2023-11-28 10:45:12] I: radiomics.script: Processing input...
[VTK] [2023-11-28 10:45:12] E: radiomics.script: Error extracting features!
[VTK] Traceback (most recent call last):
[VTK] File "C:\Users\Ali Doruk\AppData\Local\slicer.org\Slicer 5.6.0\slicer.org\Extensions-32390\SlicerRadiomics\Lib\site-packages\radiomics\scripts\ __init__.py", line 135, in run
[VTK] results = self._processCases(caseGenerator)
[VTK] File "C:\Users\Ali Doruk\AppData\Local\slicer.org\Slicer 5.6.0\slicer.org\Extensions-32390\SlicerRadiomics\Lib\site-packages\radiomics\scripts\ __init__.py", line 233, in _processCases
[VTK] setting_overrides = self._parseOverrides()
[VTK] File "C:\Users\Ali Doruk\AppData\Local\slicer.org\Slicer 5.6.0\slicer.org\Extensions-32390\SlicerRadiomics\Lib\site-packages\radiomics\scripts\ __init__.py", line 353, in _parseOverrides
[VTK] settingsSchema = yaml.safe_load(schema)['mapping']['setting']['mapping']
[VTK] File "C:\Users\Ali Doruk\AppData\Local\slicer.org\Slicer 5.6.0\slicer.org\Extensions-32390\SlicerRadiomics\Lib\site-packages\ruamel\yaml\main.py", line 1105, in safe_load
[VTK] error_deprecation('safe_load', 'load', arg="typ='safe', pure=True")
[VTK] File "C:\Users\Ali Doruk\AppData\Local\slicer.org\Slicer 5.6.0\slicer.org\Extensions-32390\SlicerRadiomics\Lib\site-packages\ruamel\yaml\main.py", line 1037, in error_deprecation
[VTK] raise AttributeError(s)
[VTK] AttributeError: 
[VTK] "safe_load()" has been removed, use
[VTK] 
[VTK] yaml = YAML(typ='safe', pure=True)
[VTK] yaml.load(...)
[VTK] 
[VTK] instead of file "C:\Users\Ali Doruk\AppData\Local\slicer.org\Slicer 5.6.0\slicer.org\Extensions-32390\SlicerRadiomics\Lib\site-packages\radiomics\scripts\ __init__.py", line 353
[VTK] 
[VTK] settingsSchema = yaml.safe_load(schema)['mapping']['setting']['mapping']
[VTK] 
[VTK] 
..Done
[2023-11-28 10:45:12] I: radiomics.script: Starting PyRadiomics (version: v3.1.0)
[2023-11-28 10:45:12] I: radiomics.script: Processing input...
[2023-11-28 10:45:12] E: radiomics.script: Error extracting features!
Traceback (most recent call last):
  File "C:\Users\Ali Doruk\AppData\Local\slicer.org\Slicer 5.6.0\slicer.org\Extensions-32390\SlicerRadiomics\Lib\site-packages\radiomics\scripts\ __init__.py", line 135, in run
    results = self._processCases(caseGenerator)
  File "C:\Users\Ali Doruk\AppData\Local\slicer.org\Slicer 5.6.0\slicer.org\Extensions-32390\SlicerRadiomics\Lib\site-packages\radiomics\scripts\ __init__.py", line 233, in _processCases
    setting_overrides = self._parseOverrides()
  File "C:\Users\Ali Doruk\AppData\Local\slicer.org\Slicer 5.6.0\slicer.org\Extensions-32390\SlicerRadiomics\Lib\site-packages\radiomics\scripts\ __init__.py", line 353, in _parseOverrides
    settingsSchema = yaml.safe_load(schema)['mapping']['setting']['mapping']
  File "C:\Users\Ali Doruk\AppData\Local\slicer.org\Slicer 5.6.0\slicer.org\Extensions-32390\SlicerRadiomics\Lib\site-packages\ruamel\yaml\main.py", line 1105, in safe_load
    error_deprecation('safe_load', 'load', arg="typ='safe', pure=True")
  File "C:\Users\Ali Doruk\AppData\Local\slicer.org\Slicer 5.6.0\slicer.org\Extensions-32390\SlicerRadiomics\Lib\site-packages\ruamel\yaml\main.py", line 1037, in error_deprecation
    raise AttributeError(s)
AttributeError: 
"safe_load()" has been removed, use

  yaml = YAML(typ='safe', pure=True)
  yaml.load(...)

instead of file "C:\Users\Ali Doruk\AppData\Local\slicer.org\Slicer 5.6.0\slicer.org\Extensions-32390\SlicerRadiomics\Lib\site-packages\radiomics\scripts\ __init__.py", line 353

      settingsSchema = yaml.safe_load(schema)['mapping']['setting']['mapping']

```