# Slicer v. 5.6.0. Radiomics-module error while extracting features?

**URL:** <https://discourse.slicer.org/t/slicer-v-5-6-0-radiomics-module-error-while-extracting-features/33280>\
**Category:** Support\
**Tags:** radiomics, pyradiomics\
**Created:** [December 7, 2023, 8:23am UTC](https://discourse.slicer.org/t/slicer-v-5-6-0-radiomics-module-error-while-extracting-features/33280 "2023-12-07T08:23:50Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![Magnus](https://avatars.discourse-cdn.com/v4/letter/m/e9c0ed/32.png) [@Magnus](https://discourse.slicer.org/u/Magnus)\
**Post date:** [December 7, 2023, 8:23am UTC](https://discourse.slicer.org/t/slicer-v-5-6-0-radiomics-module-error-while-extracting-features/33280/1 "2023-12-07T08:23:51Z")

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Hello,

Updated slicer to the latest version (5.6.0). Now I get an error while trying to extract radiomic features using the Radiomics module. See following error message. What can I do?

[2023-12-07 09:15:38] I: radiomics.script: Starting PyRadiomics (version: v3.1.0)  
[2023-12-07 09:15:38] I: radiomics.script: Processing input…  
[2023-12-07 09:15:38] E: radiomics.script: Error extracting features!  
Traceback (most recent call last):  
File “C:\Users\magnu\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\magnu\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\magnu\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\magnu\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\magnu\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\magnu\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']

```

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<div class="post-metadata">

**Author:** ![pieper](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pieper/32/8_2.png) [@pieper](https://discourse.slicer.org/u/pieper)\
**Post date:** [December 7, 2023, 12:25pm UTC](https://discourse.slicer.org/t/slicer-v-5-6-0-radiomics-module-error-while-extracting-features/33280/2 "2023-12-07T12:25:25Z")

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Thanks for reporting - the same issue is being tracked here with a proposed change. Maybe you could test the fix?

> <https://github.com/AIM-Harvard/pyradiomics/pull/857>
>
> I recently found the SlicerRadiomics extension does not work in 3D Slicer and be…low is the issue that I decribed in.
> https://github.com/AIM-Harvard/SlicerRadiomics/issues/80
> 
> I tried to modify the code with the help of @pieper :
> 1. Add the code below to the top of the file:
> \`from ruamel.yaml import YAML\`
> 2. Add the code below before line 353:
> \`yaml = YAML(typ='safe', pure=True) \`
> 3. Change what was in line 353 to:
> \`settingsSchema = yaml.load(schema)\['mapping'\]\['setting'\]\['mapping'\]\`

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<div class="post-metadata">

**Author:** ![Magnus](https://avatars.discourse-cdn.com/v4/letter/m/e9c0ed/32.png) [@Magnus](https://discourse.slicer.org/u/Magnus)\
**Post date:** [December 7, 2023, 1:08pm UTC](https://discourse.slicer.org/t/slicer-v-5-6-0-radiomics-module-error-while-extracting-features/33280/3 "2023-12-07T13:08:16Z")

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Thank you. Good to know it might not be my fault.

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<div class="post-metadata">

**Author:** ![Magnus](https://avatars.discourse-cdn.com/v4/letter/m/e9c0ed/32.png) [@Magnus](https://discourse.slicer.org/u/Magnus)\
**Post date:** [December 7, 2023, 1:41pm UTC](https://discourse.slicer.org/t/slicer-v-5-6-0-radiomics-module-error-while-extracting-features/33280/4 "2023-12-07T13:41:20Z")

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However, I will have to wait for a fix, since I can’t edit any sourcecode myself (if I understood the fix correctly).

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<div class="post-metadata">

**Author:** ![Magnus](https://avatars.discourse-cdn.com/v4/letter/m/e9c0ed/32.png) [@Magnus](https://discourse.slicer.org/u/Magnus)\
**Post date:** [December 7, 2023, 2:06pm UTC](https://discourse.slicer.org/t/slicer-v-5-6-0-radiomics-module-error-while-extracting-features/33280/5 "2023-12-07T14:06:16Z")

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I can extract the features when not specifying the binWidth or binCount in the settings, when running pyradiomics from the command-prompt. However it returns a lot of 0 or 1 indicating problems with the binWidth, but when I try to change the size or count of the bin, it returns the above mentioned error.

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<div class="post-metadata">

**Author:** ![pieper](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pieper/32/8_2.png) [@pieper](https://discourse.slicer.org/u/pieper)\
**Post date:** [December 7, 2023, 2:26pm UTC](https://discourse.slicer.org/t/slicer-v-5-6-0-radiomics-module-error-while-extracting-features/33280/6 "2023-12-07T14:26:05Z")

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If you aren’t able to apply/test the fix, you should be able to use older versions of Slicer and SlicerRadiomics.