radiomics problem

mhs · March 10, 2024, 1:52pm

why i use radiomics to image feature extraction but no data

pieper · March 10, 2024, 4:37pm

You should check the error log. It’s possible you need to update to the latest. You might be seeing this issue:

github.com/AIM-Harvard/SlicerRadiomics

Error extracting features

opened 04:52PM - 03 Dec 23 UTC

closed 04:12AM - 09 Jan 24 UTC

DanXieJY

Hi, I've been trying to use the newly updated SlicerRadiomics package to extract… radiomics features, but the error below prompted every time I clicked apply. There were only table titles in the tables. At first I thought it was due to the setting of my machine. But after I tried 3 different machines, including win and linux, the same thing happened. I've tried Slicer 5.3-5.6, and even manually changed the py files but nothing worked. Hope someone could help me fix this problem. Thanks!! [2023-12-04 00:42:47] I: radiomics.script: Processing input... [2023-12-04 00:42:47] E: radiomics.script: Error extracting features! Traceback (most recent call last): File "/home/ubuntu/Slicer-5.6.0-linux-amd64/slicer.org/Extensions-32390/SlicerRadiomics/lib/python3.9/site-packages/radiomics/scripts/__init__.py", line 135, in run results = self._processCases(caseGenerator) File "/home/ubuntu/Slicer-5.6.0-linux-amd64/slicer.org/Extensions-32390/SlicerRadiomics/lib/python3.9/site-packages/radiomics/scripts/__init__.py", line 233, in _processCases setting_overrides = self._parseOverrides() File "/home/ubuntu/Slicer-5.6.0-linux-amd64/slicer.org/Extensions-32390/SlicerRadiomics/lib/python3.9/site-packages/radiomics/scripts/__init__.py", line 353, in _parseOverrides settingsSchema = yaml.safe_load(schema)['mapping']['setting']['mapping'] File "/home/ubuntu/Slicer-5.6.0-linux-amd64/slicer.org/Extensions-32390/SlicerRadiomics/lib/python3.9/site-packages/ruamel/yaml/main.py", line 1105, in safe_load error_deprecation('safe_load', 'load', arg="typ='safe', pure=True") File "/home/ubuntu/Slicer-5.6.0-linux-amd64/slicer.org/Extensions-32390/SlicerRadiomics/lib/python3.9/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 "/home/ubuntu/Slicer-5.6.0-linux-amd64/slicer.org/Extensions-32390/SlicerRadiomics/lib/python3.9/site-packages/radiomics/scripts/__init__.py", line 353 settingsSchema = yaml.safe_load(schema)['mapping']['setting']['mapping']

mhs · March 11, 2024, 3:16am

how do i update to the latest version

pieper · March 11, 2024, 11:56am

You can get the latest preview release as described here:

https://slicer.readthedocs.io/en/latest/user_guide/getting_started.html

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