search

AIM-Harvard / pyradiomics

Open-source python package for the extraction of Radiomics features from 2D and 3D images and binary masks. Support: https://discourse.slicer.org/c/community/radiomics
http://pyradiomics.readthedocs.io/
BSD 3-Clause "New" or "Revised" License
1.14k stars 493 forks source link

How can i get wavelet images when using parameter file to extract features? #551

Closed yuwon-shin closed 4 years ago

yuwon-shin commented 4 years ago

HI,

I'm extracting features from MRI images(nii.gz). Could you please tell me how can I show only the wavelet-LLL images.

Here's my codes.

extractor = featureextractor.RadiomicsFeatureExtractor(paramsFile)

for case_id in patient_id : image = sitk.ReadImage(path + case_id+"/"+"T2.nii.gz") label = sitk.ReadImage(path + case_id+"/"+"T2_v4.nii.gz") features[case_id] = extractor.execute(image,label)

Thanks!

fedorov commented 4 years ago

Did you look at this function: https://github.com/Radiomics/pyradiomics/blob/master/radiomics/imageoperations.py#L772?

yuwon-shin commented 4 years ago

Hi Fedorov,

Yes i’v seen that function! But i don’t know exactly how to use that function when collectively extract features by parameter file. Some other image setting like Resampling/ normalize are contained in the file, so that function is not work at same condition, simply. Can you tell me how?

Many Thanks.

JoostJM commented 4 years ago

@yuwon-shin, check out the section on the parameter file (under customizing the extraction). There you can find details on how the paramter file is build. Bascially, you have 3 sections: Setting, ImageType and FeatureClass. These respectively customize the settings (e.g. resampling/normalization), the filters to apply to the image (e.g. Wavelet) and which features to extract (e.g. GLCM).