JoostJM
commented
4 years ago @kevin-why,
currently, this is not possible if you use PyRadiomics on the command-line. However, in interactive Python it'll be quite easy:
import SimpleITK as sitk
from radiomics import featureextractor
ma = sitk.ReadImage(r'path/to/mask.nrrd')
ma_arr = sitk.GetArrrayFromImage(ma)
for l in (2, 3, 4):
ma_arr[ma_arr == l] = 1
ma_merged = sitk.GetImageFromArray(ma_arr)
ma_merged.CopyInformation(ma) # geometric information
extractor = featureextractor.RadiomicsFeatureExtractor(r'path/to/params.yaml')
features = extractor.execute(r'path/to/image.nrrd', ma_merged, label=1) # You can pass in a SimpleITK.Image object directly for image and/or mask
# Features will be a dict with featurename:feature value
Describe the bug When I use the pyradiomics，I wonder how to merge several labels into one label.(There are 4 labels in my test image, I need to extract the features of them as a whole)
PyRadiomics configuration I used the 【Params.yaml】download from here, I tried to modify the label number in the file. 【label:1→label：1,2.3.4】but unfortunately it doesn't work.
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