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bhklab / med-imagetools

Transparent and reproducible medical image processing pipelines in Python.

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Exporting multiple ROIs using regex in StructureSetToSegmentation

jmarsil opened this issue · comments

commented
  1. Could I pass a list of regexes here?
 self.make_binary_mask = StructureSetToSegmentation(roi_names="GTV-1")

If not it would be cool to assign a list of regexes to a standardized OAR name. Use the regex when the name is given in roi_names.

  1. If multiple structures are output, are the masks saved to different directories? Could we add a function to compress and save all masks in one file (useful for my OAR pipeline). Maybe a setting that combines all masks from ROI export and runs an argmax. Don't know if this already has been implemented in imgtools.
commented

@mkazmier can you add me as a contributor?