Ontology-guided Radiomics Analysis Workflow (O-RAW)
Radiomics is high-throughput automated tumour feature extraction from medical images. This has shown potential for quantifying tumour phenotype and predicting treatment response. The three major challenges of radiomics research and clinical adoption are:
We propose an open-source Ontology-guided Radiomics Analysis Workflow (O-RAW) to address the above challenges in the following manner: (i) distributing a free and open-source software package for radiomics analysis, (ii) deploying a standard lexicon to uniquely describe features in common usage and (iii) provide methods to publish radiomic features as a semantically-interoperable data graph object complying to FAIR (Findable Accessible Interoperable Reusable) data principles.
If you publish any work which uses this package, please cite the following publication:
Shi, Zhenwei, Alberto Traverso, Johan van Soest, Andre Dekker, and Leonard Wee. “Ontology‐guided Radiomics Analysis Workflow (O‐RAW).” Medical Physics (2019). https://aapm.onlinelibrary.wiley.com/doi/pdf/10.1002/mp.13844
O-RAW is still under development. Although we have tested and evaluated the workflow under many different situations, errors and bugs still happen unfortunately. Please use it cautiously. If you find any, please contact us and we would fix them ASAP.
O-RAW is dependent on several tools and packages that are listed below.
python -m pip install -r pyrex_requirements.txt
under command line to install the required packages. We provide a test dataset in ./data
. This dataset has a series of CT, PET & MRI scans with RTSTRUCT. The configuration file for test “./pyradiomics-master/Py-rex-master/ParamsSettings/Pyradiomics_Params.yaml”
Execute:
python ./HelloORAW.py
Or try ./Notebook/O-RAW-notebook.ipynb
Results in ./RFstore
O-RAW may not be used for commercial purposes. This package is freely available to browse, download, and use for scientific
and educational purposes as outlined in the Creative Commons Attribution 3.0 Unported License.
1Department of Radiation Oncology (MAASTRO Clinic), GROW-School for Oncology and Development Biology, Maastricht University Medical Centre, The Netherlands.