piotrsobecki/PCa-radiomics-experiments

README

What is this repository for?

PCa classification optimisation experiments based on the radiomics features - simple models that base on the sklearn classifiers. See: https://www.researchgate.net/publication/317660491_MRI_imaging_texture_features_in_prostate_lesions_classification https://www.researchgate.net/publication/317721536_Feature_Extraction_Optimized_For_Prostate_Lesion_Classification

Python scripts with experiments base on the corresponding .json configuration files (see example for very brief documentation)

How do set up the project?

• Download ProstateX data
• Enforce correct directory structure

Directory structure

/{project.dir}/data/ProstateX/train/DOI

/{project.dir}/data/ProstateX/train/ktrans

/{project.dir}/data/ProstateX/train/lesion-information/

/{project.dir}/data/ProstateX/train/lesion-information/

/{project.dir}/data/ProstateX/train/lesion-information/ProstateX.csv (if absent generated automatically by Dataset) - a dataset file containing data merged from patients mhd files and meta-data files (csv)

/{project.dir}/data/ProstateX/train/lesion-information/ProstateX-DataInfo-Test.docx

/{project.dir}/data/ProstateX/train/lesion-information/ProstateX-Findings.csv

/{project.dir}/data/ProstateX/train/lesion-information/ProstateX-Images.csv

/{project.dir}/data/ProstateX/train/lesion-information/ProstateX-Images-KTrans.csv

/{project.dir}/data/ProstateX/train/screenshots (optional)