Decoding Radiomics: A Step-by-Step Guide to Machine Learning Workflow in Hand-Crafted and Deep Learning Radiomics Studies

Maurizio Cè, Marius Dumitru Chiriac, Andrea Cozzi, Laura Macrì, Francesca Lucrezia Rabaiotti, Giovanni Irmici, Deborah Fazzini, Gianpaolo Carrafiello, Michaela Cellina

Although radiomics research has experienced rapid growth in recent years, with numerous studies dedicated to the automated extraction of diagnostic and prognostic information from various imaging modalities, such as CT, PET, and MRI, only a small fraction of these findings has successfully transitioned into clinical practice. This gap is primarily due to the significant methodological challenges involved in radiomics research, which emphasize the need for a rigorous evaluation of study quality. While many technical aspects may lie outside the expertise of most radiologists, having a foundational knowledge is essential for evaluating the quality of radiomics workflows and contributing, together with data scientists, to the development of models with a real-world clinical impact. This review is designed for the new generation of radiologists, who may not have specialized training in machine learning or radiomics, but will inevitably play a role in this evolving field. The paper has two primary objectives: first, to provide a clear, systematic guide to radiomics study pipeline, including study design, image preprocessing, feature selection, model training and validation, and performance evaluation. Furthermore, given the critical importance of evaluating the robustness of radiomics studies, this review offers a step-by-step guide to the application of the METhodological RadiomICs Score (METRICS, 2024)—a newly proposed tool for assessing the quality of radiomics studies. This roadmap aims to support researchers and reviewers alike, regardless of their machine learning expertise, in utilizing this tool for effective study evaluation.