Harmonization in Magnetic Resonance Imaging: A Survey of Acquisition, Image-level, and Feature-level Methods

Modern medical imaging technologies have greatly advanced neuroscience research and clinical diagnostics. However, imaging data collected across different scanners, acquisition protocols, or imaging sites often exhibit substantial heterogeneity, known as "batch effects" or "site effects". These non-biological sources of variability can obscure true biological signals, reduce reproducibility and statistical power, and severely impair the generalizability of learning-based models across datasets. Image harmonization aims to eliminate or mitigate such site-related biases while preserving meaningful biological information, thereby improving data comparability and consistency. This review provides a comprehensive overview of key concepts, methodological advances, publicly available datasets, current challenges, and future directions in the field of medical image harmonization, with a focus on magnetic resonance imaging (MRI). We systematically cover the full imaging pipeline, and categorize harmonization approaches into prospective acquisition and reconstruction strategies, retrospective image-level and feature-level methods, and traveling-subject-based techniques. Rather than providing an exhaustive survey, we focus on representative methods, with particular emphasis on deep learning-based approaches. Finally, we summarize the major challenges that remain and outline promising avenues for future research.