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

Magnetic resonance imaging (MRI) has 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 is grounded in the central hypothesis that site-related biases can be eliminated or mitigated 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, and evaluation metrics in the field of MRI harmonization. We systematically cover the full imaging pipeline and categorize harmonization approaches into prospective acquisition and reconstruction, retrospective image-level and feature-level methods, and traveling-subject-based techniques. By synthesizing existing methods and evidence, we revisit the central hypothesis of image harmonization and show that, although site invariance can be achieved with current techniques, further evaluation is required to verify the preservation of biological information. To this end, we summarize the remaining challenges and highlight key directions for future research, including the need for standardized validation benchmarks, improved evaluation strategies, and tighter integration of harmonization methods across the imaging pipeline.