Large-scale multi-sequence pretraining for generalizable MRI analysis in versatile clinical applications

Multi-sequence magnetic resonance imaging (MRI) is essential for clinical diagnosis because it enables comprehensive characterization of complex anatomy. However, its substantial heterogeneity limits the generalizability of deep learning models and hinders clinical translation. Here we present MARS, a large-scale MRI foundation model with a novel pretraining strategy that disentangles anatomy-invariant features from sequence-specific variations to learn robust and generalizable representations for diverse clinical applications. We collected 64 datasets spanning 10 anatomical structures and multiple MRI sequences. Among these, 336,476 volumetric scans from 34 datasets (8 public and 26 private) were curated to build a large multi-organ, multi-sequence MRI pretraining corpus. We further established a benchmark of 44 downstream tasks covering diagnosis, segmentation, registration, progression prediction and report generation. MARS ranked first in 41 of 44 benchmarks, with statistically significant improvements. Its strong performance on heterogeneous and external datasets underscores MARS as a scalable foundation for versatile real-world multi-sequence MRI analysis.