CrossPan: A Comprehensive Benchmark for Cross-Sequence Pancreas MRI Segmentation and Generalization

TL;DR

CrossPan introduces a large benchmark dataset revealing that current models struggle with cross-sequence MRI segmentation, highlighting the need for better generalization methods.

Contribution

The paper provides the first systematic analysis of cross-sequence domain shifts in pancreas MRI segmentation and evaluates the effectiveness of existing generalization techniques.

Findings

Cross-sequence domain shifts cause models to fail dramatically.

Foundation models like MedSAM2 offer moderate zero-shot performance.

Semi-supervised learning is unstable on variable sequences.

Abstract

Automatic pancreas segmentation is fundamental to abdominal MRI analysis, yet deep learning models trained on one MRI sequence often fail catastrophically when applied to another-a challenge that has received little systematic investigation. We introduce CrossPan, a multi-institutional benchmark comprising 1,386 3D scans across three routinely acquired sequences (T1-weighted, T2-weighted, and Out-of-Phase) from eight centers. Our experiments reveal three key findings. First, cross-sequence domain shifts are far more severe than cross-center variability: models achieving Dice scores above 0.85 in-domain collapse to near-zero (<0.02) when transferred across sequences. Second, state-of-the-art domain generalization methods provide negligible benefit under these physics-driven contrast inversions, whereas foundation models like MedSAM2 maintain moderate zero-shot performance through contrast-invariant shape priors. Third, semi-supervised learning offers gains only under stable intensity distributions and becomes unstable on sequences with high intra-organ variability. These results establish cross-sequence generalization-not model architecture or center diversity-as the primary barrier to clinically deployable pancreas MRI segmentation. Dataset and code are available at https://crosspan.netlify.app/.