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medRxiv PreprintsInternational12 November 2026

A Multi-Cohort nnU-Net for White Matter Hyperintensity Segmentation Across 2D and 3D FLAIR Acquisitions

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Background White matter hyperintensities (WMH) are increasingly pooled across aging, cerebral small vessel disease (CSVD), and dementia cohorts that differ in both disease composition and FLAIR acquisition. Most automated segmentation tools were developed within a narrower range of populations or protocols, and few have been tested for whether segmentation accuracy and error remain consistent across conventional 2D and isotropic 3D FLAIR, or whether the choice of algorithm alters downstream clinical associations. Methods We developed a single nnU-Net model, taking FLAIR and T1-weighted images
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