MAESTRO: A Public, Generalizable Model for Stroke Lesion Segmentation from T1 MRI Across the Recovery Continuum

Abstract

Accurate stroke lesion segmentation is essential for large-scale neuroimaging studies, yet manual delineation remains labor-intensive, and existing automated methods often struggle to generalize across imaging protocols and stages of recovery. We developed MAESTRO, a deep learning framework for automated lesion segmentation across the stroke recovery continuum using T1-weighted (T1) MRI alone. We hypothesized that combining a transformer-based architecture with an image augmentation strategy would improve segmentation accuracy and robustness under heterogeneous imaging conditions. T1 MRI scans and expert-traced lesion masks from 955 stroke participants across 33 international cohorts were used to train and evaluate MAESTRO within the open-source nnU-Net framework. Performance was evaluated on a held-out test set using spatial and volumetric agreement metrics. An exploratory human-in-the-loop (HITL) evaluation compared correction of MAESTRO-generated segmentations with manual tracing from scratch. MAESTRO achieved the strongest performance across several evaluated model configurations, providing the most accurate lesion localization and lesion volume estimates (median Dice = 0.686; Pearson r = 0.861; ICC = 0.792). Segmentation performance was sensitive to lesion size and stroke chronicity but remained robust across diverse imaging conditions. Additionally, using a HITL workflow to correct MAESTRO segmentations reduced annotation time by 47.4% compared to manual tracing while improving accuracy relative to both automated and manual workflows. MAESTRO is publicly available to enable robust, automated stroke lesion segmentation from T1 MRI. When combined with human review and correction, MAESTRO offers a practical approach for generating standardized, high-quality lesion annotations, helping reduce a major practical barrier to large-scale stroke imaging studies.