Accurate and generalisable segmentation of stroke lesions from magnetic resonance imaging (MRI) is essential for advancing clinical research, prognostic modelling, and personalised interventions. Although deep learning has improved automated lesion delineation, many existing models are optimised for narrow imaging contexts and generalise poorly to independent datasets, modalities, and stroke stages. Here, we systematically evaluated stroke lesion segmentation using the nnU-Net framework across multiple heterogeneous, publicly available MRI datasets spanning acute and chronic stroke. Models were trained and tested on diffusion-weighted imaging (DWI), fluid-attenuated inversion recovery (FLAIR), and T1-weighted MRI, and evaluated on independent datasets. Across stroke stages, models showed robust generalisation, with segmentation accuracy approaching reported inter-rater reliability. Performance varied with imaging modality and training data characteristics. In acute stroke, DWI-trained models consistently outperformed FLAIR-based models, with only modest gains from multimodal combinations. In chronic stroke, increasing training set size improved performance, with diminishing returns beyond several hundred cases. Lesion volume was a key determinant of accuracy: smaller lesions were harder to segment, and models trained on restricted volume ranges generalised poorly. MRI image quality further constrained generalisability: models trained on lower-quality scans transferred poorly, whereas those trained on higher-quality data generalised well to noisier images. Discrepancies between predictions and reference masks were often attributable to limitations in manual annotations. Together, these findings show that automated lesion segmentation can approach human-level performance while identifying key factors governing generalisability and informing the development of lesion segmentation tools.
Large networks and ensembles often lead medical image segmentation challenges, but their storage and inference demands complicate deployment. We present LightMedSeg-ISLES, a 1.26-million-parameter pipeline for T1-weighted stroke lesion segmentation in ISLES'26. On a 146-case held-out cohort, flip test-time augmentation produces 0.618 mean Dice and 0.599 lesion-wise F1. A 102.35-million-parameter nnU-Net ResEnc-L produces 0.634 Dice and 0.544 lesion-wise F1 after size filtering. LightMedSeg therefore retains 97.5% of nnU-Net's Dice with 81.4× fewer parameters while improving lesion-wise F1 by 0.055. Its four-pass TTA operating point requires 4.7× fewer FLOPs per standardized patch than nnU-Net. It also slightly exceeds filtered UNETR++ and nnFormer. Longer training and stronger augmentation add 0.0358 Dice without increasing capacity, establishing a strong single-checkpoint alternative to much larger models.
Giorgi Nikvashvili, Hanxue Gu, Jie Bao +2
University of California, Berkeley, Berkeley, CA, USA · University of California, San Francisco, San Francisco, CA, USA
When the blood supply to the brain is obstructed by a clot, oxygen delivery to brain tissues becomes insufficient, leading to cellular necrosis. In healthcare settings, accurately identifying and delineating ischemic lesion boundaries is essential for treatment and surgical planning. However, ischemic stroke lesions vary widely in shape, size, and location, and in grayscale MRI modalities such as T1W they may resemble surrounding brain structures. This makes lesion detection and segmentation a challenging task for clinicians. This study introduces a novel VRU-Net architecture, derived from visual features, residual connections, and a U-shaped network, for detecting and segmenting ischemic stroke lesions in 3D magnetic resonance imaging scans. The proposed method first uses a modified VGG model to identify ischemic stroke in separate 2D slices. Then, a U-shaped segmentation model with residual blocks segments the lesion in each slice. This procedure is applied independently to the axial, sagittal, and coronal planes, and the final output is generated by aggregating the three segmentation results. To improve both performance and processing speed, a high-performance classifier is applied before the segmentation model in a sequential framework. This strategy reduces unnecessary segmentation of non-lesion slices and improves overall accuracy. In addition, decomposing 3D images into 2D slices reduces model complexity while allowing information from three anatomical planes to support more accurate lesion localization. The proposed model is trained on the Anatomical Tracings of Lesions After Stroke dataset and outperforms state-of-the-art models in terms of accuracy and Dice coefficient. Moreover, the segmentation output provides feedback that helps the classification model reduce false-positive predictions.
Objectives: Quantitative assessment of infarct hypodensity on non-contrast computed tomography (NCCT), including net water uptake (NWU), requires manual or semi-manual lesion delineation, often guided by CT perfusion or diffusion-weighted MRI, limiting clinical applicability. Automated segmentation on NCCT could enable efficient biomarker extraction such as NWU but remains challenging across heterogeneous multicenter data. This study aimed to develop and externally test a domain-aware deep learning framework for ischemic stroke segmentation on NCCT and assess its suitability for NWU quantification. Materials & Methods: In this retrospective multicenter study of 801 patients from four datasets, an nnU-Net-based model was trained on NCCT scans from the University Medical Center Hamburg-Eppendorf and the Acute Ischemic Stroke Dataset. To adapt to new domains, the model was fine-tuned on target-domain subsets from Boston (n=11) and ISLES (n=75), with evaluation on held-out cases not used for fine-tuning. Automated segmentations and NWU values were compared with expert references. Results: For lesions ≥ 30 mL, median Dice was 0.68 (Boston) and 0.56 (ISLES). Including smaller lesions, which predominated in ISLES, median Dice was 0.54 (interquartile range [IQR] 0.30-0.70) for acute lesion segmentation (Boston dataset) and 0.20 (IQR 0.03-0.41) for NCCT lesion segmentations when compared to post-treatment infarct (primary target of the ISLES challenge). Automated NWU mean absolute error was 1.37 percentage points (SD 1.61, Boston). Conclusion: Target-domain adaptation supported NCCT-only infarct segmentation across heterogeneous external cohorts, although performance varied across domains. The approach enabled low-error NWU quantification from baseline NCCT without advanced imaging, supporting further prospective clinical evaluation.
Linus Britt, Maximilian Nielsen, Susan Klapproth +5
Institute for Applied Medical Informatics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany · Institute of Computational Neuroscience, University Medical Center Hamburg-Eppendorf, Hamburg, Germany · Department of Diagnostic and Interventional Neuroradiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany +4