MedNet-PVS: A MedNeXt-Based Deep Learning Model for Automated Segmentation of Perivascular Spaces

Zhen Xuen Brandon Low; Rory Zhang; Hang Min; William Pham; Lucy Vivash; Jasmine Moses; Miranda Lynch; Karina Dorfman; Cassandra Marotta; Shaun Koh; Jacob Bunyamin; Ella Rowsthorn; Alex Jarema; Himashi Peiris; Zhaolin Chen; Sandy R. Shultz; David K. Wright; Dexiao Kong; Sharon L. Naismith; Terence J. O'Brien; Ying Xia; Meng Law; Benjamin Sinclair

arXiv · 2508.20256

MedNet-PVS: A MedNeXt-Based Deep Learning Model for Automated Segmentation of Perivascular Spaces

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Abstract

Enlarged perivascular spaces (PVS) are increasingly recognized as biomarkers of cerebral small vessel disease, Alzheimer's disease, stroke, and aging-related neurodegeneration. However, manual segmentation of PVS is time-consuming and subject to moderate inter-rater reliability, while existing automated deep learning models have moderate performance and typically fail to generalize across diverse clinical and research MRI datasets. We adapted MedNeXt-L-k5, a Transformer-inspired 3D encoder-decoder convolutional network, for automated PVS segmentation. Two models were trained: one using a homogeneous dataset of 200 T2-weighted (T2w) MRI scans from the Human Connectome Project-Aging (HCP-Aging) dataset and another using 40 heterogeneous T1-weighted (T1w) MRI volumes from seven studies across six scanners. Model performance was evaluated using internal 5-fold cross validation (5FCV) and leave-one-site-out cross validation (LOSOCV). MedNeXt-L-k5 models trained on the T2w images of the HCP-Aging dataset achieved voxel-level Dice scores of 0.88+/-0.06 (white matter, WM), comparable to the reported inter-rater reliability of that dataset, and the highest yet reported in the literature. The same models trained on the T1w images of the HCP-Aging dataset achieved a substantially lower Dice score of 0.58+/-0.09 (WM). Under LOSOCV, the model had voxel-level Dice scores of 0.38+/-0.16 (WM) and 0.35+/-0.12 (BG), and cluster-level Dice scores of 0.61+/-0.19 (WM) and 0.62+/-0.21 (BG). MedNeXt-L-k5 provides an efficient solution for automated PVS segmentation across diverse T1w and T2w MRI datasets. MedNeXt-L-k5 did not outperform the nnU-Net, indicating that the attention-based mechanisms present in transformer-inspired models to provide global context are not required for high accuracy in PVS segmentation.

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Zhen Xuen Brandon Low, Rory Zhang, Hang Min, William Pham, Lucy Vivash, Jasmine Moses, Miranda Lynch, Karina Dorfman, Cassandra Marotta, Shaun Koh, Jacob Bunyamin, Ella Rowsthorn, Alex Jarema, Himashi Peiris, Zhaolin Chen, Sandy R. Shultz, David K. Wright, Dexiao Kong, Sharon L. Naismith, Terence J. O'Brien, Ying Xia, Meng Law, Benjamin Sinclair. 2025-08-27. MedNet-PVS: A MedNeXt-Based Deep Learning Model for Automated Segmentation of Perivascular Spaces. https://arxiv.org/abs/2508.20256

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