segcsvdWMH: A Convolutional Neural Network-Based Tool for Quantifying White Matter Hyperintensities in Heterogeneous Patient Cohorts

White matter hyperintensities (WMH) of presumed vascular origin are a magnetic resonance imaging (MRI)-based biomarker of cerebral small vessel disease (CSVD). WMH are associated with cognitive decline and increased risk of stroke and dementia, and are commonly observed in aging, vascular cognitive impairment, and neurodegenerative diseases. The reliable and rapid measurement of WMH in large-scale multisite clinical studies with heterogeneous patient populations remains challenging, where the diversity of imaging characteristics across studies adds additional complexity to this task. We present segcsvd_WMH, a convolutional neural network-based tool developed to provide reliable and accurate WMH quantification across diverse clinical datasets. segcsvd_WMH was developed using a large dataset consisting of over 700 fluid-attenuated inversion recovery MRI scans from seven multisite studies, spanning a wide range of clinical populations, WMH burdens, and imaging protocols. Model training incorporated anatomical information through a novel hierarchical segmentation approach, together with extensive data augmentation techniques to improve performance across varied imaging conditions. Benchmarked against three widely available segmentation tools, segcsvd_WMH demonstrated superior accuracy, achieving mean Dice score improvements of 7.8% ± 9.7% over HyperMapp3r, 21.8% ± 8.6% over SAMSEG, and 43.5% ± 7.1% over WMH-SynthSeg across four diverse test datasets. segcsvd_WMH also maintained consistently high Dice scores across these test datasets (mean DSC = 0.86 ± 0.08), and exhibited strong, stable correlations with periventricular, deep, and total WMH ground truth volumes (mean r = 0.99 ± 0.01). Additionally, segcsvd_WMH was robust to low and moderate levels of simulated MRI spike noise artifacts and maintained strong performance across a range of binary segmentation thresholds and WMH burden levels. These findings suggest that segcsvd_WMH may provide more accurate and robust WMH segmentation performance for heterogeneous clinical datasets characterized by varying degrees of CSVD severity.