Deep Learning-Based Assessment of Brainstem Volume Changes in Spinocerebellar Ataxia Type 2 (SCA2): A Study on Patients and Preclinical Subjects

Spinocerebellar ataxia type 2 (SCA2) is a neurodegenerative disorder marked by progressive brainstem and cerebellar atrophy, leading to gait ataxia. Quantifying this atrophy in magnetic resonance imaging (MRI) is critical for tracking disease progression in both symptomatic patients and preclinical subjects. However, manual segmentation of brainstem subregions (mesencephalon, pons, and medulla) is time-consuming and prone to human error. This work presents an automated deep learning framework to assess brainstem atrophy in SCA2. Using T1-weighted MRI scans from patients, preclinical carriers, and healthy controls, a U-shaped convolutional neural network (CNN) was trained to segment brainstem subregions and quantify volume loss. The model achieved strong agreement with manual segmentations, significantly outperforming four U-Net-based benchmarks (mean Dice scores: whole brainstem 0.96 vs. 0.93–0.95, pons 0.96 vs. 0.91–0.94, mesencephalon 0.96 vs. 0.89–0.93, and medulla 0.95 vs. 0.91–0.93). Results revealed severe atrophy in preclinical and symptomatic cohorts, with pons volumes reduced by nearly 50% compared to controls (p < 0.001). The mesencephalon and medulla showed milder degeneration, underscoring regional vulnerability differences. This automated approach enables rapid, precise assessment of brainstem atrophy, advancing early diagnosis and monitoring in SCA2.