BrainSignsNET: Deep Learning-Based 3D Anatomical Landmark Detection in Human Brain Imaging

Accurate detection of anatomical landmarks in brain Magnetic Resonance Imaging (MRI) scans is essential for reliable spatial normalization, image alignment, and quantitative neuroimaging analyses. In this study, we introduce BrainSignsNET, a deep learning framework designed for robust three-dimensional (3D) landmark detection. Our approach leverages a multi-task 3D convolutional neural network that integrates an attention decoder branch with a multi-class decoder branch to generate precise 3D heatmaps, from which landmark coordinates are extracted. The model was trained and internally validated on T1-weighted Magnetization-Prepared Rapid Gradient-Echo (MPRAGE) scans from the Alzheimer’s Disease Neuroimaging Initiative (ADNI), the Baltimore Longitudinal Study of Aging (BLSA), and the Biomarkers of Cognitive Decline in Adults at Risk for AD (BIOCARD) datasets and externally validated on a clinical dataset from the Johns Hopkins Hydrocephalus Clinic. The study encompassed 14,472 scans from 6,299 participants, representing a diverse demographic profile with a significant proportion of older adult participants, particularly those over 70 years of age. Extensive preprocessing and data augmentation strategies, including traditional MRI corrections and tailored 3D transformations, ensured data consistency and improved model generalizability. Performance metrics demonstrated that on internal validation BrainSignsNET achieved an overall mean Euclidean distance of 2.32 ± 0.41 mm and 94.8% of landmarks localized within their anatomically defined 3D volumes in the external validation dataset. This improvement in accurate anatomical landmark detection on brain MRI scans should benefit many imaging tasks, including registration, alignment, and quantitative analyses.