Integrated 3D Modeling and Functional Simulation of the Human Amygdala: A Novel Anatomical and Computational Analyses

The amygdala plays a central role in emotion, memory, and decision-making and comprises approximately 13 distinct nuclei with connectivity. Despite its functional importance, high-resolution subnuclear mapping is challenging. This study aimed to construct a 3D model of the anatomical location of the amygdala in the brain and a functional dynamic model of the amygdala, integrating deep learning and elastic shape metrics. We used multimodal datasets from the Julich-Brain Atlas, BigBrain Project, and FreeSurfer, which were aligned with the Montreal Neurological Institute (MNI) and Colin 27 spaces. Subnuclei segmentation was performed using a Bayesian Fully Convolutional Network (FCN), and geometric morphometrics were analyzed using elastic shape analysis on the unit sphere. Functional dynamics were simulated using a MATLAB-based model of the amygdala incorporating theta (4-8 Hz) and gamma (30-40 Hz) oscillations with spike-timing-dependent plasticity (STDP). The mean MNI coordinates of the left and right amygdalae were (-20, -4, -15) and (22, -2, -15), respectively, with an inter-amygdalar distance of 42.48 mm. The Dice Similarity Coefficients (DSCs) for FCN-based subnuclear segmentation were as follows: basolateral amygdala (BLA) nucleus = 0.89 ± 0.03, centromedial nucleus = 0.83 ± 0.04, and cortical nucleus = 0.81 ± 0.05. Principal component analysis of elastic shape metrics revealed post-traumatic stress disorder (PTSD)-related morphological deviations, with the first principal component (PC1) accounting for 38% of the variance (p < 0.01). Oscillatory simulations captured the BLA rhythm dynamics and STDP-induced synaptic changes. This study presents a comprehensive 3D model of the human amygdala that bridges anatomical accuracy with computational modeling. Unlike prior models that focus solely on structural or functional domains, our approach integrates subnuclear segmentation, morphometrics, and real-time functional simulation. This study introduces a fully integrated anatomical-functional 3D model of the human amygdala, providing a translational platform for neuromodulation targeting, psychiatric diagnostics, and computational neuroengineering applications.