MUSA: A Multimodal MRI-Based Major Depressive Disorder Classification Model with a Unified ROI Semantic Space

Major depressive disorder (MDD) is a common disabling psychiatric disorder mainly diagnosed through clinical interviews and rating-scale assessments. Magnetic resonance imaging (MRI) provides a promising basis for computer-aided MDD identification, particularly through multimodal models that can integrate structural and functional brain information. However, existing multimodal MRI fusion models often use data-level fusion or post hoc feature concatenation, potentially overlooking differences in spatial resolution, voxel organization, and region of interest (ROI)-level semantic correspondence. To address this issue, this study proposes MUSA, a unified ROI semantic space model for multimodal MRI-based MDD classification. An Automated Anatomical Labeling (AAL) atlas-guided ROI semantic space establishes consistent brain-region correspondence across heterogeneous MRI features. An ROI-level 3D Vision Transformer (3D ViT) encodes ROI voxel information into fixed-dimensional representations, allowing structural, local functional, and connectivity information to be organized and integrated within a consistent brain-region semantic space. Experiments on 2380 participants from REST-meta-MDD validated MUSA for MDD and normal controls (NCs) classification. The feature combination of white matter (WM), functional connectivity (FC), regional homogeneity (ReHo), and degree centrality (DC) achieved 79.20% ± 0.65% accuracy and an AUC of 87.08% ± 0.51%. Brain-region importance analysis identified classifier-derived discriminative patterns across frontoparietal, sensorimotor, visual, temporal, and limbic-related regions.