Moving Beyond Functional Connectivity: Time-Series Modeling for fMRI-Based Brain Disorder Classification

Functional magnetic resonance imaging (fMRI) enables non-invasive brain disorder classification by capturing blood-oxygen-level-dependent (BOLD) signals. However, most existing methods rely on functional connectivity (FC) via Pearson correlation, which reduces 4D BOLD signals to static 2D matrices-discarding temporal dynamics and capturing only linear inter-regional relationships. In this work, we benchmark state-of-the-art temporal models (e.g., time-series models: PatchTST, TimesNet, TimeMixer) on raw BOLD signals across five public datasets. Results show these models consistently outperform traditional FC-based approaches, highlighting the value of directly modeling temporal information such as cycle-like oscillatory fluctuations and drift-like slow baseline trends. Building on this insight, we propose DeCI, a simple yet effective framework that integrates two key principles: (i) Cycle and Drift Decomposition to disentangle cycle and drift within each ROI (Region of Interest); and (ii) Channel-Independence to model each ROI separately, improving robustness and reducing overfitting. Extensive experiments demonstrate that DeCI achieves superior classification accuracy and generalization compared to both FC-based and temporal baselines. Our findings advocate for a shift toward end-to-end temporal modeling in fMRI analysis to better capture complex brain dynamics. The code is available at https://github.com/Levi-Ackman/DeCI.