A pretrained foundation model for headache disorders based on magnetoencephalography

Abstract Objective: Foundation models have demonstrated transformative potential in medical AI but remain underexplored in functional neuroimaging, particularly magnetoencephalography (MEG). This study aims to develop a domain-specific, self-supervised MEG clinical foundation model tailored for headache disorders to address the challenges of high-dimensional data and limited labeled datasets in clinical research. Approach: We developed a transformer-based model pretrained on a large-scale dataset comprising multi-state MEG recordings (resting-state, auditory, and somatosensory stimulation) from 416 participants (362 headache patients and 54 healthy controls). The model utilized a self-supervised masked-signal reconstruction strategy to learn latent spatiotemporal representations of neural activity. We evaluated the model’s performance through signal reconstruction, visualization of attention weights, and downstream classification tasks comparing model-derived features against original MEG signals for migraine diagnosis. Main results: The pretrained model successfully reconstructed both continuous MEG signals and stimulus-specific evoked responses, effectively capturing intrinsic spatiotemporal brain dynamics. Visualization of the model’s attention weights demonstrated spatial alignment with corresponding sensory brain regions, confirming its neurophysiological interpretability. Furthermore, classifiers trained on features extracted from the pretrained model significantly outperformed those using original MEG signals in identifying migraine patients, revealing distinct neural response patterns. Significance: This study introduces a scalable, data-efficient framework for clinical MEG analysis that significantly reduces reliance on manual feature extraction and labeled data. It demonstrates the efficacy of foundation models in decoding complex neural dynamics, offering promising implications for understanding neuropathology and facilitating precision diagnostics in neurology.