Brain decoding aims to reconstruct visual perception of human subject from fMRI signals, which is crucial for understanding brain’s perception mechanisms. Existing methods are confined to the single-subject paradigm due to substantial brain variability, which leads to weak generalization across individuals and incurs high training costs, exacerbated by limited availability of fMRI data. To address these challenges, we propose MindAligner, an explicit functional alignment framework for cross-subject brain decoding from limited fMRI data. The proposed MindAligner enjoys several merits. First, we learn a Brain Transfer Matrix (BTM) that projects the brain signals of an arbitrary new subject to one of the known subjects, enabling seamless use of pre-trained decoding models. Second, to facilitate reliable BTM learning, a Brain Functional Alignment module is proposed to perform soft cross-subject brain alignment under different visual stimuli with a multi-level brain alignment loss, uncovering fine-grained functional correspondences with high interpretability. Experiments indicate that MindAligner not only outperforms existing methods in visual decoding under data-limited conditions, but also provides valuable neuroscience insights in cross-subject functional analysis. The code will be made publicly available.

Deciphering how visual stimuli are transformed into cortical responses is a fundamental challenge in computational neuroscience. This visual-to-neural mapping is inherently a one-to-many relationship, as identical visual inputs reliably evoke variable hemodynamic responses across trials, contexts, and subjects. However, existing deterministic methods struggle to simultaneously model this biological variability while capturing the underlying functional consistency that encodes stimulus information. To address these limitations, we propose SynBrain, a generative framework that simulates the transformation from visual semantics to neural responses in a probabilistic and biologically interpretable manner. SynBrain introduces two key components: (i) BrainVAE models neural representations as continuous probability distributions via probabilistic learning while maintaining functional consistency through visual semantic constraints; (ii) A Semantic-to-Neural Mapper acts as a semantic transmission pathway, projecting visual semantics into the neural response manifold to facilitate high-fidelity fMRI synthesis. Experimental results demonstrate that SynBrain surpasses state-of-the-art methods in subject-specific visual-to-fMRI encoding performance. Furthermore, SynBrain adapts efficiently to new subjects with few-shot data and synthesizes high-quality fMRI signals that are effective in improving data-limited fMRI-to-image decoding performance. Beyond that, SynBrain reveals functional consistency across trials and subjects, with synthesized signals capturing interpretable patterns shaped by biological neural variability. Our code is available at https://github.com/MichaelMaiii/SynBrain.

Understanding and decoding human brain activity from electroencephalography (EEG) signals is a fundamental problem in neuroscience and artificial intelligence, with applications ranging from cognition and emotion recognition to clinical diagnosis and brain–computer interfaces. While recent EEG foundation models have made progress in generalized brain decoding by leveraging unified architectures and large-scale pretraining, they inherit a scale-agnostic dense modeling paradigm from NLP and vision. This design overlooks an intrinsic property of neural activity—cross-scale spatiotemporal structure. Different EEG task patterns span a broad range of temporal and spatial scales, from brief neural activations to slow-varying rhythms, and from localized cortical activations to large-scale distributed interactions. Ignoring this diversity may lead to suboptimal representations and weakened generalization ability. To address these limitations, we propose CSBrain, a Cross-scale Spatiotemporal Brain foundation model for generalized EEG decoding. CSBrain introduces two key components: (i) Cross-scale Spatiotemporal Tokenization (CST), which aggregates multi-scale features within localized temporal windows and anatomical brain regions into compact scale-aware token representations; and (ii) Structured Sparse Attention (SSA), which models cross-window and cross-region dependencies for diverse decoding tasks, further enriching scale diversities while eliminating the spurious dependencies. CST and SSA are alternately stacked to progressively integrate cross-scale spatiotemporal dependencies. Extensive experiments across 11 representative EEG tasks and 16 datasets demonstrate that CSBrain consistently outperforms both task-specific models and strong foundation baselines. These results establish cross-scale modeling as a key inductive bias for generalized EEG decoding and highlight CSBrain as a robust backbone for future brain–AI research.