fMRI foundation models increasingly aggregate heterogeneous data across brain states, cohorts, and acquisition settings, yet pretraining domains are commonly treated as a flat mixture and downstream tasks are adapted independently. We study whether measured learning relations can organize both stages without modifying the backbone. During pretraining, a lightweight Brain-DiT proxy estimates difficulty and directed facilitation across ten fMRI domains, yielding a priority-guided cumulative domain curriculum combined with high-to-low-noise timestep scheduling and joint consolidation. During adaptation, controlled first- and higher-order transfer across fifteen tasks constructs a directed taskonomy, from which budgeted integer programming (BIP) selects directly supervised source tasks and target-specific routes. The joint priority-domain and high-to-low-timestep curriculum reduces v-NMSE, PSD-NMSE, and FC-MSE by 6.5%, 16.3%, and 10.5%, respectively, relative to uniform sampling over both dimensions, and shows strong downstream performance across six in- and out-of-domain tasks. The taskonomy reveals asymmetric, target-dependent transfer, while exploratory sealed-test evaluation shows larger descriptive gains for BIP policies when higher-order route spaces are available than for matched random controls. Together, these findings support organizing fMRI pretraining and adaptation by measured learning relations rather than treating domains and tasks as independent flat sets.
Current fMRI foundation models primarily rely on a limited range of brain states and mismatched pretraining tasks, restricting their ability to learn generalized representations across diverse brain states. We present Brain-DiT, a universal multi-state fMRI foundation model pretrained on 349,898 sessions from 24 datasets spanning resting, task, naturalistic, disease, and sleep states. Unlike prior fMRI foundation models that rely on masked reconstruction in the raw-signal space or a latent space, Brain-DiT adopts metadata-conditioned diffusion pretraining with a Diffusion Transformer (DiT), enabling the model to learn multi-scale representations that capture both fine-grained functional structure and global semantics. Across extensive evaluations and ablations on 7 downstream tasks, we find consistent evidence that diffusion-based generative pretraining is a stronger proxy than reconstruction or alignment, with metadata-conditioned pretraining further improving downstream performance by disentangling intrinsic neural dynamics from population-level variability. We also observe that downstream tasks exhibit distinct preferences for representational scale: ADNI classification benefits more from global semantic representations, whereas age/sex prediction comparatively relies more on fine-grained local structure.
Cognitive tasks are organized by shared and specialized neural processes. Masked fMRI reconstruction provides a common self-supervised objective for quantifying transfer relations among task states, but existing reconstruction-based taskonomies mainly study one-to-one transfer from a single source task to a target. Here, we extend an fMRI cognitive taskonomy from single-source to multi-source transfer across 23 Human Connectome Project task states and use Boolean Integer Programming (BIP) to analyze budget-constrained task allocation. We train 1,127 task-specific and transfer models. Single-source transfer is directional and paradigm structured: motor states transfer well within the motor paradigm but provide limited support to most non-motor targets, consistent with a shared sensorimotor execution system and effector-specific representations. Multi-source transfer depends on the composition of the source set, suggesting that many-to-one task relations are not fully captured by pairwise taskonomy alone. Across supervision budgets, BIP repeatedly allocates direct supervision to several 0-back and 2-back working-memory states, although these states are not consistently the strongest individual sources. This pattern may reflect the integration of perceptual, attentional, and executive processes in working-memory tasks. Together, these findings reveal a cross-paradigm-limited motor cluster and working-memory states with high priority under the specified global allocation objective. Our study extends reconstruction-based fMRI taskonomy from one-to-one transfer to many-to-one task relations and budget-constrained task dependencies.
Brain foundation models (BFMs) are self-supervised Transformers pretrained on fMRI data. We posit that these models should capture each subject's cognitive performance from their fMRI signal. Yet across three state-of-the-art BFMs and every readout we test, they predict cognition worse than a linear regression from the ∼80K parameters of the functional connectivity matrix (FC). The gap widens with scale: BrainLM's 650M model predicts cognition worse than its 111M. We attribute this to a \textbf{variance allocation problem}: BFM pretraining captures the variance components that dominate fMRI but not the higher-order structure that predicts cognition. Our per-cumulant analysis of the reconstructed signal shows that the second-order covariance is partially preserved, while the third-order co-skewness tensor is largely destroyed. To recover what BFMs lose, we design a linear pipeline that projects the fMRI signal into the subspace that best preserves its co-skewness and computes FC there. This \textbf{exceeds raw FC and every pretrained BFM} on every dataset and parcellation we test, outperforming prior state-of-the-art under controlled evaluation \textbf{with no pretraining and no GPU}. We \textbf{recover the raw-FC ceiling on BrainLM's forward pass} by finetuning with a loss targeted at this same subspace. This shows that the bottleneck is the pretraining objective, not the architecture or the model size.
Giovanni Marraffini, Gabriel Mahuas, Trinidad Borrell +2