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.
Scaling laws have guided large-model development in computer vision and natural language processing, but the relationships among data, model size, and compute remain unclear for functional magnetic resonance imaging (fMRI) foundation models. Here, we conduct a controlled empirical study using pretraining data from more than 200 source datasets and over 10,000 GPU-hours of experiments. Holding the pretraining framework and downstream protocol fixed, we vary pretraining data size, model size, and training duration. Downstream performance generally improves with compute, yet models using similar compute can perform substantially differently. Additional pretraining data bring larger gains at larger model sizes, suggesting that data and model size should be scaled together. At matched compute, increasing pretraining data benefits more tasks than increasing model size, although the pattern varies across tasks. We then use in-distribution (ID) downstream performance to select the combination of pretraining data size, model size, and training duration at two fixed compute budgets. The resulting models are locked before out-of-distribution (OOD) evaluation. They achieve the highest average performance across the evaluated OOD tasks among the compared fMRI foundation models while using less pretraining compute. Overall, our results show that compute alone does not characterize fMRI scaling: performance depends on how pretraining data, model size, and training duration are combined.