fMRI Encoding Models

Increasingly complex neural models predict blood-oxygen-level-dependent (BOLD) responses to naturalistic stimuli, but the predictive value of this added complexity remains unclear. We ask when pretrained stimulus representations help and how much downstream complexity is needed, with and without recent measured BOLD history. We compare linear diagnostic references and nonlinear predictors across HCP movie fMRI (154 subjects), BOLD Moments (10 subjects), and Algonauts 2025 (4 subjects). Under a shared offline protocol, models are fitted on training subjects and evaluated on held-out subjects viewing largely familiar stimuli, without refitting. Pretrained visual features generally improve prediction over raw pixels; for linear autoregression, this advantage becomes more pronounced over longer rollouts (recursive predictions without additional measured BOLD). Measured BOLD history provides substantial gains that generally diminish {as rollouts lengthen}. Nonlinear stimulus-only predictors can improve on linear readouts, whereas linear autoregression provides a strong history-conditioned baseline. Controls examine context length, regularization, fitting procedures, and model capacity. Regional response consistency across subjects is associated with held-out prediction accuracy, while less consistent regions tend to gain more from measured history. In paired simulations with fixed linear neural dynamics, slower hemodynamic responses generally sustain high temporal prediction correlations over longer rollouts, illustrating how the observation process can contribute to predictive persistence. Together, these findings support evaluating stimulus representations and downstream complexity separately, using history-conditioned linear prediction as a diagnostic reference under matched inputs and measurement availability.

Encoding models that predict brain activation responses to images have traditionally been trained to maximize accuracy when predicting observed brain data. However, their internal representations may not reflect individual human perception. In this work, we investigate whether we can fine-tune brain encoding models to better align their representations with individuals' similarity judgments. Using similarity judgments of 100 images from 8 participants in the Natural Scenes Dataset (NSD), we adapt a generic human similarity judgment model (DreamSim) separately for each participant to obtain personalized perceptual similarity models. These models are then used to obtain subject-specific similarity structure across images in their encoding model training sets. We fine-tune each participant's baseline encoder in two conditions, aligning its representations with either generic or personalized similarity judgments, with the same initialization and objective. We find that baseline brain encoders reflect within-subject perceptual similarity more strongly than measured fMRI responses and preserve intersubject correlations present in measured fMRI, but fail to reflect those of human perceptual similarity judgments. Fine-tuning with generic, population-level perceptual similarity information results in better alignment with human judgments than baseline encoders, but these models still fail to capture intersubject correlations of human judgments. However, fine-tuning with personalized perceptual similarity information results in models that are the most aligned with human perceptual similarity judgments and also reflect intersubject correlations of human judgments. Our framework provides an approach for bootstrapping human similarity judgment data into more individualized, human-aligned brain encoding models of vision.

Current fMRI encoding models frame prediction as deterministic regression, yet identical stimuli evoke a distribution of neural responses (arising from physiological noise, hemodynamic variability, and cognitive fluctuations) that a single point estimate cannot capture. This work introduces MultiFlow, a generative fMRI encoding framework based on Conditional Flow Matching (CFM) and a formulation termed Stimulus-Informed Source Flow Matching (SISFM). SISFM generalises CFM by conditioning the source distribution on the stimulus: a learnable temporal convolution shapes the source mean with an HRF-length receptive field, while a variance head shrinks its scale, shortening the expected transport path. SISFM is instantiated with a Diffusion Transformer (DiT-X) decoder parameterising the velocity field, with sub-layer Attention Residuals, heterogeneous fusion of ten frozen vision, audio, language, and audiovisual backbones, and per-subject Yeo-network heads. On the Algonauts 2025 dataset, a single MultiFlow checkpoint recovers most of the benefit of large deterministic ensembles: it trails the 1000-model TRIBE ensemble in-distribution by 0.003 PCC (0.3163 vs. 0.3195), and the strongest in- and out-of-distribution ensembles (VIBE-20, MedARC-50) by 0.010 and 0.009 PCC, using a single trained model rather than an ensemble of 20-1000. The same checkpoint also provides stimulus-conditioned uncertainty estimates and sample-based diversity.

Understanding how the brain parses actions and events from time-varying natural inputs is a central challenge in neuroscience. Recent work has used deep neural network (DNN) models to build stimulus-computable fMRI encoding models that predict single-voxel responses to complex natural videos. However, the majority of video-computable encoding models predict responses using simple linear mappings from model tokens, overlooking the spatiotemporal structure shared by video representations and neural responses. Recent cross-attention encoding models address this limitation for static images, enabling flexible stimulus-dependent weighting of image content across space. Here, we extend this framework to naturalistic video, using per-parcel cross-attention to dynamically route features from a self-supervised video model (V-JEPA-2) across both space and time, fitting this model to fMRI responses to short video clips. We compare joint spatiotemporal attention with factorized and selectively constrained alternatives, and find that joint routing improves predictions of brain responses to held-out videos across higher visual regions, most consistently in lateral and dorsal visual areas associated with dynamic motion perception. Moreover, our method provides interpretable, stimulus-specific attention maps that dynamically follow moving objects, revealing which locations and temporal moments contribute to each neural response. We further show that attention maps from parcels in different category-selective networks (face-, body-, scene-selective) differentially weight content in accordance with expected semantic selectivity. Together, this work provides a new computational framework for understanding how visual information is adaptively weighted by cortical populations during dynamic visual perception.

Understanding the relationship between deep visual representations and the human visual system is a fundamental challenge in computational neuroscience. While modern vision models achieve strong performance in image recognition, their correspondence with the hierarchical organization of the human visual cortex remains an open question. In this study, we propose CHASMBrain, a novel hierarchical two-stage framework for image-to-fMRI encoding. Our architecture leverages a dual-stream Mamba design to explicitly separate and process global semantic tokens and local spatial patches, motivated by the functional organization of the visual cortex. A coarse-to-fine strategy is employed: Stage 1 predicts denoised ROI-level activations, while Stage 2 refines these coarse responses into full voxel-level predictions using a Mamba-VAE. Experiments on the Natural Scenes Dataset (NSD) demonstrate that our method achieves a Pearson correlation of 0.429 and an MSE of 0.261, outperforming all evaluated baselines including ridge regression and DINOv2 linear probes. Beyond predictive performance, causal branch-ablation experiments reveal an asymmetric specialization: the patch stream is specifically locked to early visual cortex (retinotopic regions), while the CLS stream contributes broader semantic context to higher-order areas -- a correspondence that holds causally, not merely correlationally. Cross-subject transfer experiments further show that the learned backbone generalizes across individuals with minimal per-subject adaptation, suggesting the model captures a shared, subject-agnostic visual representation.

Recent progress in task-optimized neural networks has established encoding models as a powerful tool for predicting brain responses to naturalistic stimuli, yet most existing approaches rely on unimodal representations. The emergence of omni-modal foundation models and rich multimodal neural datasets enables encoding models that jointly integrate visual, auditory, and linguistic information across subjects. We introduce MIRAGE, a brain encoding framework for predicting whole-brain fMRI responses to naturalistic audiovisual stimuli. MIRAGE achieves state-of-the-art performance via a native multimodal backbone and adaptive feature gating across layers. These representations are then combined with a transformer-based brain encoder and a subject-specific linear head over the cortical parcels. Controlled comparisons show that natively multimodal features consistently outperform post-hoc aggregation of independent unimodal features, across architectural levels and backbones. Beyond predictive accuracy, the learned attention weights are directly inspectable to interpret the modality-specific gating profile over the backbone, and each modality traces a distinct anatomical pattern across cortex. Together, these results propose adaptive layer-wise aggregation of natively multimodal features as a generalizable, interpretable, and accurate approach for whole-brain encoding.

Functional MRI data exhibit high-dimensional spatiotemporal structure, making both prediction and decoding challenging. In this work, we investigate neural integral-operator-based models for encoding and decoding tasks in fMRI, with particular emphasis on the role of nonlocal spatiotemporal context. We implement a latent neural integral operator framework that performs fixed point iterations in an auxiliary space from which classification and stimuli prediction is performed via a decoder. We evaluate our model on two open-source fMRI datasets. Our experiments examine both decoding of stimuli from fMRI recordings and encoding of fMRI dynamics from stimulus representations. A main focus is the effect of spatiotemporal context: we systematically compare short and long temporal windows, as well as the use of visual cortex vs whole brain recordings, and analyze their influence on performance and latent-space geometry. Across tasks and datasets, larger temporal windows generally improve results and produce more structured learned representations. In decoding experiments, the learned latent space often provides clearer class separation than the raw data. In encoding experiments, although absolute performance remains moderate due to the difficulty of the task, longer temporal windows still yield consistent gains. These findings suggest that neural integral operators provide a promising framework for modeling fMRI dynamics and that broader spatiotemporal context can be beneficial for both prediction and representation learning. More broadly, the results indicate that exploiting distributed nonlocal structure in brain dynamics requires model architectures specifically designed to capture such dependencies.

Encoding models provide a powerful framework for linking continuous stimulus features to neural activity; however, traditional voxelwise approaches are limited by measurement noise, inter-subject variability, and redundancy arising from spatially correlated voxels encoding overlapping neural signals. Here, we propose an independent component (IC)-based encoding framework that dissociates stimulus-driven and noise-driven signals in fMRI data. We decompose continuous fMRI data from naturalistic story listening into ICs using one subset of the data, and train encoding models on independent data to predict IC time series from large language model representations of linguistic input. Across subjects, a subset of ICs exhibited consistently high predictivity. These ICs were spatially and temporally consistent across subjects and included cognitive networks known to respond during story listening (auditory and language). Auditory component time series were strongly correlated with acoustic stimulus features, highlighting the interpretability of identified component time series. Components identified as noise or motion-related artifacts by ICA-AROMA showed uniformly poor predictive performance, confirming that highly predicted components reflect genuine stimulus-related neural signals rather than confounds. Overall, IC-based encoding models enable analyses at the level of functional networks, accommodating the variability in network locations across individuals and providing interpretable results that are easy to compare across subjects. Code provided at: https://github.com/kamyahari/IC-Encoding-Models.git