Predicting individual face-selective topography using naturalistic stimuli

Enhancing neural encoding models for naturalistic perception with a multi-level integration of deep neural networks and cortical networks

Cognitive neuroscience aims to develop computational models that can accurately predict and explain neural responses to sensory inputs in the cortex. Recent studies attempt to leverage the representation power of deep neural networks (DNNs) to predict the brain response and suggest a correspondence between artificial and biological neural networks in their feature representations. However, typical voxel-wise encoding models tend to rely on specific networks designed for computer vision tasks, leading to suboptimal brain-wide correspondence during cognitive tasks. To address this challenge, this work proposes a novel approach that upgrades voxel-wise encoding models through multi-level integration of features from DNNs and information from brain networks. Our approach combines DNN feature-level ensemble learning and brain atlas-level model integration, resulting in significant improvements in predicting whole-brain neural activity during naturalistic video perception. Furthermore, this multi-level integration framework enables a deeper understanding of the brain's neural representation mechanism, accurately predicting the neural response to complex visual concepts. We demonstrate that neural encoding models can be optimized by leveraging a framework that integrates both data-driven approaches and theoretical insights into the functional structure of the cortical networks.

Cross-movie prediction of individualized functional topography

Participant-specific, functionally defined brain areas are usually mapped with functional localizers and estimated by making contrasts between responses to single categories of input. Naturalistic stimuli engage multiple brain systems in parallel, provide more ecologically plausible estimates of real-world statistics, and are friendly to special populations. The current study shows that cortical functional topographies in individual participants can be estimated with high fidelity from naturalistic stimuli. Importantly, we demonstrate that robust, individualized estimates can be obtained even when participants watched different movies, were scanned with different parameters/scanners, and were sampled from different institutes across the world. Our results create a foundation for future studies that allow researchers to estimate a broad range of functional topographies based on naturalistic movies and a normative database, making it possible to integrate high-level cognitive functions across datasets from laboratories worldwide.

Modeling naturalistic face processing in humans with deep convolutional neural networks

Deep convolutional neural networks (DCNNs) trained for face identification can rival and even exceed human-level performance. The ways in which the internal face representations in DCNNs relate to human cognitive representations and brain activity are not well understood. Nearly all previous studies focused on static face image processing with rapid display times and ignored the processing of naturalistic, dynamic information. To address this gap, we developed the largest naturalistic dynamic face stimulus set in human neuroimaging research (700+ naturalistic video clips of unfamiliar faces). We used this naturalistic dataset to compare representational geometries estimated from DCNNs, behavioral responses, and brain responses. We found that DCNN representational geometries were consistent across architectures, cognitive representational geometries were consistent across raters in a behavioral arrangement task, and neural representational geometries in face areas were consistent across brains. Representational geometries in late, fully connected DCNN layers, which are optimized for individuation, were much more weakly correlated with cognitive and neural geometries than were geometries in late-intermediate layers. The late-intermediate face-DCNN layers successfully matched cognitive representational geometries, as measured with a behavioral arrangement task that primarily reflected categorical attributes, and correlated with neural representational geometries in known face-selective topographies. Our study suggests that current DCNNs successfully capture neural cognitive processes for categorical attributes of faces but less accurately capture individuation and dynamic features.

Inferring Brain State Dynamics Underlying Naturalistic Stimuli Evoked Emotion Changes With dHA-HMM

The brain functional mechanisms underlying emotional changes have been primarily studied based on the traditional task design with discrete and simple stimuli. However, the brain state transitions when exposed to continuous and naturalistic stimuli with rich affection variations remain poorly understood. This study proposes a dynamic hyperalignment algorithm (dHA) to functionally align the inter-subject neural activity. The hidden Markov model (HMM) was used to study how the brain dynamics responds to emotion during long-time movie-viewing activity. The results showed that dHA significantly improved inter-subject consistency and allowed more consistent temporal HMM states across participants. Afterward, grouping the emotions in a clustering dendrogram revealed a hierarchical grouping of the HMM states. Further emotional sensitivity and specificity analyses of ordered states revealed the most significant differences in happiness and sadness. We then compared the activation map in HMM states during happiness and sadness and found significant differences in the whole brain, but strong activation was observed during both in the superior temporal gyrus, which is related to the early process of emotional prosody processing. A comparison of the inter-network functional connections indicates unique functional connections of the memory retrieval and cognitive network with the cerebellum network during happiness. Moreover, the persistent bilateral connections among salience, cognitive, and sensorimotor networks during sadness may reflect the interaction between high-level cognitive networks and low-level sensory networks. The main results were verified by the second session of the dataset. All these findings enrich our understanding of the brain states related to emotional variation during naturalistic stimuli.

Using child-friendly movie stimuli to study the development of face, place, and object regions from age 3 to 12 years

Scanning young children while they watch short, engaging, commercially-produced movies has emerged as a promising approach for increasing data retention and quality. Movie stimuli also evoke a richer variety of cognitive processes than traditional experiments, allowing the study of multiple aspects of brain development simultaneously. However, because these stimuli are uncontrolled, it is unclear how effectively distinct profiles of brain activity can be distinguished from the resulting data. Here we develop an approach for identifying multiple distinct subject-specific Regions of Interest (ssROIs) using fMRI data collected during movie-viewing. We focused on the test case of higher-level visual regions selective for faces, scenes, and objects. Adults (N = 13) were scanned while viewing a 5.6-min child-friendly movie, as well as a traditional localizer experiment with blocks of faces, scenes, and objects. We found that just 2.7 min of movie data could identify subject-specific face, scene, and object regions. While successful, movie-defined ssROIS still showed weaker domain selectivity than traditional ssROIs. Having validated our approach in adults, we then used the same methods on movie data collected from 3 to 12-year-old children (N = 122). Movie response timecourses in 3-year-old children's face, scene, and object regions were already significantly and specifically predicted by timecourses from the corresponding regions in adults. We also found evidence of continued developmental change, particularly in the face-selective posterior superior temporal sulcus. Taken together, our results reveal both early maturity and functional change in face, scene, and object regions, and more broadly highlight the promise of short, child-friendly movies for developmental cognitive neuroscience.

Processing of visual and non-visual naturalistic spatial information in the "parahippocampal place area"

The "parahippocampal place area" (PPA) in the human ventral visual stream exhibits increased hemodynamic activity correlated with the perception of landscape photos compared to faces or objects. Here, we investigate the perception of scene-related, spatial information embedded in two naturalistic stimuli. The same 14 participants were watching a Hollywood movie and listening to its audio-description as part of the open-data resource studyforrest.org. We model hemodynamic activity based on annotations of selected stimulus features, and compare results to a block-design visual localizer. On a group level, increased activation correlating with visual spatial information occurring in the movie is overlapping with a traditionally localized PPA. Activation correlating with semantic spatial information occurring in the audio-description is more restricted to the anterior PPA. On an individual level, we find significant bilateral activity in the PPA of nine individuals and unilateral activity in one individual. Results suggest that activation in the PPA generalizes to spatial information embedded in a movie and an auditory narrative, and may call for considering a functional subdivision of the PPA.

Shared neural codes for visual and semantic information about familiar faces in a common representational space

Our brain processes faces of close others differently than faces of visually familiar individuals. While both types of faces activate similar visual areas, faces of close others activate areas involved in processing social and semantic information. Here, we used between-subject linear classifiers trained on hyperaligned brain data to investigate the neural code for visual and semantic information about familiar others. The identity of both visually and personally familiar faces could be decoded across participants from brain activity in visual areas. Instead, only the identity of personally familiar faces could be decoded in areas involved in social cognition. Our results suggest that individually distinctive information associated with familiar faces is embedded in a neural code that is shared across brains.

Processes evoked by seeing a personally familiar face encompass recognition of visual appearance and activation of social and person knowledge. Whereas visual appearance is the same for all viewers, social and person knowledge may be more idiosyncratic. Using between-subject multivariate decoding of hyperaligned functional magnetic resonance imaging data, we investigated whether representations of personally familiar faces in different parts of the distributed neural system for face perception are shared across individuals who know the same people. We found that the identities of both personally familiar and merely visually familiar faces were decoded accurately across brains in the core system for visual processing, but only the identities of personally familiar faces could be decoded across brains in the extended system for processing nonvisual information associated with faces. Our results show that personal interactions with the same individuals lead to shared neural representations of both the seen and unseen features that distinguish their identities.

An empirical evaluation of functional alignment using inter-subject decoding

Inter-individual variability in the functional organization of the brain presents a major obstacle to identifying generalizable neural coding principles. Functional alignment-a class of methods that matches subjects' neural signals based on their functional similarity-is a promising strategy for addressing this variability. To date, however, a range of functional alignment methods have been proposed and their relative performance is still unclear. In this work, we benchmark five functional alignment methods for inter-subject decoding on four publicly available datasets. Specifically, we consider three existing methods: piecewise Procrustes, searchlight Procrustes, and piecewise Optimal Transport. We also introduce and benchmark two new extensions of functional alignment methods: piecewise Shared Response Modelling (SRM), and intra-subject alignment. We find that functional alignment generally improves inter-subject decoding accuracy though the best performing method depends on the research context. Specifically, SRM and Optimal Transport perform well at both the region-of-interest level of analysis as well as at the whole-brain scale when aggregated through a piecewise scheme. We also benchmark the computational efficiency of each of the surveyed methods, providing insight into their usability and scalability. Taking inter-subject decoding accuracy as a quantification of inter-subject similarity, our results support the use of functional alignment to improve inter-subject comparisons in the face of variable structure-function organization. We provide open implementations of all methods used.

The neural basis of intelligence in fine-grained cortical topographies

Intelligent thought is the product of efficient neural information processing, which is embedded in fine-grained, topographically organized population responses and supported by fine-grained patterns of connectivity among cortical fields. Previous work on the neural basis of intelligence, however, has focused on coarse-grained features of brain anatomy and function because cortical topographies are highly idiosyncratic at a finer scale, obscuring individual differences in fine-grained connectivity patterns. We used a computational algorithm, hyperalignment, to resolve these topographic idiosyncrasies and found that predictions of general intelligence based on fine-grained (vertex-by-vertex) connectivity patterns were markedly stronger than predictions based on coarse-grained (region-by-region) patterns. Intelligence was best predicted by fine-grained connectivity in the default and frontoparietal cortical systems, both of which are associated with self-generated thought. Previous work overlooked fine-grained architecture because existing methods could not resolve idiosyncratic topographies, preventing investigation where the keys to the neural basis of intelligence are more likely to be found.

An fMRI dataset in response to "The Grand Budapest Hotel", a socially-rich, naturalistic movie

Naturalistic stimuli evoke strong, consistent, and information-rich patterns of brain activity, and engage large extents of the human brain. They allow researchers to compare highly similar brain responses across subjects, and to study how complex representations are encoded in brain activity. Here, we describe and share a dataset where 25 subjects watched part of the feature film "The Grand Budapest Hotel" by Wes Anderson. The movie has a large cast with many famous actors. Throughout the story, the camera shots highlight faces and expressions, which are fundamental to understand the complex narrative of the movie. This movie was chosen to sample brain activity specifically related to social interactions and face processing. This dataset provides researchers with fMRI data that can be used to explore social cognitive processes and face processing, adding to the existing neuroimaging datasets that sample brain activity with naturalistic movies.

A new virtue of phantom MRI data: explaining variance in human participant data

Background: Magnetic resonance imaging (MRI) is an important yet complex data acquisition technology for studying the brain. MRI signals can be affected by many factors and many sources of variance are often simply attributed to "noise". Unexplained variance in MRI data hinders the statistical power of MRI studies and affects their reproducibility. We hypothesized that it would be possible to use phantom data as a proxy of scanner characteristics with a simplistic model of seasonal variation to explain some variance in human MRI data. Methods: We used MRI data from human participants collected in several studies, as well as phantom data collected weekly for scanner quality assurance (QA) purposes. From phantom data we identified the variables most likely to explain variance in acquired data and assessed their statistical significance by using them to model signal-to-noise ratio (SNR), a fundamental MRI QA metric. We then included phantom data SNR in the models of morphometric measures obtained from human anatomical MRI data from the same scanner. Results: Phantom SNR and seasonal variation, after multiple comparisons correction, were statistically significant predictors of the volume of gray brain matter. However, a sweep over 16 other brain matter areas and types revealed no statistically significant predictors among phantom SNR or seasonal variables after multiple comparison correction. Conclusions: Seasonal variation and phantom SNR may be important factors to account for in MRI studies. Our results show weak support that seasonal variations are primarily caused by biological human factors instead of scanner performance variation. The phantom QA metric and scanning parameters are useful for more than just QA. Using QA metrics, scanning parameters, and seasonal variation data can help account for some variance in MRI studies, thus making them more powerful and reproducible.

Hyperalignment: Modeling shared information encoded in idiosyncratic cortical topographies

Information that is shared across brains is encoded in idiosyncratic fine-scale functional topographies. Hyperalignment captures shared information by projecting pattern vectors for neural responses and connectivities into a common, high-dimensional information space, rather than by aligning topographies in a canonical anatomical space. Individual transformation matrices project information from individual anatomical spaces into the common model information space, preserving the geometry of pairwise dissimilarities between pattern vectors, and model cortical topography as mixtures of overlapping, individual-specific topographic basis functions, rather than as contiguous functional areas. The fundamental property of brain function that is preserved across brains is information content, rather than the functional properties of local features that support that content. In this Perspective, we present the conceptual framework that motivates hyperalignment, its computational underpinnings for joint modeling of a common information space and idiosyncratic cortical topographies, and discuss implications for understanding the structure of cortical functional architecture.