Enhanced hyperalignment via spatial prior information

Functional alignment between subjects is an important assumption of functional magnetic resonance imaging (fMRI) group-level analysis. However, it is often violated in practice, even after alignment to a standard anatomical template. Hyperalignment, based on sequential Procrustes orthogonal transformations, has been proposed as a method of aligning shared functional information into a common high-dimensional space and thereby improving inter-subject analysis. Though successful, current hyperalignment algorithms have a number of shortcomings, including difficulties interpreting the transformations, a lack of uniqueness of the procedure, and difficulties performing whole-brain analysis. To resolve these issues, we propose the ProMises (Procrustes von Mises-Fisher) model. We reformulate functional alignment as a statistical model and impose a prior distribution on the orthogonal parameters (the von Mises-Fisher distribution). This allows for the embedding of anatomical information into the estimation procedure by penalizing the contribution of spatially distant voxels when creating the shared functional high-dimensional space. Importantly, the transformations, aligned images, and related results are all unique. In addition, the proposed method allows for efficient whole-brain functional alignment. In simulations and application to data from four fMRI studies we find that ProMises improves inter-subject classification in terms of between-subject accuracy and interpretability compared to standard hyperalignment algorithms.Comment: 28 pages, 9 figure

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

Supervised Hyperalignment for multi-subject fMRI data alignment

Hyperalignment has been widely employed in Multivariate Pattern (MVP) analysis to discover the cognitive states in the human brains based on multi-subject functional Magnetic Resonance Imaging (fMRI) datasets. Most of the existing HA methods utilized unsupervised approaches, where they only maximized the correlation between the voxels with the same position in the time series. However, these unsupervised solutions may not be optimum for handling the functional alignment in the supervised MVP problems. This paper proposes a Supervised Hyperalignment (SHA) method to ensure better functional alignment for MVP analysis, where the proposed method provides a supervised shared space that can maximize the correlation among the stimuli belonging to the same category and minimize the correlation between distinct categories of stimuli. Further, SHA employs a generalized optimization solution, which generates the shared space and calculates the mapped features in a single iteration, hence with optimum time and space complexities for large datasets. Experiments on multi-subject datasets demonstrate that SHA method achieves up to 19% better performance for multi-class problems over the state-of-the-art HA algorithms

Modeling Semantic Encoding in a Common Neural Representational Space

Encoding models for mapping voxelwise semantic tuning are typically estimated separately for each individual, limiting their generalizability. In the current report, we develop a method for estimating semantic encoding models that generalize across individuals. Functional MRI was used to measure brain responses while participants freely viewed a naturalistic audiovisual movie. Word embeddings capturing agent-, action-, object-, and scene-related semantic content were assigned to each imaging volume based on an annotation of the film. We constructed both conventional within-subject semantic encoding models and between-subject models where the model was trained on a subset of participants and validated on a left-out participant. Between-subject models were trained using cortical surface-based anatomical normalization or surface-based whole-cortex hyperalignment. We used hyperalignment to project group data into an individual’s unique anatomical space via a common representational space, thus leveraging a larger volume of data for out-of-sample prediction while preserving the individual’s fine-grained functional–anatomical idiosyncrasies. Our findings demonstrate that anatomical normalization degrades the spatial specificity of between-subject encoding models relative to within-subject models. Hyperalignment, on the other hand, recovers the spatial specificity of semantic tuning lost during anatomical normalization, and yields model performance exceeding that of within-subject models

Improved fMRI-based Pain Prediction using Bayesian Group-wise Functional Registration

In recent years, neuroimaging has undergone a paradigm shift, moving away from the traditional brain mapping approach toward developing integrated, multivariate brain models that can predict categories of mental events. However, large interindividual differences in brain anatomy and functional localization after standard anatomical alignment remain a major limitation in performing this analysis, as it leads to feature misalignment across subjects in subsequent predictive models

Enhanced hyperalignment via spatial prior information

Functional alignment between subjects is an important assumption of functional magnetic resonance imaging (fMRI) group-level analysis. However, it is often violated in practice, even after alignment to a standard anatomical template. Hyperalignment, based on sequential Procrustes orthogonal transformations, has been proposed as a method of aligning shared functional information into a common high-dimensional space and thereby improving inter-subject analysis. Though successful, current hyperalignment algorithms have a number of shortcomings, including difficulties interpreting the transformations, a lack of uniqueness of the procedure, and difficulties performing whole-brain analysis. To resolve these issues, we propose the ProMises (Procrustes von Mises–Fisher) model. We reformulate functional alignment as a statistical model and impose a prior distribution on the orthogonal parameters (the von Mises–Fisher distribution). This allows for the embedding of anatomical information into the estimation procedure by penalizing the contribution of spatially distant voxels when creating the shared functional high-dimensional space. Importantly, the transformations, aligned images, and related results are all unique. In addition, the proposed method allows for efficient whole-brain functional alignment. In simulations and application to data from four fMRI studies we find that ProMises improves inter-subject classification in terms of between-subject accuracy and interpretability compared to standard hyperalignment algorithms

Modeling Semantic Encoding in a Common Neural Representational Space

Encoding models for mapping voxelwise semantic tuning are typically estimated separately for each individual, limiting their generalizability. In the current report, we develop a method for estimating semantic encoding models that generalize across individuals. Functional MRI was used to measure brain responses while participants freely viewed a naturalistic audiovisual movie. Word embeddings capturing agent-, action-, object-, and scene-related semantic content were assigned to each imaging volume based on an annotation of the film. We constructed both conventional within-subject semantic encoding models and between-subject models where the model was trained on a subset of participants and validated on a left-out participant. Between-subject models were trained using cortical surface-based anatomical normalization or surface-based whole-cortex hyperalignment. We used hyperalignment to project group data into an individual’s unique anatomical space via a common representational space, thus leveraging a larger volume of data for out-of-sample prediction while preserving the individual’s fine-grained functional–anatomical idiosyncrasies. Our findings demonstrate that anatomical normalization degrades the spatial specificity of between-subject encoding models relative to within-subject models. Hyperalignment, on the other hand, recovers the spatial specificity of semantic tuning lost during anatomical normalization, and yields model performance exceeding that of within-subject models

AN EVALUATION OF HYPERALIGNMENT ON REPRODUCIBILITY AND PREDICTION ACCURACY FOR FMRI DATA

Functional magnetic resonance imaging (fMRI) is a neuroimaging technique which measures a person's brain activity using changes in the blood flow in response to neural activity. Recently, resting state fMRI (rs-fMRI) has become a ubiquitous tool for measuring connectivity and examining the functional architecture of the human brain. Here, we used a publicly available rs-fMRI dataset to investigate the performance of the hyperalignment algorithm, on several fMRI analyses. The research employs the use of the image intra-class correlation coefficient and functional connectome fingerprinting to evaluate the reproducibility of both the unaligned and hyperaligned data, and developed a predictive model to investigate whether hyperalignment improves the prediction of certain behavioral measures. Overall, our results illustrate the utility of the hyperalignment algorithm for studying inter-individual variation in brain activity