Summary We present a high-dimensional model of the representational space in human ventral temporal (VT) cortex in which dimensions are response-tuning functions that are common across individuals and patterns of response are modeled as weighted sums of basis patterns associated with these response-tunings. We map response pattern vectors, measured with fMRI, from individual subjects’ voxel spaces into this common model space using a new method, ‘hyperalignment’. Hyperalignment parameters based on responses during one experiment – movie-viewing – identified 35 common response-tuning functions that captured fine-grained distinctions among a wide range of stimuli in the movie and in two category perception experiments. Between-subject classification (BSC, multivariate pattern classification based on other subjects’ data) of response pattern vectors in common model space greatly exceeded BSC of anatomically-aligned responses and matched within-subject classification. Results indicate that population codes for complex visual stimuli in VT cortex are based on response-tuning functions that are common across individuals.

A major challenge for systems neuroscience is to break the neural code. Computational algorithms for encoding information into neural activity and extracting information from measured activity afford understanding of how percepts, memories, thought, and knowledge are represented in patterns of brain activity. The past decade and a half has seen significant advances in the development of methods for decoding human neural activity, such as multivariate pattern classification, representational similarity analysis, hyperalignment, and stimulus-model-based encoding and decoding. This article reviews these advances and integrates neural decoding methods into a common framework organized around the concept of high-dimensional representational spaces.

Recent years have seen an increase in the popularity of multivariate pattern (MVP) analysis of functional magnetic resonance (fMRI) data, and, to a much lesser extent, magneto- and electro-encephalography (M/EEG) data. We present CoSMoMVPA, a lightweight MVPA (MVP analysis) toolbox implemented in the intersection of the Matlab and GNU Octave languages, that treats both fMRI and M/EEG data as first-class citizens. CoSMoMVPA supports all state-of-the-art MVP analysis techniques, including searchlight analyses, classification, correlations, representational similarity analysis, and the time generalization method. These can be used to address both data-driven and hypothesis-driven questions about neural organization and representations, both within and across: space, time, frequency bands, neuroimaging modalities, individuals, and species. It uses a uniform data representation of fMRI data in the volume or on the surface, and of M/EEG data at the sensor and source level. Through various external toolboxes, it directly supports reading and writing a variety of fMRI and M/EEG neuroimaging formats, and, where applicable, can convert between them. As a result, it can be integrated readily in existing pipelines and used with existing preprocessed datasets. CoSMoMVPA overloads the traditional volumetric searchlight concept to support neighborhoods for M/EEG and surface-based fMRI data, which supports localization of multivariate effects of interest across space, time, and frequency dimensions. CoSMoMVPA also provides a generalized approach to multiple comparison correction across these dimensions using Threshold-Free Cluster Enhancement with state-of-the-art clustering and permutation techniques. CoSMoMVPA is highly modular and uses abstractions to provide a uniform interface for a variety of MVP measures. Typical analyses require a few lines of code, making it accessible to beginner users. At the same time, expert programmers can easily extend its functionality. CoSMoMVPA comes with extensive documentation, including a variety of runnable demonstration scripts and analysis exercises (with example data and solutions). It uses best software engineering practices including version control, distributed development, an automated test suite, and continuous integration testing. It can be used with the proprietary Matlab and the free GNU Octave software, and it complies with open source distribution platforms such as NeuroDebian. CoSMoMVPA is Free/Open Source Software under the permissive MIT license.Website: http://cosmomvpa.orgSource code: https://github.com/CoSMoMVPA/CoSMoMVPA

Evidence of category specificity from neuroimaging in the human visual system is generally limited to a few relatively coarse categorical distinctions—e.g., faces versus bodies, or animals versus artifacts—leaving unknown the neural underpinnings of fine-grained category structure within these large domains. Here we use functional magnetic resonance imaging (fMRI) to explore brain activity for a set of categories within the animate domain, including six animal species—two each from three very different biological classes: primates, birds, and insects. Patterns of activity throughout ventral object vision cortex reflected the biological classes of the stimuli. Specifically, the abstract representational space—measured as dissimilarity matrices defined between species-specific multivariate patterns of brain activity—correlated strongly with behavioral judgments of biological similarity of the same stimuli. This biological class structure was uncorrelated with structure measured in retinotopic visual cortex, which correlated instead with a dissimilarity matrix defined by a model of V1 cortex for the same stimuli. Additionally, analysis of the shape of the similarity space in ventral regions provides evidence for a continuum in the abstract representational space—with primates at one end and insects at the other. Further investigation into the cortical topography of activity that contributes to this category structure reveals the partial engagement of brain systems active normally for inanimate objects in addition to animate regions.

Current models of the functional architecture of human cortex emphasize areas that capture coarse-scale features of cortical topography but provide no account for population responses that encode information in fine-scale patterns of activity. Here, we present a linear model of shared representational spaces in human cortex that captures fine-scale distinctions among population responses with response-tuning basis functions that are common across brains and models cortical patterns of neural responses with individual-specific topographic basis functions. We derive a common model space for the whole cortex using a new algorithm, searchlight hyperalignment, and complex, dynamic stimuli that provide a broad sampling of visual, auditory, and social percepts. The model aligns representations across brains in occipital, temporal, parietal, and prefrontal cortices, as shown by between-subject multivariate pattern classification and intersubject correlation of representational geometry, indicating that structural principles for shared neural representations apply across widely divergent domains of information. The model provides a rigorous account for individual variability of well-known coarse-scale topographies, such as retinotopy and category selectivity, and goes further to account for fine-scale patterns that are multiplexed with coarse-scale topographies and carry finer distinctions.