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.org Source code: https://github.com/CoSMoMVPA/CoSMoMVPA.

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.

Traditional tests of concept knowledge generate scores to assess how well a learner understands a concept. Here, we investigated whether patterns of brain activity collected during a concept knowledge task could be used to compute a neural 'score' to complement traditional scores of an individual's conceptual understanding. Using a novel data-driven multivariate neuroimaging approach-informational network analysis-we successfully derived a neural score from patterns of activity across the brain that predicted individual differences in multiple concept knowledge tasks in the physics and engineering domain. These tasks include an fMRI paradigm, as well as two other previously validated concept inventories. The informational network score outperformed alternative neural scores computed using data-driven neuroimaging methods, including multivariate representational similarity analysis. This technique could be applied to quantify concept knowledge in a wide range of domains, including classroom-based education research, machine learning, and other areas of cognitive science.

Fine-grained functional organization of cortex is not well-conserved across individuals. As a result, individual differences in cortical functional architecture are confounded by topographic idiosyncrasies-i.e., differences in functional-anatomical correspondence. In this study, we used hyperalignment to align information encoded in topographically variable patterns to study individual differences in fine-grained cortical functional architecture in a common representational space. We characterized the structure of individual differences using three common functional indices, and assessed the reliability of this structure across independent samples of data in a natural vision paradigm. Hyperalignment markedly improved the reliability of individual differences across all three indices by resolving topographic idiosyncrasies and accommodating information encoded in spatially fine-grained response patterns. Our results demonstrate that substantial individual differences in cortical functional architecture exist at fine spatial scales, but are inaccessible with anatomical normalization alone.

Shared information content is represented across brains in idiosyncratic functional topographies. Hyperalignment addresses these idiosyncrasies by using neural responses to project individuals' brain data into a common model space while maintaining the geometric relationships between distinct patterns of activity or connectivity. The dimensions of this common model capture functional profiles that are shared across individuals such as cortical response profiles collected during a common time-locked stimulus presentation (e.g. movie viewing) or functional connectivity profiles. Hyperalignment can use either response-based or connectivity-based input data to derive transformations that project individuals' neural data from anatomical space into the common model space. Previously, only response or connectivity profiles were used in the derivation of these transformations. In this study, we developed a new hyperalignment algorithm, hybrid hyperalignment, that derives transformations based on both response-based and connectivity-based information. We used three different movie-viewing fMRI datasets to test the performance of our new algorithm. Hybrid hyperalignment derives a single common model space that aligns response-based information as well as or better than response hyperalignment while simultaneously aligning connectivity-based information better than connectivity hyperalignment. These results suggest that a single common information space can encode both shared cortical response and functional connectivity profiles across individuals.

As smartphone usage has become increasingly prevalent in our society, so have rates of depression, particularly among young adults. Individual differences in smartphone usage patterns have been shown to reflect individual differences in underlying affective processes such as depression (Wang et al., 2018). In the current study, a positive relationship was identified between smartphone screen time (e.g., phone unlock duration) and resting-state functional connectivity (RSFC) between the subgenual cingulate cortex (sgCC), a brain region implicated in depression and antidepressant treatment response, and regions of the ventromedial/orbitofrontal cortex (OFC), such that increased phone usage was related to stronger connectivity between these regions. This cluster was subsequently used to constrain subsequent analyses looking at individual differences in depressive symptoms in the same cohort and observed partial replication in a separate cohort. Similar analyses were subsequently performed on metrics of circadian rhythm consistency showing a negative relationship between connectivity of the sgCC and OFC. The data and analyses presented here provide relatively simplistic preliminary analyses which replicate and provide an initial step in combining functional brain activity and smartphone usage patterns to better understand issues related to mental health. Smartphones are a prevalent part of modern life and the usage of mobile sensing data from smartphones promises to be an important tool for mental health diagnostics and neuroscience research.

No abstract available

Subject-specific, functionally defined areas are conventionally estimated with functional localizers and a simple contrast analysis between responses to different stimulus categories. Compared with functional localizers, naturalistic stimuli provide several advantages such as stronger and widespread brain activation, greater engagement, and increased subject compliance. In this study we demonstrate that a subject's idiosyncratic functional topography can be estimated with high fidelity from that subject's fMRI data obtained while watching a naturalistic movie using hyperalignment to project other subjects' localizer data into that subject's idiosyncratic cortical anatomy. These findings lay the foundation for developing an efficient tool for mapping functional topographies for a wide range of perceptual and cognitive functions in new subjects based only on fMRI data collected while watching an engaging, naturalistic stimulus and other subjects' localizer data from a normative sample.

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.

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.

Humans prioritize different semantic qualities of a complex stimulus depending on their behavioral goals. These semantic features are encoded in distributed neural populations, yet it is unclear how attention might operate across these distributed representations. To address this, we presented participants with naturalistic video clips of animals behaving in their natural environments while the participants attended to either behavior or taxonomy. We used models of representational geometry to investigate how attentional allocation affects the distributed neural representation of animal behavior and taxonomy. Attending to animal behavior transiently increased the discriminability of distributed population codes for observed actions in anterior intraparietal, pericentral, and ventral temporal cortices. Attending to animal taxonomy while viewing the same stimuli increased the discriminability of distributed animal category representations in ventral temporal cortex. For both tasks, attention selectively enhanced the discriminability of response patterns along behaviorally relevant dimensions. These findings suggest that behavioral goals alter how the brain extracts semantic features from the visual world. Attention effectively disentangles population responses for downstream read-out by sculpting representational geometry in late-stage perceptual areas.

Variation in cortical connectivity profiles is typically modeled as having a coarse spatial scale parcellated into interconnected brain areas. We created a high-dimensional common model of the human connectome to search for fine-scale structure that is shared across brains. Projecting individual connectivity data into this new common model connectome accounts for substantially more variance in the human connectome than do previous models. This newly discovered shared structure is closely related to fine-scale distinctions in representations of information. These results reveal a shared fine-scale structure that is a major component of the human connectome that coexists with coarse-scale, areal structure. This shared fine-scale structure was not captured in previous models and was, therefore, inaccessible to analysis and study.

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.

How does STEM knowledge learned in school change students' brains? Using fMRI, we presented photographs of real-world structures to engineering students with classroom-based knowledge and hands-on lab experience, examining how their brain activity differentiated them from their "novice" peers not pursuing engineering degrees. A data-driven MVPA and machine-learning approach revealed that neural response patterns of engineering students were convergent with each other and distinct from novices' when considering physical forces acting on the structures. Furthermore, informational network analysis demonstrated that the distinct neural response patterns of engineering students reflected relevant concept knowledge: learned categories of mechanical structures. Information about mechanical categories was predominantly represented in bilateral anterior ventral occipitotemporal regions. Importantly, mechanical categories were not explicitly referenced in the experiment, nor does visual similarity between stimuli account for mechanical category distinctions. The results demonstrate how learning abstract STEM concepts in the classroom influences neural representations of objects in the world.

Encouraged by a rise of reciprocal interest between the machine learning and neuroscience communities, several recent studies have demonstrated the explanatory power of statistical learning techniques for the analysis of neural data. In order to facilitate a wider adoption of these methods, neuroscientific research needs to ensure a maximum of transparency to allow for comprehensive evaluation of the employed procedures. We argue that such transparency requires "neuroscience-aware" technology for the performance of multivariate pattern analyses of neural data that can be documented in a comprehensive, yet comprehensible way. Recently, we introduced PyMVPA, a specialized Python framework for machine learning based data analysis that addresses this demand. Here, we review its features and applicability to various neural data modalities.

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.

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.

The Python programming language is steadily increasing in popularity as the language of choice for scientific computing. The ability of this scripting environment to access a huge code base in various languages, combined with its syntactical simplicity, make it the ideal tool for implementing and sharing ideas among scientists from numerous fields and with heterogeneous methodological backgrounds. The recent rise of reciprocal interest between the machine learning (ML) and neuroscience communities is an example of the desire for an inter-disciplinary transfer of computational methods that can benefit from a Python-based framework. For many years, a large fraction of both research communities have addressed, almost independently, very high-dimensional problems with almost completely non-overlapping methods. However, a number of recently published studies that applied ML methods to neuroscience research questions attracted a lot of attention from researchers from both fields, as well as the general public, and showed that this approach can provide novel and fruitful insights into the functioning of the brain. In this article we show how PyMVPA, a specialized Python framework for machine learning based data analysis, can help to facilitate this inter-disciplinary technology transfer by providing a single interface to a wide array of machine learning libraries and neural data-processing methods. We demonstrate the general applicability and power of PyMVPA via analyses of a number of neural data modalities, including fMRI, EEG, MEG, and extracellular recordings.