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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., (Copyright © 2011 Elsevier Inc. All rights reserved.)

Current neuroimaging software offer users an incredible opportunity to analyze their data in different ways, with different underlying assumptions. Several sophisticated software packages (e.g., AFNI, BrainVoyager, FSL, FreeSurfer, Nipy, R, SPM) are used to process and analyze large and often diverse (highly multi-dimensional) data. However, this heterogeneous collection of specialized applications creates several issues that hinder replicable, efficient, and optimal use of neuroimaging analysis approaches: (1) No uniform access to neuroimaging analysis software and usage information; (2) No framework for comparative algorithm development and dissemination; (3) Personnel turnover in laboratories often limits methodological continuity and training new personnel takes time; (4) Neuroimaging software packages do not address computational efficiency; and (5) Methods sections in journal articles are inadequate for reproducing results. To address these issues, we present Nipype (Neuroimaging in Python: Pipelines and Interfaces; http://nipy.org/nipype), an open-source, community-developed, software package, and scriptable library. Nipype solves the issues by providing Interfaces to existing neuroimaging software with uniform usage semantics and by facilitating interaction between these packages using Workflows. Nipype provides an environment that encourages interactive exploration of algorithms, eases the design of Workflows within and between packages, allows rapid comparative development of algorithms and reduces the learning curve necessary to use different packages. Nipype supports both local and remote execution on multi-core machines and clusters, without additional scripting. Nipype is Berkeley Software Distribution licensed, allowing anyone unrestricted usage. An open, community-driven development philosophy allows the software to quickly adapt and address the varied needs of the evolving neuroimaging community, especially in the context of increasing demand for reproducible research.

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.

Neuroimaging (e.g. fMRI) data are increasingly used to attempt to identify not only brain regions of interest (ROIs) that are especially active during perception, cognition, and action, but also the qualitative causal relations among activity in these regions (known as effective connectivity; Friston, 1994). Previous investigations and anatomical and physiological knowledge may somewhat constrain the possible hypotheses, but there often remains a vast space of possible causal structures. To find actual effective connectivity relations, search methods must accommodate indirect measurements of nonlinear time series dependencies, feedback, multiple subjects possibly varying in identified regions of interest, and unknown possible location-dependent variations in BOLD response delays. We describe combinations of procedures that under these conditions find feed-forward sub-structure characteristic of a group of subjects. The method is illustrated with an empirical data set and confirmed with simulations of time series of non-linear, randomly generated, effective connectivities, with feedback, subject to random differences of BOLD delays, with regions of interest missing at random for some subjects, measured with noise approximating the signal to noise ratio of the empirical data.

Brain-imaging research has largely focused on localizing patterns of activity related to specific mental processes, but recent work has shown that mental states can be identified from neuroimaging data using statistical classifiers. We investigated whether this approach could be extended to predict the mental state of an individual using a statistical classifier trained on other individuals, and whether the information gained in doing so could provide new insights into how mental processes are organized in the brain. Using a variety of classifier techniques, we achieved cross-validated classification accuracy of 80% across individuals (chance = 13%). Using a neural network classifier, we recovered a low-dimensional representation common to all the cognitive-perceptual tasks in our data set, and we used an ontology of cognitive processes to determine the cognitive concepts most related to each dimension. These results revealed a small organized set of large-scale networks that map cognitive processes across a highly diverse set of mental tasks, suggesting a novel way to characterize the neural basis of cognition.

Decoding patterns of neural activity onto cognitive states is one of the central goals of functional brain imaging. Standard univariate fMRI analysis methods, which correlate cognitive and perceptual function with the blood oxygenation-level dependent (BOLD) signal, have proven successful in identifying anatomical regions based on signal increases during cognitive and perceptual tasks. Recently, researchers have begun to explore new multivariate techniques that have proven to be more flexible, more reliable, and more sensitive than standard univariate analysis. Drawing on the field of statistical learning theory, these new classifier-based analysis techniques possess explanatory power that could provide new insights into the functional properties of the brain. However, unlike the wealth of software packages for univariate analyses, there are few packages that facilitate multivariate pattern classification analyses of fMRI data. Here we introduce a Python-based, cross-platform, and open-source software toolbox, called PyMVPA, for the application of classifier-based analysis techniques to fMRI datasets. PyMVPA makes use of Python's ability to access libraries written in a large variety of programming languages and computing environments to interface with the wealth of existing machine learning packages. We present the framework in this paper and provide illustrative examples on its usage, features, and programmability.

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.

Over the past decade, object recognition work has confounded voxel response detection with potential voxel class identification. Consequently, the claim that there are areas of the brain that are necessary and sufficient for object identification cannot be resolved with existing associative methods (e.g., the general linear model) that are dominant in brain imaging methods. In order to explore this controversy we trained full brain (40,000 voxels) single TR (repetition time) classifiers on data from 10 subjects in two different recognition tasks on the most controversial classes of stimuli (house and face) and show 97.4% median out-of-sample (unseen TRs) generalization. This performance allowed us to reliably and uniquely assay the classifier's voxel diagnosticity in all individual subjects' brains. In this two-class case, there may be specific areas diagnostic for house stimuli (e.g., LO) or for face stimuli (e.g., STS); however, in contrast to the detection results common in this literature, neither the fusiform face area nor parahippocampal place area is shown to be uniquely diagnostic for faces or places, respectively.

A mode-based clustering method is developed for identifying spatially dense clusters in brain maps. This type of clustering focuses on identifying clusters in brain maps independent of their shape or overall variance. This can be useful for both localization in terms of interpretation and for subsequent graphical analysis that might require more coherent or dense regions of interest as starting points. The method automatically does signal/noise sharpening through density mode seeking. We also discuss the problem of parameter selection with this method and propose a new method involving 2-parameter control surface, in which we show that the same cluster solution results from tradeoff of these 2 parameters (the local density k and the radius r of the spherical kernel). We benchmark the new dense mode clustering by using several artificially created data sets and brain imaging data sets from an event perception task by perturbing the data set with noise and measuring three kinds of deviation from the original cluster solution. We present benchmark results that demonstrate that the mode clustering method consistently outperforms the commonly used single-linkage clustering, k means method (centroid method) and Ward's method (variance method).