title: A toolbox for representational similarity analysis.
abstract: Neuronal population codes are increasingly being investigated with multivariate pattern-information analyses. A key challenge is to use measured brain-activity patterns to test computational models of brain information processing. One approach to this problem is representational similarity analysis (RSA), which characterizes a representation in a brain or computational model by the distance matrix of the response patterns elicited by a set of stimuli. The representational distance matrix encapsulates what distinctions between stimuli are emphasized and what distinctions are de-emphasized in the representation. A model is tested by comparing the representational distance matrix it predicts to that of a measured brain region. RSA also enables us to compare representations between stages of processing within a given brain or model, between brain and behavioral data, and between individuals and species. Here, we introduce a Matlab toolbox for RSA. The toolbox supports an analysis approach that is simultaneously data- and hypothesis-driven. It is designed to help integrate a wide range of computational models into the analysis of multichannel brain-activity measurements as provided by modern functional imaging and neuronal recording techniques. Tools for visualization and inference enable the user to relate sets of models to sets of brain regions and to statistically test and compare the models using nonparametric inference methods. The toolbox supports searchlight-based RSA, to continuously map a measured brain volume in search of a neuronal population code with a specific geometry. Finally, we introduce the linear-discriminant t value as a measure of representational discriminability that bridges the gap between linear decoding analyses and RSA. In order to demonstrate the capabilities of the toolbox, we apply it to both simulated and real fMRI data. The key functions are equally applicable to other modalities of brain-activity measurement. The toolbox is freely available to the community under an open-source license agreement (http://www.mrc-cbu.cam.ac.uk/methods-and-resources/toolboxes/license/).
authors.affiliation: MRC Cognition and Brain Sciences Unit, Cambridge, United Kingdom.
authors.forename: Hamed
authors.initials: H
authors.lastname: Nili
authors.affiliation: Department of Computer Science, University of Bath, Bath, United Kingdom.
authors.forename: Cai
authors.initials: C
authors.lastname: Wingfield
authors.affiliation: MRC Cognition and Brain Sciences Unit, Cambridge, United Kingdom.
authors.forename: Alexander
authors.initials: A
authors.lastname: Walther
authors.affiliation: MRC Cognition and Brain Sciences Unit, Cambridge, United Kingdom; Department of Experimental Psychology, University of Cambridge, Cambridge, United Kingdom.
authors.forename: Li
authors.initials: L
authors.lastname: Su
authors.affiliation: Department of Experimental Psychology, University of Cambridge, Cambridge, United Kingdom.
authors.forename: William
authors.initials: W
authors.lastname: Marslen-Wilson
authors.affiliation: MRC Cognition and Brain Sciences Unit, Cambridge, United Kingdom.
authors.forename: Nikolaus
authors.initials: N
authors.lastname: Kriegeskorte
mesh_terms: D001921:Brain / Q000166:cytology / Q000502:physiology; D003198:Computer Simulation; D001330:Electronic Data Processing; D006801:Humans; D008962:Models, Theoretical
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