Neuroinformatics

, Volume 7, Issue 1, pp 37–53

PyMVPA: a Python Toolbox for Multivariate Pattern Analysis of fMRI Data

  • Michael Hanke
  • Yaroslav O. Halchenko
  • Per B. Sederberg
  • Stephen José Hanson
  • James V. Haxby
  • Stefan Pollmann
Article

Abstract

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.

Keywords

Python Neuroimaging software Image analysis MVPA Scripting Machine learning Functional magnetic resonance imaging 

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Copyright information

© Humana Press Inc. 2009

Authors and Affiliations

  • Michael Hanke
    • 1
    • 2
  • Yaroslav O. Halchenko
    • 3
    • 4
  • Per B. Sederberg
    • 5
    • 6
  • Stephen José Hanson
    • 3
    • 7
  • James V. Haxby
    • 8
    • 9
  • Stefan Pollmann
    • 1
    • 2
    • 10
  1. 1.Department of Experimental PsychologyUniversity of MagdeburgMagdeburgGermany
  2. 2.Center for Advanced ImagingMagdeburgGermany
  3. 3.Psychology DepartmentRutgers NewarkNewarkUSA
  4. 4.Computer Science DepartmentNew Jersey Institute of TechnologyNewarkUSA
  5. 5.Department of PsychologyPrinceton UniversityPrincetonUSA
  6. 6.Princeton Neuroscience InstitutePrinceton UniversityPrincetonUSA
  7. 7.Rutgers University Mind Brain Analysis, Rutgers NewarkNewarkUSA
  8. 8.Center for Cognitive NeuroscienceDartmouth CollegeHanoverUSA
  9. 9.Department of Psychological and Brain SciencesDartmouth CollegeHanoverUSA
  10. 10.Center for Behavioral Brain SciencesMagdeburgGermany

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