Coordinate-Based Meta-Analysis of fMRI Studies with R

This paper outlines how to conduct a simple meta-analysis of neuroimaging foci of activation in R. In particular, the first part of this paper reviews the nature of fMRI data, and briefly overviews the existing packages that can be used to analyze fMRI data in R. The second part illustrates how to handle fMRI data by showing how to visualize the results of different neuroimaging studies in a so-called orthographic view, where the spatial distribution of the foci of activation from different fMRI studies can be inspected visually. Functional MRI (fMRI) is one of the most important and powerful tools of neuroscientific research. Although not as commonly used for fMRI analysis as some specific applications such as SPM (Friston et al., 2006), AFNI (Cox and Hyde, 1997), or FSL (Smith et al., 2004), R does provide several packages that can be employed in neuroimaging research. These packages deal with a variety of topics, ranging from reading and manipulating fMRI datasets, to implementing sophisticated statistical models. The goal of this paper is to provide a brief introduction to fMRI analysis, and the various R packages that can be used to carry it out. As an example, it will show how to use simple R commands to read fMRI images and plot results from previous studies, which can then be visually compared. This is a special form of meta-analysis, and a common way to compare results from the existing literature.

Andrea Stocco

CRAN packages used

fmri, RNiftyReg, AnalyzeFMRI, RfmriVC, arf3DS4, BHMSMAfMRI, neuRosim, oro.nifti, spatstat

CRAN Task Views implied by cited packages

MedicalImaging, ChemPhys, Spatial, SpatioTemporal, Survival


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For attribution, please cite this work as

Stocco, "The R Journal: Coordinate-Based Meta-Analysis of fMRI Studies with R ", The R Journal, 2014

BibTeX citation

  author = {Stocco, Andrea},
  title = {The R Journal: Coordinate-Based Meta-Analysis of fMRI Studies with R },
  journal = {The R Journal},
  year = {2014},
  note = {},
  doi = {10.32614/RJ-2014-020},
  volume = {6},
  issue = {2},
  issn = {2073-4859},
  pages = {5-15}