Spatial Bayesian Methods for Task Functional MRI Studies

Performs a spatial Bayesian general linear model (GLM) for task functional magnetic resonance imaging (fMRI) data on the cortical surface. Additional models include group analysis and inference to detect thresholded areas of activation. Includes direct support for the 'CIFTI' neuroimaging file format. For more information see A. F. Mejia, Y. R. Yue, D. Bolin, F. Lindgren, M. A. Lindquist (2020) and D. Spencer, Y. R. Yue, D. Bolin, S. Ryan, A. F. Mejia (2022) .

BayesfMRI

The BayesfMRI R package includes the main function BayesGLM, which implements a spatial Bayesian GLM for task fMRI. It also contains a wrapper function BayesGLM_cifti, for CIFTI cortical surface fMRI data.

Citation

If you use BayesfMRI please cite the following papers:

Name	APA Citation
Spatial Bayesian GLM	Mejia, A. F., Yue, Y., Bolin, D., Lindgren, F., & Lindquist, M. A. (2020). A Bayesian general linear modeling approach to cortical surface fMRI data analysis. Journal of the American Statistical Association, 115(530), 501-520.
Multi-session Spatial Bayesian GLM	Spencer, D., Yue, Y. R., Bolin, D., Ryan, S., & Mejia, A. F. (2022). Spatial Bayesian GLM on the cortical surface produces reliable task activations in individuals and groups. NeuroImage, 249, 118908.

You can also obtain citation information from within R like so:

citation("BayesfMRI")

Installation

You can install BayesfMRI from CRAN with:

install.packages("BayesfMRI")

Vignette/Demo

See this link to view the tutorial vignette.

Important Note on Dependencies:

BayesfMRI depends on the ciftiTools package, which requires an installation of Connectome Workbench. It can be installed from the HCP website.

The INLA package is required, which, due to a CRAN policy, will not be installed automatically. You can obtain it by running install.packages("INLA",repos=c(getOption("repos"),INLA="https://inla.r-inla-download.org/R/stable"), dep=FALSE). For more information, see the INLA website. Note: INLA must be installed before installing BayesfMRI.

On Mac platforms, an installation of Xcode is necessary to build the C++ code included in BayesfMRI.

Testing the INLA Installation:

Sometimes INLA does not install properly. Installation issues with INLA will prevent BayesfMRI from functioning. We recommend verifying a successful INLA installation by running the example model available on the INLA website.