BayesBrainMap

R package BayesBrainMap implementing Bayesian brain mapping for individual functional topography and connectivity

CRAN status R-CMD-check Codecov test coverage

This package contains functions implementing the BrainMap model proposed in Mejia et al. (2019) and the spatial BrainMap model proposed in proposed in Mejia et al. (2020+). (Previously, these models were named “Template ICA” and were contained in the package templateICAr.) For both models, subject-level brain networks are estimated as deviations from known population-level networks, which can be estimated using standard ICA algorithms or provided as a parcellation. Both models employ an expectation-maximization algorithm for estimation of the latent brain networks and unknown model parameters.

BrainMap consists of three steps. The main functions associated with each step are listed below.

  1. Prior estimation: estimate_prior. Can export the results with export_prior.
  2. BrainMap model estimation (single-subject): BrainMap.
  3. Identification of areas of engagement in each network (or deviation from the prior mean): engagements.

Citation

If you use BayesBrainMap please cite the following papers:

Name APA Citation
BrainMap Mejia, A. F., Nebel, M. B., Wang, Y., Caffo, B. S., & Guo, Y. (2020). Template Independent Component Analysis: targeted and reliable estimation of subject-level brain networks using big data population priors. Journal of the American Statistical Association, 115(531), 1151-1177.
Spatial BrainMap Mejia, A. F., Bolin, D., Yue, Y. R., Wang, J., Caffo, B. S., & Nebel, M. B. (2022). Template Independent Component Analysis with spatial priors for accurate subject-level brain network estimation and inference. Journal of Computational and Graphical Statistics, (just-accepted), 1-35.

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

citation("BayesBrainMap")

Installation

You can install the development version of BayesBrainMap from Github with:

# install.packages("devtools")
devtools::install_github("mandymejia/BayesBrainMap")

Important Notes on Dependencies:

To analyze or visualize CIFTI-format data, BayesBrainMap depends on the ciftiTools package, which requires an installation of Connectome Workbench. It can be installed from the HCP website.

For fitting the BrainMap model with surface-based priors (spatial_model=TRUE in BrainMap()), INLA is required. Due to a CRAN policy, INLA cannot 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=TRUE). Alternatively, dep=FALSE can be used along with manual installation of dependencies as necessary to avoid installing all of the many INLA dependencies, most of which are not actually required. Binaries for alternative Linux builds can be added with the command inla.binary.install(). Note that INLA is not required for standard BrainMap.

Depending on the analysis, PARDISO may reduce computation time. To obtain a free academic license forINLA-PARDISO, run inla.pardiso() in R after running library(INLA). Provide an academic email address. Once you obtain a license, point to it using INLA::inla.setOption(pardiso.license = "pardiso.lic") followed by INLA::inla.pardiso.check() to ensure that PARDISO is successfully installed and running.