Estimate Brain Networks and Connectivity with Population-Derived Priors
Combine additive terms in string
Block diagonal matrix
Bdiag m2
BrainMap
Check for required parallel packages
Check required packages for the data format
Cholesky-based FC sampling
Compute LL for EM Bayesian brain mapping
Compute posterior mean and precision of s
Compute SPDE and prior precision matrices for S
PCA-based Dimension Reduction and Prewhitening
Dual Regression wrapper
EM Algorithms for Bayesian brain maps
engagements
Estimate IW dof parameter nu based on method of moments
Universally estimate IW dof parameter nu based on method of moments, s...
Estimate Cholesky FC prior
Estimate empirical FC prior
Estimate IW FC prior
Estimate prior from DR estimates (when there are two measurements)
Estimate prior from DR
Estimate prior
Estimation of effective sample size
Export prior
Bayesian brain mapping
Format engagement name
Get FORMAT from format
Compute inverse covariance matrix for AR process (up to a constant sca...
GSR
Half log determinant
hpf
Engagements of (spatial) Bayesian brain mapping
Check for INLA
Compute theoretical Inverse-Wishart variance of correlation matrix ele...
Compute theoretical Inverse-Wishart variance of covariance matrix elem...
Compute likelihood in SPDE model for ESS estimation
Log-likelihood SQUAREM
Compute part of kappa log-likelihood
Kappa log-likelihood
Create a mask based on vertices that are invalid
Make 2D INLA mesh
Make INLA mesh from "surf" object
Make permutation matrix
Normalize BOLD data
Orthonormalizes a square, invertible matrix
Plot engagements
Plot fit_BBM estiamte
Plot prior
Plot prior
Plot prior
Plot prior
Plot prior
Plot prior
Estimate residual autocorrelation for prewhitening
Check Q2_max
Remove brain structure from CIFTI prior
Resample CIFTI prior
Remove nuisance ICs from data
scale
Compute matrix square root of X'X
Apply data structure to priors
Summarize a "bMap_eng.cifti" object
Summarize a "bMap_eng.matrix" object
Summarize a "bMap_eng.nifti" object
Summarize a "bMap.cifti" object
Summarize a "bMap.matrix" object
Summarize a "bMap.nifti" object
Summarize a "prior.cifti" object
Summarize a "prior.gifti" object
Summarize a "prior.matrix" object
Summarize a "prior.nifti" object
TR
Update A for VB FC Bayesian brain mapping using Cholesky prior for FC
Update A for VB FC Bayesian brain mapping using IW prior on FC
Update S for VB FC Bayesian brain mapping
Update tau for VB FC Bayesian brain mapping
Parameter Estimates in EM Algorithm for Bayesian brain map
Update theta SQUAREM
Compute the overall error between empirical and theoretical variance o...
Compute the error between empirical and theoretical variance of covari...
varTol
VB_FC_BBM
Implements Bayesian brain mapping with population-derived priors, including the original model described in Mejia et al. (2020) <doi:10.1080/01621459.2019.1679638>, the model with spatial priors described in Mejia et al. (2022) <doi:10.1080/10618600.2022.2104289>, and the model with population-derived priors on functional connectivity described in Mejia et al. (2025) <doi:10.1093/biostatistics/kxaf022>. Population-derived priors are based on templates representing established brain network maps, for example derived from independent component analysis (ICA), parcellations, or other methods. Model estimation is based on expectation-maximization or variational Bayes algorithms. Includes direct support for 'CIFTI', 'GIFTI', and 'NIFTI' neuroimaging file formats.
Useful links