Estimate Brain Networks and Connectivity with ICA and Empirical Priors

[Up] [Top]

Documentation for package ‘templateICAr’ version 0.8.8

Help Pages

templateICAr-package templateICAr: Estimate Brain Networks and Connectivity with ICA and Empirical Priors
activations Activations of (spatial) template ICA
bdiag_m2 Bdiag m2
Chol_samp_fun Cholesky-based FC sampling
dim_reduce PCA-based Dimension Reduction and Prewhitening
EM_templateICA EM Algorithms for Template ICA Models
EM_templateICA.independent EM Algorithms for Template ICA Models
EM_templateICA.spatial EM Algorithms for Template ICA Models
estimate.ESS Estimation of effective sample size
estimate_nu Universally estimate IW dof parameter nu based on method of moments, so that no empirical variance is under-estimated
estimate_nu_matrix Estimate IW dof parameter nu based on method of moments
estimate_template Estimate template
estimate_template.cifti Estimate template
estimate_template.gifti Estimate template
estimate_template.nifti Estimate template
estimate_template_FC Estimate FC template
estimate_template_from_DR Estimate template from DR
export_template Export template
getInvCovAR Compute inverse covariance matrix for AR process (up to a constant scaling factor)
Gibbs_AS_posteriorCPP Use a Gibbs sampler for the A and S variables (E-step of the EM)
groupICA.cifti Perform group ICA based on CIFTI data
IW_var Compute theoretical Inverse-Wishart variance of covariance matrix elements
IW_var_cor Compute theoretical Inverse-Wishart variance of correlation matrix elements
lik Compute likelihood in SPDE model for ESS estimation
make_mesh Make INLA mesh from '"surf"' object
make_mesh_2D Make 2D INLA mesh
norm_BOLD Normalize BOLD data
orthonorm Orthonormalizes a square, invertible matrix
plot.template.cifti Plot template
plot.template.gifti Plot template
plot.template.matrix Plot template
plot.template.nifti Plot template
plot.tICA.cifti Plot template
plot.tICA.matrix Plot template
plot.tICA.nifti Plot template
plot.tICA_act.cifti Plot activations
print.summary.template.cifti Summarize a '"template.cifti"' object
print.summary.template.gifti Summarize a '"template.gifti"' object
print.summary.template.matrix Summarize a '"template.matrix"' object
print.summary.template.nifti Summarize a '"template.nifti"' object
print.summary.tICA.cifti Summarize a '"tICA.cifti"' object
print.summary.tICA.matrix Summarize a '"tICA.matrix"' object
print.summary.tICA.nifti Summarize a '"tICA.nifti"' object
print.summary.tICA_act.cifti Summarize a '"tICA_act.cifti"' object
print.summary.tICA_act.matrix Summarize a '"tICA_act.matrix"' object
print.summary.tICA_act.nifti Summarize a '"tICA_act.nifti"' object
print.template.cifti Summarize a '"template.cifti"' object
print.template.gifti Summarize a '"template.gifti"' object
print.template.matrix Summarize a '"template.matrix"' object
print.template.nifti Summarize a '"template.nifti"' object
print.tICA.cifti Summarize a '"tICA.cifti"' object
print.tICA.matrix Summarize a '"tICA.matrix"' object
print.tICA.nifti Summarize a '"tICA.nifti"' object
print.tICA_act.cifti Summarize a '"tICA_act.cifti"' object
print.tICA_act.matrix Summarize a '"tICA_act.matrix"' object
print.tICA_act.nifti Summarize a '"tICA_act.nifti"' object
pw_estimate Estimate residual autocorrelation for prewhitening
resample_template Resample CIFTI template
sqrt_XtX Compute matrix square root of X'X
summary.template.cifti Summarize a '"template.cifti"' object
summary.template.gifti Summarize a '"template.gifti"' object
summary.template.matrix Summarize a '"template.matrix"' object
summary.template.nifti Summarize a '"template.nifti"' object
summary.tICA.cifti Summarize a '"tICA.cifti"' object
summary.tICA.matrix Summarize a '"tICA.matrix"' object
summary.tICA.nifti Summarize a '"tICA.nifti"' object
summary.tICA_act.cifti Summarize a '"tICA_act.cifti"' object
summary.tICA_act.matrix Summarize a '"tICA_act.matrix"' object
summary.tICA_act.nifti Summarize a '"tICA_act.nifti"' object
templateICA Template ICA
templateICAr templateICAr: Estimate Brain Networks and Connectivity with ICA and Empirical Priors
UpdateTheta_FCtemplateICAcpp Update parameters (M-step of the EM)
UpdateTheta_templateICA Parameter Estimates in EM Algorithm for Template ICA Model
UpdateTheta_templateICA.independent Parameter Estimates in EM Algorithm for Template ICA Model
UpdateTheta_templateICA.spatial Parameter Estimates in EM Algorithm for Template ICA Model
UT2mat Transform upper-triangular elements to matrix form
var_sq_err Compute the error between empirical and theoretical variance of covariance matrix elements
var_sq_err_constrained Compute the overall error between empirical and theoretical variance of CORRELATION matrix elements