Estimate Brain Networks and Connectivity with ICA and Empirical Priors

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Documentation for package ‘templateICAr’ version 0.10.0

• DESCRIPTION file.
• Package NEWS.

Help Pages

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)
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
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