# Spatial Bayesian Methods for Task Functional MRI Studies

## Documentation for package ‘BayesfMRI’ version 0.3.11

- DESCRIPTION file.

## Help Pages

.findTheta | Perform the EM algorithm of the Bayesian GLM fitting
.getSqrtInvCpp | Get the prewhitening matrix for a single data location
.initialKP | Find the initial values of kappa2 and phi
.logDetQt | Find the log of the determinant of Q_tilde
act_prevalance | Activations prevalence.
aic_Param | aic
ar_order_Param | ar_order
ar_smooth_Param | ar_smooth
BayesGLM | BayesGLM
BayesGLM2 | Group-level Bayesian GLM
BayesGLM_cifti | BayesGLM for CIFTI
BayesGLM_group | Group-level Bayesian GLM
Bayes_Param | Bayes
cderiv | Central derivative
combine_sessions_Param | combine_sessions
contrasts_Param | contrasts
emTol_Param | emTol
EM_Param | EM
faces_Param | faces
HRF | Canonical (double-gamma) HRF
id_activations | Identify task activations
INLA_Description | INLA
is.BfMRI.sess | Validate a '"BfMRI.sess"' object.
make_HRFs | Make HRFs
make_mask | Mask out invalid data
make_mesh | Make Mesh
mask_Param_vertices | mask: vertices
max.threads_Param | max.threads
mesh_Param_either | mesh: either
mesh_Param_inla | mesh: INLA only
num.threads_Param | num.threads
plot.act_BayesGLM_cifti | S3 method: use 'view_xifti_surface' to plot a '"act_BayesGLM_cifti"' object
plot.BayesGLM2_cifti | S3 method: use 'view_xifti_surface' to plot a '"BayesGLM2_cifti"' object
plot.BayesGLM_cifti | S3 method: use 'view_xifti_surface' to plot a '"BayesGLM_cifti"' object
plot.prev_BayesGLM_cifti | S3 method: use 'view_xifti' to plot a '"prev_BayesGLM_cifti"' object
print.act_BayesGLM | Summarize a '"act_BayesGLM"' object
print.act_BayesGLM_cifti | Summarize a '"act_BayesGLM_cifti"' object
print.BayesGLM | Summarize a '"BayesGLM"' object
print.BayesGLM2 | Summarize a '"BayesGLM2"' object
print.BayesGLM2_cifti | Summarize a '"BayesGLM2_cifti"' object
print.BayesGLM_cifti | Summarize a '"BayesGLM_cifti"' object
print.prev_BayesGLM | Summarize a '"prev_BayesGLM"' object
print.prev_BayesGLM_cifti | Summarize a '"prev_BayesGLM_cifti"' object
print.summary.act_BayesGLM | Summarize a '"act_BayesGLM"' object
print.summary.act_BayesGLM_cifti | Summarize a '"act_BayesGLM_cifti"' object
print.summary.BayesGLM | Summarize a '"BayesGLM"' object
print.summary.BayesGLM2 | Summarize a '"BayesGLM2"' object
print.summary.BayesGLM2_cifti | Summarize a '"BayesGLM2_cifti"' object
print.summary.BayesGLM_cifti | Summarize a '"BayesGLM_cifti"' object
print.summary.prev_BayesGLM | Summarize a '"prev_BayesGLM"' object
print.summary.prev_BayesGLM_cifti | Summarize a '"prev_BayesGLM_cifti"' object
pw_estimate | Estimate residual autocorrelation for prewhitening
pw_smooth | Smooth AR coefficients and white noise variance
return_INLA_Param | return_INLA
scale_BOLD_Param | scale_BOLD
scale_design_Param | scale_design
seed_Param | seed
session_names_Param | session_names
summary.act_BayesGLM | Summarize a '"act_BayesGLM"' object
summary.act_BayesGLM_cifti | Summarize a '"act_BayesGLM_cifti"' object
summary.BayesGLM | Summarize a '"BayesGLM"' object
summary.BayesGLM2 | Summarize a '"BayesGLM2"' object
summary.BayesGLM2_cifti | Summarize a '"BayesGLM2_cifti"' object
summary.BayesGLM_cifti | Summarize a '"BayesGLM_cifti"' object
summary.prev_BayesGLM | Summarize a '"prev_BayesGLM"' object
summary.prev_BayesGLM_cifti | Summarize a '"prev_BayesGLM_cifti"' object
task_names_Param | task_names
trim_INLA_Param | trim_INLA
verbose_Param | verbose
vertex_areas | Surface area of each vertex
vertices_Param | vertices