# Spatial Bayesian Methods for Task Functional MRI Studies

## Documentation for package ‘BayesfMRI’ version 0.11.0

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

BayesfMRI-package | BayesfMRI: Spatial Bayesian Methods for Task Functional MRI Studies
.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
activations | Identify field activations
aic_Param | aic
ar_order_Param | ar_order
ar_smooth_Param | ar_smooth
BayesfMRI | BayesfMRI: Spatial Bayesian Methods for Task Functional MRI Studies
BayesGLM | BayesGLM for CIFTI
BayesGLM2 | Group-level Bayesian GLM
Bayes_Param | Bayes
BOLD_Param_BayesGLM | BOLD
brainstructures_Param_BayesGLM | brainstructures
buffer_Param | buffer
Connectome_Workbench_Description | Connectome Workbench
contrasts_Param | contrasts
design_Param_BayesGLM | design
do_QC | Mask out invalid data
emTol_Param | emTol
EM_Param | EM
faces_Param | faces
field_names_Param | field_names
fit_bayesglm | fit_bayesglm
hpf_Param_BayesGLM | hpf
id_activations | Identify field activations
INLA_Description | INLA
INLA_Latent_Fields_Limit_Description | INLA Latent Fields
make_mesh | Make Mesh
mask_Param_vertices | mask: vertices
max_threads_Param | max_threads
mean_var_Tol_Param | mean and variance tolerance
mesh_Param_either | mesh: either
mesh_Param_inla | mesh: INLA only
nbhd_order_Param | nbhd_order
nuisance_Param_BayesGLM | nuisance
n_threads_Param | n_threads
plot.act_BGLM | S3 method: use 'view_xifti' to plot a '"act_BGLM"' object
plot.BGLM | S3 method: use 'view_xifti' to plot a '"BGLM"' object
plot.BGLM2 | S3 method: use 'view_xifti' to plot a '"BGLM2"' object
plot.prev_BGLM | S3 method: use 'view_xifti' to plot a '"prev_BGLM"' object
prevalence | Activations prevalence.
print.act_BGLM | Summarize a '"act_BGLM"' object
print.act_fit_bglm | Summarize a '"act_fit_bglm"' object
print.BGLM | Summarize a '"BGLM"' object
print.BGLM2 | Summarize a '"BGLM2"' object
print.fit_bglm | Summarize a '"fit_bglm"' object
print.fit_bglm2 | Summarize a '"fit_bglm2"' object
print.prev_BGLM | Summarize a '"prev_BGLM"' object
print.prev_fit_bglm | Summarize a '"prev_fit_bglm"' object
print.summary.act_BGLM | Summarize a '"act_BGLM"' object
print.summary.act_fit_bglm | Summarize a '"act_fit_bglm"' object
print.summary.BGLM | Summarize a '"BGLM"' object
print.summary.BGLM2 | Summarize a '"BGLM2"' object
print.summary.fit_bglm | Summarize a '"fit_bglm"' object
print.summary.fit_bglm2 | Summarize a '"fit_bglm2"' object
print.summary.prev_BGLM | Summarize a '"prev_BGLM"' object
print.summary.prev_fit_bglm | Summarize a '"prev_fit_bglm"' object
resamp_res_Param_BayesGLM | resamp_res
return_INLA_Param | return_INLA
scale_BOLD | Scale the BOLD timeseries
scale_BOLD_Param | scale_BOLD
scrub_Param_BayesGLM | scrub
seed_Param | seed
session_names_Param | session_names
summary.act_BGLM | Summarize a '"act_BGLM"' object
summary.act_fit_bglm | Summarize a '"act_fit_bglm"' object
summary.BGLM | Summarize a '"BGLM"' object
summary.BGLM2 | Summarize a '"BGLM2"' object
summary.fit_bglm | Summarize a '"fit_bglm"' object
summary.fit_bglm2 | Summarize a '"fit_bglm2"' object
summary.prev_BGLM | Summarize a '"prev_BGLM"' object
summary.prev_fit_bglm | Summarize a '"prev_fit_bglm"' object
surfaces_Param_BayesGLM | surfaces
trim_INLA_Param | trim_INLA
TR_Param_BayesGLM | TR
verbose_Param | verbose
vertex_areas | Surface area of each vertex
vertices_Param | vertices
vol2spde | Construct a triangular mesh from a 3D volumetric mask