BayesfMRI0.11.0 package

Identification of areas of activation in a General Linear Model using ...

Identify activations using joint posterior probabilities

Identify field activations

aic

Corrected AIC

ar_order

ar_smooth

Bayes

BayesfMRI: Spatial Bayesian Methods for Task Functional MRI Studies

Bayes GLM arg checks

Format fit_bayesglm results into "xifti" objects

Format design

Format nuisance

Format scrub

Is a valid design?

Is a valid nuisance?

Is a valid scrub?

Get session_names for GLM

BayesGLM for CIFTI

Group-level Bayesian GLM

Beta posterior theta sampling

BOLD

brainstructures

buffer

cbind if first argument might be NULL

Check INLA and PARDISO

Sample from the multivariate normal distribution with Cholesky(Q)

Connectome Workbench

contrasts

Function to prepare objects for use in Rcpp functions

design

Set column values to zero for sparse matrix

Mask out invalid data

Perform the EM algorithm of the Bayesian GLM fitting

Get the prewhitening matrix for a single data location

Find the initial values of kappa2 and phi

Find the log of the determinant of Q_tilde

Expected log-likelihood function

EM

emTol

Extract Estimates of Activation

F logwt

faces

field_names

fit_bayesglm

Create FEM matrices

Get number of locations for various masks

Extracts posterior density estimates for hyperparameters

Extracts posterior density estimates for hyperparameters for volumetri...

Classical GLM

Classical GLM for multiple models

Standardize data variance, and prewhiten if applicable

Fixed point function for the joint BayesGLM EM update algorithm

Objective function for the BayesGLM EM algorithm

hpf

The fix point function for the initialization of kappa2 and phi

Objective function for the initialization of kappa2 and phi

Import INLA dependencies

INLA

INLA Latent Fields

Intersection mask for BayesGLM or activations result

Is a matrix or data.frame?

Function to optimize over kappa2

Make log_kappa and log_tau

Make A matrix with resampling framework

Make A matrix

Make data list for estimate_model

Make Mesh

Make the full SPDE precision based on theta, the spde, and the number ...

Make replicates

Make sqrtInv_all

mask: vertices

max_threads

mean and variance tolerance

mesh: either

mesh: INLA only

n_threads

nbhd_order

The negative of the objective function for kappa

The negative of the objective function for kappa without Sig_inv

Streamlined negative objective function for kappa2 using precompiled v...

Streamlined negative objective function for kappa2 using precompiled v...

nuisance

S3 method: use view_xifti to plot a "act_BGLM" object

S3 method: use view_xifti to plot a "BGLM" object

S3 method: use view_xifti to plot a "BGLM2" object

S3 method: use view_xifti to plot a "prev_BGLM" object

Find values for coefficients used in objective function for kappa2

Activations prevalence.

Estimate residual autocorrelation for prewhitening

Smooth AR coefficients and white noise variance

Q prime

Sample from a multivariate normal with mean and precision

resamp_res

Retroactively mask activations

Retroactively mask locations from fit_bglm result.

Retroactively mask locations from mesh.

return_INLA

Sequential 2-means on array B

Sequential 2-means variable selection

scale_BOLD

Scale the BOLD timeseries

Scale the design matrix

scrub

seed

session_names

Organize data for Bayesian GLM

SPDE from mesh model

SPDE from voxel model

Calculate the SPDE covariance

Summarize a "act_BGLM" object

Summarize a "act_fit_bglm" object

Summarize a "BGLM" object

Summarize a "BGLM2" object

Summarize a "fit_bglm" object

Summarize a "fit_bglm2" object

Summarize a "prev_BGLM" object

Summarize a "prev_fit_bglm" object

surfaces

TR

Trim INLA object

trim_INLA

Trace of Q beta' beta

Trace approximation function

Hutchinson estimator of the trace

Unmask data

Validate spatial

verbose

Surface area of each vertex

vertices

Construct a triangular mesh from a 3D volumetric mask