activations: Identify field activations
In mandymejia/BayesfMRI: Spatial Bayesian Methods for Task Functional MRI Studies

activations

R Documentation

Identify field activations

Description

Identify areas of activation for each field from the result of BayesGLM or fit_bayesglm.

Usage

activations(
  x,
  Bayes = TRUE,
  gamma = NULL,
  alpha = 0.05,
  correction = c("FWER", "FDR", "none"),
  fields = NULL,
  sessions = NULL,
  verbose = 1
)

id_activations(
  x,
  Bayes = TRUE,
  gamma = NULL,
  alpha = 0.05,
  correction = c("FWER", "FDR", "none"),
  fields = NULL,
  sessions = NULL,
  verbose = 1
)

Arguments

`x`	Result of `BayesGLM` or `fit_bayesglm` model call, of class `"BGLM"` or `"fit_bglm"`.
`Bayes`	Use spatial Bayesian modeling to identify activations based on the joint posterior distribution? Default: `TRUE`. If `FALSE`, activations will be based on classical (massive univariate) GLM model, with multiple comparisons correction (see `correction`). Note that `TRUE` is only applicable if `x` includes Bayesian results (i.e. `x <- BayesGLM(..., Bayes = TRUE)` was run.)
`gamma`	Activation threshold, for example `1` for 1 percent signal change if `scale_BOLD=="mean"` during model estimation. Setting a `gamma` is required for the Bayesian method; `NULL` (default) will use a `gamma` of zero for the classical method.
`alpha`	Significance level for inference. Default: `0.05`.
`correction`	For the classical method only: Type of multiple comparisons correction: `"FWER"` (Bonferroni correction, the default), `"FDR"` (Benjamini Hochberg), or `"none"`.
`fields`	The field(s) to identify activations for. Give either the name(s) as a character vector, or the numerical indices. If `NULL` (default), analyze all fields.
`sessions`	The session(s) to identify activations for. Give either the name(s) as a character vector, or the numerical indices. If `NULL` (default), analyze the first session.
`verbose`	`1` (default) to print occasional updates during model computation; `2` for occasional updates as well as running INLA in verbose mode (if `Bayes`), or `0` for no printed updates.