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R/rox_args_docs_BayesGLM.R
#' BOLD
#'
#' @param BOLD fMRI timeseries data in CIFTI format ("*.dtseries.nii").
#' For single-session analysis this can be a file path to a CIFTI file or a
#' \code{"xifti"} object from the \code{ciftiTools} package. For multi-session
#' analysis this can be a vector of file paths or a list of \code{"xifti"}
#' objects.
#'
#' If \code{BOLD} is a \code{"xifti"} object(s), the surfaces, if any, will be
#' used for the spatial model. However, if \code{surfL} and \code{surfR} are
#' provided, they will override any surfaces in \code{BOLD}.
#'
#' @name BOLD_Param_BayesGLM
NULL
#' design
#'
#' @param design A numeric matrix or \code{data.frame}, or a
#' \code{"BayesfMRI_design"} object from \code{make_design}. Can also
#' be an array where the third dimension is the same length as the number of
#' data locations, to model each location with its own design.
#'
#' @name design_Param_BayesGLM
NULL
#' TR
#'
#' @param TR Temporal resolution of the data, in seconds.
#'
#' @name TR_Param_BayesGLM
NULL
#' brainstructures
#'
#' @param brainstructures Character vector indicating which brain structure(s)
#' of \code{BOLD} to analyze: \code{"left"} cortex; \code{"right"} cortex;
#' and/or \code{"subcortical"} structures. Or \code{"all"} to model all three.
#' Default: \code{c("left","right")} (cortex only).
#'
#' @name brainstructures_Param_BayesGLM
NULL
#' surfaces
#'
#' @param surfL,surfR For cortex spatial model. Left and right cortex surface
#' geometry in GIFTI format ("*.surf.gii"). These can be a file path to
#' a GIFTI file or a \code{"surf"} object from \code{ciftiTools}.
#'
#' Surfaces can alternatively be provided through the \code{$surf} metadata in
#' \code{BOLD} if it is \code{"xifti"} data. If neither are provided, by default the
#' HCP group-average fs_LR inflated surfaces included in \code{ciftiTools} will be
#' used for the cortex spatial model.
#'
#' @name surfaces_Param_BayesGLM
NULL
#' resamp_res
#'
#' @param resamp_res For cortex spatial model. The number of vertices to which
#' each cortical surface should be resampled, or \code{NULL} to not resample.
#'
#' For computational feasibility, a value of \code{10000} (default) or lower is
#' recommended for Bayesian spatial modeling. If \code{Bayes=FALSE},
#' \code{resamp_res} can be set to \code{NULL} for full-resolution classical
#' modeling.
#'
#' @name resamp_res_Param_BayesGLM
NULL
#' nuisance
#'
#' @param nuisance (Optional) A \eqn{T \times N_{nuis}} matrix of nuisance signals,
#' where \eqn{T} is the number of timepoints and \eqn{N} is the number of
#' nuisance signals, or a list of these for multi-session analysis. Nuisance
#' signals are regressed from the fMRI data and design matrix prior to GLM
#' computation. Nuisance signals can include motion regressors, HRF derivatives
#' not being modeled as tasks, and other sources of noise.
#'
#' Detrending/high-pass filtering is accomplished by adding DCT bases to the
#' nuisance matrix; see the parameters \code{hpf} and \code{DCT}.
#'
#' Do not add spike regressors for scrubbing to the \code{nuisance} matrix.
#' Rather, provide these in \code{scrub} so that their corresponding timepoints
#' are also removed from the BOLD data after nuisance regression.
#'
#' @name nuisance_Param_BayesGLM
NULL
#' scrub
#'
#' @param scrub (Optional) A \eqn{T \times N_{scrub}} matrix of spike regressors
#' (one 1 value at the timepoint to scrub, and 0 for all other values), or a
#' logical vector indicating the timepoints to scrub (\code{TRUE} to scrub, and
#' \code{FALSE} to keep). For multi-session data, a session-length list of
#' such matrices or logical vectors.
#'
#' The spike regressors will be included in the nuisance
#' regression, and afterwards the timepoints indicated in \code{scrub} will be
#' removed from the BOLD data and design matrix.
#'
#' @name scrub_Param_BayesGLM
NULL
#' hpf
#'
#' @param hpf Add DCT bases to \code{nuisance} to apply a temporal high-pass
#' filter to the data, for detrending? \code{hpf} is the filter frequency.
#' Use \code{NULL} to skip detrending. Detrending is strongly recommended for
#' fMRI data, to help reduce the autocorrelation in the residuals, so
#' \code{NULL} will induce a warning. Use \code{"already"} to disable the
#' warning while skipping highpass filtering.
#'
#' Using at least two DCT bases is as sufficient for detrending as using linear
#' and quadratic drift terms in the nuisance matrix. So if DCT detrending is
#' being used here, there is no need to add linear and quadratic drift terms to
#' \code{nuisance}.
#'
#' @name hpf_Param_BayesGLM
NULL
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