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#' Read a CIFTI file
#'
#' Read in a CIFTI file as a \code{"xifti"} object.
#'
#' First, metadata is obtained with \code{\link{info_cifti}}. Then, if no
#' resampling is requested, the \code{-cifti-convert -to-gifti-ext} Workbench
#' Command is used to "flatten" the data and save it as a metric or label GIFTI
#' file, which is read in and separated by brainstructure according to the metadata
#' (\code{\link{read_cifti_convert}}). Otherwise, if sampling is requested,
#' then the CIFTI is separated into its GIFTI and NIFTI components, resampled,
#' and then re-assembled (\code{\link{read_cifti_separate}}). The former is
#' much faster for large CIFTI files, so the latter is only used when necessary
#' for resampling.
#'
#' If \code{cifti_fname} is not provided, then only the surfaces are read in.
#'
#' @inheritSection labels_Description Label Levels
#'
#' @inheritParams cifti_fname_Param
#' @inheritParams surfL_fname_Param
#' @inheritParams surfR_fname_Param
#' @inheritParams brainstructures_Param_all
#' @inheritParams idx_Param
#' @param resamp_res Resolution to resample the cortical data and surface to.
#' Default: \code{NULL} (do not resample). If not \code{NULL}, the data will
#' have to be read in with \code{-cifti-separate}, which is slower than
#' \code{-cifti-convert -to-gifti-ext}.
#' @inheritParams resamp_method_Param
#' @inheritParams area_original_Param
#' @param flat Should the result be flattened into a single matrix?
#'
#' If \code{FALSE} (default), the result will be a \code{"xifti"} object.
#'
#' If \code{TRUE}, the result will be a \eqn{T \times G} matrix (\eqn{T}
#' measurements, \eqn{G} grayordinates not including the medial wall if it's
#' excluded from the ROI). All below arguments will be ignored because the
#' brain structures cannot be identified. Surfaces will not be appended.
#' Resampling is also not possible. \code{flat==TRUE} is the fastest way to
#' read in just the CIFTI data.
#'
#' If \code{TRUE}, the grayordinates will be ordered by left cortex, right
#' cortex, and then subcortex. Subcortical voxels will be ordered by alphabetical
#' label. However, where each brainstructure (and subcortical structure) begins
#' and ends cannot be determined. The medial wall locations and subcortical
#' brain mask are also not included. The data matrix will be identical to that
#' created by \code{-cifti-convert -to-gifti-ext}.
#' @param mwall_values If the medial wall locations are not indicated in the
#' CIFTI, use these values to infer the medial wall mask. Default:
#' \code{c(NA, NaN)}. If \code{NULL}, do not attempt to infer the medial wall.
#' @inheritParams verbose_Param_FALSE
#' @param ... Additional arguments to \code{\link{read_cifti_convert}} or
#' \code{\link{read_cifti_separate}}.
#'
#' @return If \code{!flat}, a \code{"xifti"} object. Otherwise, a \eqn{T \times G}
#' matrix (\eqn{T} measurements, \eqn{G} grayordinates).
#'
#' @family common
#' @family reading
#' @export
#'
#' @section Connectome Workbench:
#' This function interfaces with the \code{"-cifti-convert"} Workbench command if
#' resampling is not needed, and the \code{"-cifti-separate"} Workbench command
#' if resampling is needed.
#'
read_cifti <- function(
cifti_fname=NULL,
surfL_fname=NULL, surfR_fname=NULL,
brainstructures="all", idx=NULL,
resamp_res=NULL, resamp_method=c("barycentric", "adaptive"),
areaL_original_fname=NULL, areaR_original_fname=NULL,
flat=FALSE,
mwall_values=c(NA, NaN), verbose=FALSE, ...){
if (is.null(cifti_fname)) {
if (is.null(surfL_fname) && is.null(surfR_fname)) {
warning("`cifti_fname`, `surfL_fname` and `surfR_fname` were all NULL: Nothing to read!\n")
return(template_xifti())
} else {
xifti <- template_xifti()
xifti <- add_surf(xifti, surfL=surfL_fname, surfR=surfR_fname)
if (!is.null(resamp_res)) {
if (!is.null(xifti$surf$cortex_left)) {
xifti$surf$cortex_left <- resample_surf(xifti$surf$cortex_left, resamp_res, "left")
}
if (!is.null(xifti$surf$cortex_right)) {
xifti$surf$cortex_right <- resample_surf(xifti$surf$cortex_right, resamp_res, "right")
}
}
return(xifti)
}
}
# ----------------------------------------------------------------------------
# Handle flat method. --------------------------------------------------------
# ----------------------------------------------------------------------------
if (flat) {
if (!is.null(resamp_res)) {
ciftiTools_warn(paste(
"Resampling is not possible with the flat method.",
"Ignoring `resamp_res`.\n"
))
}
return( read_cifti_flat(cifti_fname, idx=idx) )
}
# ----------------------------------------------------------------------------
# Check arguments. -----------------------------------------------------------
# ----------------------------------------------------------------------------
require_separate_method <- !is.null(resamp_res)
brainstructures <- match_input(
brainstructures, c("left","right","subcortical","all"),
user_value_label="brainstructures"
)
if ("all" %in% brainstructures) {
brainstructures <- c("left","right","subcortical")
}
# ----------------------------------------------------------------------------
# Read. ----------------------------------------------------------------------
# ----------------------------------------------------------------------------
if (!require_separate_method) {
return(read_cifti_convert(
cifti_fname,
surfL_fname=surfL_fname, surfR_fname=surfR_fname,
brainstructures=brainstructures, idx=idx,
mwall_values=mwall_values, verbose=verbose,
...
))
} else {
return(read_cifti_separate(
cifti_fname,
surfL_fname=surfL_fname, surfR_fname=surfR_fname,
brainstructures=brainstructures, idx=idx,
resamp_res=resamp_res, resamp_method=resamp_method,
areaL_original_fname=areaL_original_fname, areaR_original_fname=areaR_original_fname,
mwall_values=mwall_values, verbose=verbose,
...
))
}
}
#' @rdname read_cifti
#' @export
readCIfTI <- function(
cifti_fname=NULL,
surfL_fname=NULL, surfR_fname=NULL,
brainstructures="all", idx=NULL,
resamp_res=NULL, resamp_method=c("barycentric", "adaptive"),
areaL_original_fname=NULL, areaR_original_fname=NULL,
flat=FALSE,
mwall_values=c(NA, NaN), verbose=FALSE, ...){
read_cifti(
cifti_fname=cifti_fname,
surfL_fname=surfL_fname, surfR_fname=surfR_fname,
brainstructures=brainstructures, idx=idx,
resamp_res=resamp_res, resamp_method=resamp_method,
areaL_original_fname=areaL_original_fname, areaR_original_fname=areaR_original_fname,
flat=flat,
mwall_values=mwall_values, verbose=verbose, ...
)
}
#' @rdname read_cifti
#' @export
readcii <- function(
cifti_fname=NULL,
surfL_fname=NULL, surfR_fname=NULL,
brainstructures="all", idx=NULL,
resamp_res=NULL, resamp_method=c("barycentric", "adaptive"),
areaL_original_fname=NULL, areaR_original_fname=NULL,
flat=FALSE,
mwall_values=c(NA, NaN), verbose=FALSE, ...){
read_cifti(
cifti_fname=cifti_fname,
surfL_fname=surfL_fname, surfR_fname=surfR_fname,
brainstructures=brainstructures, idx=idx,
resamp_res=resamp_res, resamp_method=resamp_method,
areaL_original_fname=areaL_original_fname, areaR_original_fname=areaR_original_fname,
flat=flat,
mwall_values=mwall_values, verbose=verbose, ...
)
}
#' @rdname read_cifti
#' @export
read_xifti <- function(
cifti_fname=NULL,
surfL_fname=NULL, surfR_fname=NULL,
brainstructures="all", idx=NULL,
resamp_res=NULL, resamp_method=c("barycentric", "adaptive"),
areaL_original_fname=NULL, areaR_original_fname=NULL,
flat=FALSE,
mwall_values=c(NA, NaN), verbose=FALSE, ...){
read_cifti(
cifti_fname=cifti_fname,
surfL_fname=surfL_fname, surfR_fname=surfR_fname,
brainstructures=brainstructures, idx=idx,
resamp_res=resamp_res, resamp_method=resamp_method,
areaL_original_fname=areaL_original_fname, areaR_original_fname=areaR_original_fname,
flat=flat,
mwall_values=mwall_values, verbose=verbose, ...
)
}
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