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#' Load a parcellation included in \code{ciftiTools}
#'
#' Load a parcellation included in \code{ciftiTools}.
#'
#' When using these parcellations, please cite the corresponding paper(s):
#'
#' \enumerate{
#' \item{Yeo, B. T. T. et al. The organization of the human cerebral cortex estimated by intrinsic functional connectivity. J Neurophysiol 106, 1125-1165 (2011).}
#' \item{Schaefer, A. et al. Local-Global Parcellation of the Human Cerebral Cortex from Intrinsic Functional Connectivity MRI. Cereb Cortex 28, 3095-3114 (2018).}
#' \item{Kong, R. et al. Individual-Specific Areal-Level Parcellations Improve Functional Connectivity Prediction of Behavior. Cerebral Cortex (2021+) doi:10.1093/cercor/bhab101.}
#' }
#'
#' Note that the Schaefer parcels have been matched to networks from Kong (2021+).
#'
#' @param name The name of the parcellation to load:
#' \describe{
#' \item{\code{"Schaefer_100"}:}{ (2018) 100 parcels based on the "local-global" approach.}
#' \item{\code{"Schaefer_400"}:}{ (2018) 400 parcels based on the "local-global" approach.}
#' \item{\code{"Schaefer_1000"}:}{ (2018) 1000 parcels based on the "local-global" approach.}
#' \item{\code{"Yeo_7"}:}{ (2011) 7 networks based on fcMRI clustering. Networks are further divided into 51 components.}
#' \item{\code{"Yeo_17"}:}{ (2011) 17 networks based on fcMRI clustering. Networks are further divided into 114 components.}
#' }
#'
# @param map Schaefer parcels have been matched to networks from Yeo (2011) and
# Kong (2022). Available choices depend on the parcellation:
# \describe{
# \item{\code{"Schaefer_*"}:}{ \code{"Yeo_7"}, \code{"Yeo_17",} or \code{"Kong_17"}}
# \item{\code{"Yeo_*"}:}{ None available (this argument must be \code{NULL})}
# }
#' \code{NULL} (default) will load the first choice, where applicable. This
#' argument will affect the indices, colors, and names of each parcel, but not
#' the parcel boundaries.
#'
#' @return The parcellation as a dlabel \code{"xifti"} with one column. Each key
#' represents one unique parcel.
#'
#' @family reading
#' @family parcellation-related
#' @export
load_parc <- function(
name=c("Schaefer_100", "Schaefer_400", "Schaefer_1000", "Yeo_7", "Yeo_17")
) {
# Get the full parcellation name based on `name` and `map`
name <- match.arg(name,
c("Schaefer_100", "Schaefer_400", "Schaefer_1000", "Yeo_7", "Yeo_17")
)
map <- ifelse(grepl("Schaefer", name), "Kong_17", "Yeo_7")
# if (!is.null(map)) {
# map <- match.arg(map, c("Yeo_7", "Yeo_17", "Kong_17"))
# } else {
# map <- "Yeo_7"
# }
name2 <- paste(name, map, sep="__")
p_all <- c(
#Schaefer_100__Yeo_7 = "Schaefer2018_100Parcels_7Networks_order",
#Schaefer_100__Yeo_17 = "Schaefer2018_100Parcels_17Networks_order",
Schaefer_100__Kong_17 = "Schaefer2018_100Parcels_Kong2022_17Networks_order",
#Schaefer_400__Yeo_7 = "Schaefer2018_400Parcels_7Networks_order",
#Schaefer_400__Yeo_17 = "Schaefer2018_400Parcels_17Networks_order",
Schaefer_400__Kong_17 = "Schaefer2018_400Parcels_Kong2022_17Networks_order",
#Schaefer_1000__Yeo_7 = "Schaefer2018_1000Parcels_7Networks_order",
#Schaefer_1000__Yeo_17 = "Schaefer2018_1000Parcels_17Networks_order",
Schaefer_1000__Kong_17 = "Schaefer2018_1000Parcels_Kong2022_17Networks_order",
Yeo_7__Yeo_7 = "Yeo2011_7Networks.split_components",
Yeo_17__Yeo_7 = "Yeo2011_17Networks.split_components"
)
if (!(name2 %in% names(p_all))) {
stop("Invalid `name` and `map` pair. Refer to the documentation for `load_parc` for valid inputs.")
}
# Load the parcellation
p <- ciftiTools.data$parc[[p_all[name2]]]
# Format the parcellation as a \code{"xifti"}. Return it
nv <- nrow(p$map) # 32492*2=64984
np <- nrow(p$col) - 1
z <- template_xifti()
z$data$cortex_left <- p$map[seq(nv/2),,drop=FALSE]
z$data$cortex_right <- p$map[seq(nv/2+1, nv),,drop=FALSE]
z$meta$cifti <- list(
intent=3007,
brainstructures=c("left", "right"),
names="parcels",
labels=list()
#misc = ...
)
z$meta$cifti$labels <- list(
parcels = data.frame(
Key = seq(0, np),
Red = p$col$Red,
Green = p$col$Green,
Blue = p$col$Blue,
Alpha = c(0, rep(1, np))
)
)
rownames(z$meta$cifti$labels$parcels) <- rownames(p$col)
z
}
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