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#' Read only the data matrix in a CIFTI file
#'
#' Reads the CIFTI data matrix by converting it to a GIFTI using the
#' \code{-cifti-convert -to-gifti-ext} Connectome Workbench command. The result
#' will be a \eqn{T \times G} matrix (\eqn{T} measurements, \eqn{G} non-empty
#' grayordinates). All brainstructures in the CIFTI will be obtained, with no
#' indication for which brainstructure each brainordinate corresponds to.
#' Medial wall vertices and voxels outside the subcortical mask will not be
#' included. No spatial information is included. This is the fastest way to
#' read in CIFTI data.
#'
#' @inheritParams cifti_fname_Param
#' @param keep This function works by converting the CIFTI file to a GIFTI file
#' and then reading it in. Should the GIFTI file be kept? If \code{FALSE}
#' (default), write it in a temporary directory regardless of \code{write_dir}.
#' @param gifti_fname File path of GIFTI-format data to save the CIFTI as.
#' Should end with ".func.gii" for dscalar and dtseries CIFTI, and ".label.gii"
#' for dlabel CIFTI. Default: the CIFTI_fname but with the CIFTI extension
#' replaced with the appropriate GIFTI extension.
#' @inheritParams idx_Param
#' @param write_dir The directory in which to save the GIFTI, if it is being
#' kept. If \code{NULL} (default), use the current working directory.
#'
#' @importFrom gifti readgii
#'
#' @return A \eqn{T \times G} matrix, where \eqn{T} is the number of measurements
#' and \eqn{G} is the number of grayordinates in the CIFTI file.
#'
#' @keywords internal
#'
read_cifti_flat <- function(
cifti_fname, keep=FALSE, gifti_fname=NULL,
idx=NULL, write_dir=NULL) {
# ----------------------------------------------------------------------------
# Get the output file name ---------------------------------------------------
# ----------------------------------------------------------------------------
cifti_fname <- format_path(cifti_fname)
if (!is.fname(cifti_fname)) {
stop("`", cifti_fname, "` is not an existing file.")
}
# Get the components of the CIFTI and GIFTI file paths.
bname_cifti <- basename(cifti_fname)
extn_cii <- get_cifti_extn(bname_cifti)
extn_cii <- paste0(".", extn_cii) # e.g. ".dtseries.nii"
is_label = FALSE# extn_cii == ".dlabel.nii"
extn_gii <- ifelse(is_label, ".label.gii", ".func.gii")
extn_gii2 <- gsub(".", "\\.", extn_gii, fixed=TRUE)
extn_cii2 <- paste0(gsub(".", "\\.", extn_cii, fixed=TRUE), "$")
# If gifti_fname is not provided, use the CIFTI_fname but replace the
# extension with "flat.gii".
if (is.null(gifti_fname)) {
if (grepl(bname_cifti, extn_cii2)) {
gifti_fname <- gsub(extn_cii2, extn_gii2, bname_cifti)
} else {
gifti_fname <- paste0(bname_cifti, extn_gii)
}
}
if (!keep) { write_dir <- tempdir() }
gifti_fname <- format_path(gifti_fname, write_dir, mode=2)
# ----------------------------------------------------------------------------
# Write the file and read it in. ---------------------------------------------
# ----------------------------------------------------------------------------
cmd <- paste(
"-cifti-convert -to-gifti-ext",
sys_path(cifti_fname),
sys_path(gifti_fname)
)
run_wb_cmd(cmd)
# Create new GIFTI with selected columns, if specified.
if (!is.null(idx)) {
stopifnot(all(idx > 0) && all(idx == round(idx)))
idx_is_seq <- (length(idx) > 2 && all(diff(idx) == 1))
if (idx_is_seq) {
idx_string <- paste("-column", idx[1], "-up-to", idx[length(idx)])
} else {
idx_string <- paste("-column", paste(idx, collapse=" -column "))
}
gifti_fname_original <- gifti_fname
gifti_fname <- file.path(
tempdir(),
gsub(
paste0(extn_gii2, "$"), paste0("\\.sel_idx", extn_gii2),
basename(gifti_fname_original)
)
)
run_wb_cmd(paste(
"-metric-merge", sys_path(gifti_fname),
"-metric", sys_path(gifti_fname_original), idx_string
))
}
result <- readgii(gifti_fname)
do.call(cbind, result$data)
}
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