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#' Smooth a metric GIFTI file
#'
#' Smooths metric GIFTI data along the cortical surface. The results are written
#' to a new GIFTI file.
#'
#' @param original_fname The GIFTI file to smooth.
#' @param target_fname Where to save the smoothed file.
#' @param surf_fname Surface GIFTI files cortical surface along which to smooth.
#' If not provided, the default inflated surfaces will be used.
#' @param surf_FWHM The full width at half maximum (FWHM) parameter
#' for the gaussian surface smoothing kernel, in mm. Default: \code{5}
#' @param hemisphere The cortex hemisphere: \code{"left"} or \code{"right"}.
#' Only used if \code{surf_fname} is \code{NULL}.
#' @param ROI_fname The ROI to limit smoothing to, as a metric file. This is
#' used to exclude the medial wall from smoothing. If not provided (default)
#' all the data is smoothed across the surface.
#' @param zeroes_as_NA Should zero-values be treated as NA? Default: \code{FALSE}.
#' @return The smoothed GIFTI file name, invisibly
#'
#' @importFrom gifti readgii
#'
#' @family gifting
#' @export
#'
#' @section Connectome Workbench:
#' This function interfaces with the \code{"-metric-smoothing"} Workbench command.
#'
smooth_gifti <- function(
original_fname, target_fname, surf_fname=NULL, surf_FWHM=5,
hemisphere=c("left", "right"), ROI_fname=NULL, zeroes_as_NA=FALSE) {
# ----------------------------------------------------------------------------
# Check arguments. -----------------------------------------------------------
# ----------------------------------------------------------------------------
stopifnot(file.exists(original_fname))
# Use default surface if none provided.
if (is.null(surf_fname)) {
ciftiTools_warn(paste(
"No surface provided to `smooth_gifti`,",
"so using the surface included in `ciftiTools`."
))
hemisphere <- match.arg(hemisphere, c("left", "right"))
x_res <- nrow(readgii(original_fname)$data[[1]])
surf_fname <- file.path(tempdir(), paste0(hemisphere, ".surf.gii"))
surf_fname <- resample_gifti(
ciftiTools.files()$surf[hemisphere],
surf_fname, hemisphere=hemisphere, file_type="surface", resamp_res=x_res
)
}
stopifnot(file.exists(surf_fname))
# ----------------------------------------------------------------------------
# Make and run command. ------------------------------------------------------
# ----------------------------------------------------------------------------
cmd <- paste(
"-metric-smoothing",
sys_path(surf_fname), sys_path(original_fname),
surf_FWHM / (2*sqrt(2*log(2))), sys_path(target_fname)
)
if (!is.null(ROI_fname)) { cmd <- paste(cmd, "-roi", sys_path(ROI_fname)) }
if (zeroes_as_NA) { cmd <- paste(cmd, "-fix-zeros") }
run_wb_cmd(cmd)
return(invisible(target_fname))
}
#' @rdname smooth_gifti
#' @export
smoothGIfTI <- function(
original_fname, target_fname, surf_fname, surf_FWHM=5,
zeroes_as_NA=FALSE) {
smooth_gifti(
original_fname, target_fname, surf_fname, surf_FWHM, zeroes_as_NA
)
}
#' @rdname smooth_gifti
#' @export
smoothgii <- function(
original_fname, target_fname, surf_fname, surf_FWHM=5,
zeroes_as_NA=FALSE) {
smooth_gifti(
original_fname, target_fname, surf_fname, surf_FWHM, zeroes_as_NA
)
}
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