R/readrpi.R

In muschellij2/fslr: Wrapper Functions for 'FSL' ('FMRIB' Software Library) from Functional MRI of the Brain ('FMRIB')

#' @title Read NIfTI file reoriented to RPI
#' 
#' @description  This function calls the \code{\link{readnii}} function after
#' calling \code{\link{rpi_orient_file}} to force RPI orientation.
#' @param file file name of the NIfTI file. 
#' @param ... Arguments to pass to \code{\link{readnii}}
#' @param verbose print diagnostics, passed to \code{\link{rpi_orient_file}}
#' @export
#' @examples 
#' if (have.fsl()){
#' print(fsl_version())
#' in_ci <- function() {
#'  nzchar(Sys.getenv("CI"))
#'  }
#'  if (in_ci()) {
#'  destfile = tempfile(fileext = ".nii.gz")
#'  url = paste0("https://ndownloader.figshare.com/", 
#'  "files/18068546")
#'  old_url = paste0("https://github.com/muschellij2/", 
#'  "Neurohacking/files/3454385/113-01-MPRAGE2.nii.gz")
#'  dl = tryCatch(download.file(url,
#'  destfile = destfile))
#'  if (inherits(dl, "try-error") || dl != 0) {
#'  dl = download.file(old_url, destfile = destfile)
#'  }
#'  res = readrpi(destfile)
#'  }
#'  }   
readrpi <- function(file, ..., verbose = TRUE) {
  args = list(...)
  n_args = names(args)
  if ("fname" %in% n_args) {
    stop("fname cannot be specified in readrpi!")
  }
  
  L = rpi_orient_file(file = file, verbose = verbose)
  file = L$img
  nim = readnii(fname = file, ...)
  return(nim)
}