#' @title Use Freesurfers MRI Mask
#' @description This function calls \code{mri_mask} to mask an image
#' @param file (character) input filename
#' @param mask (character) mask filename
#' @param outfile (character) output filename
#' @param retimg (logical) return image of class nifti
#' @param opts (character) additional options to \code{mri_mask}
#' @param ... additional arguments passed to \code{\link{fs_cmd}}.
#' @return Character or nifti depending on \code{retimg}
#' @export
#' @examples
#' if (have_fs()) {
#' img = oro.nifti::nifti(array(rnorm(5*5*5), dim = c(5,5,5)))
#' mask = img > 1
#' res = mri_mask(img, mask)
#' }
mri_mask = function(file,
mask,
outfile = NULL,
retimg = TRUE,
opts = "",
...){
mask = checkimg(mask)
res = fs_cmd(
func = "mri_mask",
file = file,
outfile = outfile,
frontopts = opts,
opts = mask,
retimg = retimg,
samefile = FALSE,
...)
return(res)
}
#' @title MRI Normalize Help
#' @description This calls Freesurfer's \code{mri_mask} help
#'
#' @return Result of \code{fs_help}
#' @export
mri_mask.help = function(){
fs_help(func_name = "mri_mask")
}
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