R/mri_watershed.R

In freesurfer: Wrapper Functions for 'Freesurfer'

#' @title Use Freesurfers MRI Watershed Algorithm
#' @description This function calls \code{mri_watershed} to extract a brain 
#' from an image, usually for skull stripping.
#' @param file (character) input filename
#' @param outfile (character) output filename
#' @param retimg (logical) return image of class nifti
#' @param opts (character) additional options to \code{mri_watershed}
#' @param ... additional arguments passed to \code{\link{fs_cmd}}.
#' @return Character or nifti depending on \code{retimg}
#' @export
#' @examples \dontrun{
#' if (have_fs()){
#'     mri_watershed("/path/to/T1.nii.gz")
#' } 
#' }  
mri_watershed = function(file, 
                         outfile = NULL,                  
                         retimg = TRUE,
                         opts="", 
                         ...){
  res = fs_cmd(
    func = "mri_watershed",
         file = file,
         outfile = outfile,
         frontopts = opts,
         retimg = retimg,
         samefile = FALSE,
         ...)
  return(res)
}


#' @title MRI Watershed Help
#' @description This calls Freesurfer's \code{mri_watershed} help 
#'
#' @return Result of \code{fs_help}
#' @export
mri_watershed.help = function(){
  fs_help(func_name = "mri_watershed")
}