R/tracker.R

In neuroconductor-devel/freesurfer: Wrapper Functions for 'Freesurfer'

#' @title Tract Reconstruction Helper for trac-all from Freesurfer
#' @description Wrapper for the \code{trac-all} function in Freesurfer
#' 
#' @param infile Input filename (dcm or nii)
#' @param outdir Output directory
#' @param subjid subject id, if NULL, the basename of the infile will be used
#' @param verbose print diagnostic messages
#' @param opts Additional options
#'
#' @return Result of \code{\link{system}}
#' @export
tracker <- function(
  infile,
  outdir = NULL,
  subjid,
  verbose = TRUE,
  opts = ""
) {
  
  if (is.null(subjid)) {
    subjid = nii.stub(infile, bn = TRUE)
    subjid = file_path_sans_ext(subjid)
  }
  if (!is.null(infile)) {
    infile = checknii(infile)
    in_opts = paste0("-i ", infile)
  } else {
    in_opts = ""
  }
  
  if (!is.null(outdir)) {
    sd_opts = paste0(" -sd ", shQuote(outdir))
  } else {
    sd_opts = ""
  }
  
  opts = paste(
    in_opts,
    sd_opts,
    paste0(" -s ", subjid),
    opts)
  
  cmd = get_fs()
  cmd = paste0(cmd, "trac-all")
  cmd = paste(cmd, opts)
  if (verbose) {
    message(cmd, "\n")
  }
  res = system(cmd)
  return(res)
}