R/spm12_realign_est.R

In spm12r: Wrapper Functions for 'SPM' (Statistical Parametric Mapping) Version 12 from the 'Wellcome' Trust Centre for 'Neuroimaging'

#' @title SPM12 Realign (Estimate)
#'
#' @description Performs SPM12 Realignment estimation on an Image
#' @param filename Files to be realigned
#' @param fwhm Full-Width Half Max to smooth
#' @param register_to Should the files be registered to the first 
#' or the mean
#' @param add_spm_dir Add SPM12 directory from this package
#' @param spmdir SPM dir to add, will use package default directory
#' @param clean Remove scripts from temporary directory after running
#' @param verbose Print diagnostic messages
#' @param outdir Directory to copy results.  
#' If full filename given, then results will
#' be in \code{dirname(filename)}
#' @param install_dir directory to download SPM12
#' 
#' @param ... Arguments passed to \code{\link{run_spm12_script}}
#' @export
#' @return Character list of filenames from output
spm12_realign_est <- function(
  filename,
  fwhm = 5,
  register_to = c("first", "mean"),
  add_spm_dir = TRUE,
  spmdir = spm_dir(verbose = verbose,
                   install_dir = install_dir),
  clean = TRUE,
  verbose = TRUE,
  outdir = NULL,
  install_dir = NULL,
  ...
){
  
  install_spm12(verbose = verbose,
                install_dir = install_dir)
  
  ########################
  # Getting Number of Time points
  ########################
  if (verbose) {
    message("# Getting Number of Time Points\n")
  }
  time_points = ntime_points(filename)
  
  # check filenames
  filename = filename_check(filename)
  stub = nii.stub(filename, bn = TRUE)[1]
  rpfile = file.path(
    dirname(filename),
    paste0("rp_", stub, ".txt"))
  #   meanfile = file.path(dirname(filename),
  #                        paste0("mean", stub, ".nii"))
  matfile = file.path(dirname(filename),
                      paste0(stub, ".mat"))
  
  ##########################################################
  # Pasting together for a 4D file
  ##########################################################
  filename = paste0(filename, ",", time_points)
  filename = rvec_to_matlabcell(filename)
  
  register_to = match.arg(register_to, c("first", "mean"))
  register_to = switch(register_to,
                       first = 0,
                       mean = 1)
  
  jobvec = c(filename, fwhm,
             register_to, spmdir)
  names(jobvec) = c("%filename%", "%fwhm%",
                    "%registerto%", "%spmdir%")
  
  res = run_spm12_script(
    script_name = "Realign_Estimate",
    jobvec = jobvec,
    mvec = NULL,
    add_spm_dir = add_spm_dir,
    spmdir = spmdir,
    clean = clean,
    verbose = verbose,
    ...)
  stopifnot(res == 0)
  ####################
  # Copy outfiles
  ####################
  if (!is.null(outdir)) {
    file.copy(rpfile, to = outdir, overwrite = TRUE)
    #     file.copy(meanfile, to = outdir, overwrite = TRUE)
    file.copy(matfile, to = outdir, overwrite = TRUE)
  }
  outfiles = c(rp = rpfile,
               #                mean = meanfile,
               mat = matfile)
  return(outfiles)
}