#' @title Read in CT Template

#' @description Wrapper for returning a \code{nifti} object of the CT Template

#' @param ... Arguments passed to \code{\link{ct_template_fname}}

#'

#' @return Object of class \code{\link{nifti}}

#' @export

ct_template = function(...){

  fname = ct_template_fname(...)

  res = readnii(fname)

  return(res)

}

#' @title Get CT Template Filename

#' @description Wrapper for returning the filename of the CT Template

#' @param type Type of image.  \code{image} is the original image,

#' \code{brain} is the skull stripped image,

#' \code{mask} is brain mask. Values with \code{cormack} or \code{stripped}

#' are in 2 millimeter resolution, and smoothed.

#' @return Character filename

#' @export

#' @examples

#' types = c("brain", "mask", "image",

#' "cormack",

#' "stripped_cormack",

#' "stripped_hu",

#' "stripped_hu8")

#' sapply(types, ct_template_fname)

ct_template_fname = function(type = c("brain", "mask", "image",

                                      "cormack",

                                      "stripped_cormack",

                                      "stripped_hu",

                                      "stripped_hu8")){

  type = match.arg(type)

  if (type %in% c("cormack",

                  "stripped_cormack",

                  "stripped_hu",

                  "stripped_hu8")) {

    stub = paste0("scct_", type)

  } else {

    stub = "scct_unsmooth"

    brain = type %in% "brain"

    mask = type %in% "mask"

    if (brain | mask) {

      stub = paste0(stub, "_SS_0.01")

    }

    if (mask) {

      stub = paste0(stub, "_Mask")

    }

  }

  stub = paste0(stub, ".nii.gz")

  res = system.file(stub,

                    package = "ichseg")

  if (!file.exists(res)) {

    stop("Template File not found!")

  }

  return(res)

}