#' CT DICOM to NIfTI conversion

#'

#' @param basedir (character) directory to get files

#' @param merge_files Should files be merged, passed do \code{\link{dcm2nii}}

#' options

#' @param verbose print diagnostic messages

#' @param drop_dim passed to \code{\link{readnii}} for dropping empty

#' dimensions

#' @param ... Additional parameters passed to \code{\link{dcm2nii}}

#' @param ignore_roi_if_multiple additional argument to pass to

#' \code{\link{check_dcm2nii}} to remove ROI overlays if present

#'

#' @return A list or singular \code{nifti} image

#' @export

#'

#' @importFrom dcm2niir dcm2nii check_dcm2nii

#' @importFrom neurobase rescale_img check_nifti

ct_dcm2nii = function(basedir = ".", merge_files = TRUE,

                      verbose = TRUE,

                      drop_dim = TRUE, ...,

                      ignore_roi_if_multiple = FALSE,

                      fail_on_error = FALSE) {

  if (!merge_files) {

    warning(

      paste0(

      "ichseg < v0.19.0 had overridden merge_files = FALSE (bug),",

      " please be aware for reproducibility."

      )

    )

  }

  out = dcm2nii(basedir, merge_files = merge_files, verbose = verbose,

                ...)

  if (fail_on_error && out$result > 0) {

    stop("Error in result from dcm2nii and fail_on_error = TRUE")

  }

  res = check_dcm2nii(out, ignore_roi_if_multiple = ignore_roi_if_multiple)

  img = lapply(res, function(x){

    if (verbose) {

      message("# reading in image")

    }

    img = check_nifti(res, drop_dim = drop_dim)

    if (verbose) {

      message("# rescaling data")

    }

    img = rescale_img(img, min.val = -1024,

                      max.val = 3071,

                      drop_dim = drop_dim)

  })

  if (length(res) == 1) {

    img = img[[1]]

  }

  attr(img, "dcm2nii_result") = out$result

  return(img)

}