#' @title Convert AFNI File to NIFTI Image
#' @description Converts an AFNI file to an NIfTI file or \code{nifti}
#' using \code{3dAFNItoNIFTI}
#' @param file AFNI BRIK or HEAD file
#' @param outfile output filename or prefix. The default is to always use
#' \code{.nii.gz} extensions and will override if \code{outfile} has a
#' \code{.nii} extension.
#' @param opts Additional options to pass to \code{3dAFNItoNIFTI}
#' @param float Should the \code{-float} option be called in
#' \code{3dAFNItoNIFTI}
#' @param retimg Should an image be returned?
#' @param ... additional arguments to \code{\link{readnii}}
#'
#' @return If \code{retimg} then object of class nifti. Otherwise,
#' the \code{outfile} argument is returned (or a temporary filename)
#' @export
afni_3dAFNItoNIFTI = function(
file,
outfile = NULL,
opts = "",
float = TRUE,
retimg = TRUE,
...) {
func = "3dAFNItoNIFTI"
if (is.null(outfile)) {
outfile = tempfile(fileext = ".nii.gz")
}
if (float) {
opts = paste0(opts, " -float")
}
outfile = paste0(nii.stub(outfile), ".nii.gz")
opts = paste0(opts, " -prefix ", outfile)
res = afni_cmd(
file = file,
func = func,
frontopts = opts,
opts = "",
outfile = NULL,
samefile = TRUE,
quote_outfile = FALSE,
retimg = FALSE
)
if (res != 0) {
warning(paste0("Result does not indicate success ",
"- function may not work as expected!"))
}
if (retimg) {
img = readnii(outfile,
...)
} else {
img = outfile
}
attr(img, "afni_version") = afni_version()
return(img)
}
#' @rdname afni_3dAFNItoNIFTI
#' @export
afni_to_nifti = function(...) {
afni_3dAFNItoNIFTI(...)
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.