#' @title AFNI 3dABoverlap function
#' @description Wrapper for AFNI \code{3dABoverlap} function
#'
#' @param file1 nifti object or NIfTI filename for overlap
#' @param file2 nifti object or NIfTI filename for overlap
#' @param automask if \code{TRUE}, \code{automask} is run on the files.
#' If \code{FALSE}, consider input datasets as masks
#' (automask does not work on mask datasets)
#' @param ... not used
#'
#' @return Output filename of the brik
#' @export
afni_3dABoverlap = function(
file1, #source
file2,
automask = TRUE) {
func = "3dABoverlap"
cmd = get_afni()
cmd <- paste0(cmd, func)
file1 = checkimg(file1, allow_array = FALSE)
file2 = checkimg(file2, allow_array = FALSE)
opts = ""
if (!automask) {
opts = c(opts, "-no_automask")
}
opts = trimws(opts)
opts = opts[ opts != "" ]
opts = paste(opts, collapse = " ")
cmd = paste(cmd, opts, file1, file1)
res = system(cmd, intern = TRUE)
# res = res[seq(2, length(res))]
return(res)
}
#' @rdname afni_3dABoverlap
#' @export
ABoverlap = function(...) {
afni_3dABoverlap(...)
}
#' @rdname afni_3dABoverlap
#' @export
aboverlap = function(...) {
afni_3dABoverlap(...)
}
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