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#' @title Binarize Image using FSL
#' @description This function calls \code{fslmaths -bin}. The R functions wraps
#' \code{fslmaths}
#' @param file (character) image to be binarized
#' @param outfile (character) resultant image name (optional)
#' @param retimg (logical) return image of class nifti
#' @param reorient (logical) If retimg, should file be reoriented when read in?
#' Passed to \code{\link{readnii}}.
#' @param intern (logical) to be passed to \code{\link{system}}
#' @param opts (character) operations to be passed to \code{fslmaths}
#' @param ... additional arguments passed to \code{\link{readnii}}.
#' @return If \code{retimg} then object of class nifti. Otherwise,
#' Result from system command, depends if intern is TRUE or FALSE.
#' @export
#' @examples
#' set.seed(5)
#' dims = rep(10, 3)
#' arr = array(rnorm(prod(dims)), dim = dims)
#' nim = oro.nifti::nifti(arr)
#' if (have.fsl()){
#' fslbin(nim)
#' fsl_bin(nim)
#' }
#'
fslbin = function(
file,
outfile=NULL,
retimg = TRUE,
reorient = FALSE,
intern = FALSE,
opts = "",
...){
all.opts = paste("-bin ", opts, collapse = " " )
res = fslmaths(file = file, outfile = outfile,
retimg = retimg, reorient = reorient,
intern = intern, opts = all.opts, ...)
return(res)
}
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