R/spm_probs_to_seg.R

In neuroconductor-devel/spm12r: Wrapper Functions for 'SPM' (Statistical Parametric Mapping) Version 12 from the 'Wellcome' Trust Centre for 'Neuroimaging'

#' @title SPM Probability to Hard Segmentation
#'
#' @description Converts probability images from SPM 
#' segmentation to a hard, choose-one segmentation
#' @param img list of images for probabilities for each class
#' @param ties.method a character string specifying how ties are handled.  
#' See \code{\link{max.col}}.  Note, order of ties is different than 
#' \code{\link{max.col}}.
#' @export
#' @return Object of class nifti
#' @examples \dontrun{
#' spm_seg = spm12_segment(image)$outfiles
#' seg = spm_probs_to_seg(spm_seg)
#'}
spm_probs_to_seg <- function(img,
                             ties.method = c("first", "last", "random") 
){
  stopifnot(inherits(img, "list"))
  xmax = sapply(img, c)
  ties.method = match.arg(
    ties.method, 
    c("first", "last", "random")
  )
  
  maxs = max.col(xmax, 
                 ties.method = ties.method)
  res = niftiarr(img[[1]], maxs)   
  res
}