R/timeseriesN3.R

In stnava/ANTsR: ANTs in R: Quantification Tools for Biomedical Images

#' Run N3 on slices of timeseries.
#'
#' Repeatedly run N3 on slices of time series and return image
#'
#'
#' @param boldimg input matrix
#' @param mask mask to use
#' @param ncorrections levels at which to apply n3
#' @return antsImage is output
#' @author Avants BB
#' @examples
#'
#' bold <- makeImage(c(10, 10, 10, 4), rnorm(4000))
#' mask <- getMask(getAverageOfTimeSeries(bold))
#' boldn3 <- timeseriesN3(bold, mask, c(4, 2))
#'
#' @export timeseriesN3
timeseriesN3 <- function(boldimg, mask, ncorrections = c(2, 2)) {
  dim <- 4
  ismatrix <- TRUE
  if ("antsImage" %in% class(boldimg)) {
    dim <- boldimg@dimension
    if (dim != 4) {
      return(NA)
    }
    mat <- timeseries2matrix(boldimg, mask)
    ismatrix <- FALSE
  }
  if ("matrix" %in% class(boldimg)) {
    mat <- boldimg
  }
  for (i in 1:nrow(mat)) {
    perf <- makeImage(mask, mat[i, ])
    for (nc in ncorrections)
    {
      perf <- n3BiasFieldCorrection(perf, as.numeric(nc))
    }
    mat[i, ] <- perf[mask >= 1]
  }
  if (ismatrix) {
    return(mat)
  }
  if (!ismatrix) {
    return(matrix2timeseries(boldimg, mask, mat))
  }
}