R/antsMotionCorr.R

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

#' Motion Correction
#'
#' This program is a user-level registration application meant to utilize
#' ITKv4-only classes. The user can specify any number of \emph{stages} where a
#' \emph{stage} consists of -- a transform, an image metric, number of
#' iterations, shrink factors, and smoothing sigmas for each level. Specialized
#' for 4D time series data: fixed image is 3D, moving image should be the 4D
#' time series. Fixed image is a reference space or time slice.
#'
#' @param paramList antsMotionCorr parameters, as in ANTs. this is a direct call to
#' the low level \code{c++} and as such has non-standard parameters.
#' @return 0 -- Success\cr 1 -- Failure
#' @author Shrinidhi KL
#'
#' @note This function may give different results on multiple runs.
#'
#' @examples
#'
#' # boldfn <- getANTsRData( "pcasl" )
#' # bold <- antsImageRead( boldfn , 4 )
#' set.seed(123)
#' bold <- makeImage(c(10, 10, 10, 20), rnorm(10 * 10 * 10 * 20) + 1)
#' bold <- iMath(bold, "PadImage", 5)
#' aimg <- new("antsImage", "float", 3)
#' aimg <- new("antsImage", "float", 3)
#' mocoImg <- new("antsImage", "float", 4)
#' mocoParams <- new("antsMatrix", "double")
#' antsMotionCorr(list(d = 3, a = bold, o = aimg))
#' aimg2 <- new("antsImage", "float", 3)
#' antsMotionCorr(list(d = 3, a = bold, o = aimg2))
#' antsMotionCorr(list(
#'   d = 3,
#'   o = list(mocoParams, mocoImg, aimg),
#'   m = list(name = "MI", aimg, bold, 1, 32, "Regular", 0.1),
#'   t = "Rigid[0.01]", i = 25,
#'   u = 1, e = 1, s = 0, f = 1, n = 25
#' ))
#' motiondf <- as.data.frame(mocoParams)
#'
#' @export antsMotionCorr
antsMotionCorr <- function(paramList) {
  returnval <- ANTsRCore::antsMotionCorr(.int_antsProcessArguments(paramList))
}