R/ants_pipeline.R

In muschellij2/ENARSC2015: ENAR 2015 Short Course

#' @title ANTS Analysis Pipeline
#'
#' @description Run my analysis pipeline
#' @param t1 filename of T1 Image
#' @param t2 filename of T2 Image
#' @param flair filename of FLAIR Image
#' @param pd filename of PD Image
#' @param bias_correction Should Bias correction be done? 
#' @param ... pass to other stuff
#' @export
#' @return Stuff
ants_pipeline = function(t1, # filename of T1 Image
                         t2, # filename of T2 Image
                         flair, # filename of FLAIR Image
                         pd, # filename of PD Image
                         bias_correction = TRUE,
                         ...
){
  
  outdir = "~/Desktop/results"
  outdir = path.expand(outdir)
  
  options(fsl.path="/usr/local/fsl")
  
  # Data taken from http://www.osirix-viewer.com/datasets/
  
  #   outfile = file.path(outdir, paste0(nii.stub(imgs, bn=TRUE), "_N3Correct"))
  dicom_path = system.file("FLAIR_DICOM/Brainix", package="ENARSC2015")
  outfile = file.path(outdir, "FLAIR_NIfTI")
  img = dcm2nii(dicom_path, retimg = FALSE, outfile = outfile)
  
  bias_file = paste0(outfile, "_ANTS_N3Correct")
  
  bias_correct(file=outfile, outfile=bias_file)  
  
  ext = get.imgext()
  seg_file = paste0(bias_file, "_seg", ext)
  file.remove(seg_file)
  
  bias_file = paste0(bias_file, "_restore")
  
}