R/ants_brain_extraction.R

In neuroconductor-devel/ANTsR: ANTs in R: Quantification Tools for Biomedical Images

.ants_brain_extraction <- function(img) {
  # # check if called with no arguments and print usage
  # if (nchar(img) == 0) {
  #   print("usage: ants_brain_extraction( <time-series-average-image> )")
  #   return
  # }
  # 
  # # check if there is an extension
  # if (length(strsplit(img, ".", fixed = TRUE)[[1]]) < 2) {
  #   print("There appears to be no extension to the input file. Please provide a [nii|nii.gz] file.")
  #   return
  # }
  # 
  # # split the string into filename and extension
  # split_img <- strsplit(img, ".", fixed = TRUE)[[1]]
  # filename <- split_img[1]
  # if (length(split_img) == 2) {
  #   extension <- paste("", split_img[2], sep = ".")
  # } else if (length(split_img) == 3) {
  #   extension <- paste("", split_img[2], split_img[3], sep = ".")
  # }
  # 
  # bm_img <- paste(filename, "_brainmask", extension, sep = "")
  # 
  # # N3BiasFieldCorrection( 3 , img , img , 2 ) ; for( x in 1:3 ) {
  # # N3BiasFieldCorrection( 3 , img , img , 1 ) ; }

  bm_img = thresholdImage( img, "Otsu", 3 )
  bm_img = thresholdImage( bm_img,  2, 3 )
  bm_img = iMath(bm_img, "ME", 1)
  bm_img = iMath(bm_img, "GetLargestComponent")
  bm_img = iMath(bm_img, "MD", 1)
  bm_img = iMath(bm_img, "ME", 1)
  return(bm_img)
}