In muschellij2/robex: Robust Brain Extraction ('ROBEX')

Here we will skull strip an image using ROBEX (Robust Brain Extraction). First, let's load in the packages.

library(robex)
library(kirby21.t1)
library(neurobase)

The kirby21.t1 package downloads or loads T1-weighted iamges. Here we will load a filename into the file infile:

infile = kirby21.t1::get_t1_filenames(id = "113", visit = 1)
if (is.null(infile)) {
  infile = ""
}
if (!file.exists(infile)) {
  outdir = tempdir()
  try({kirby21.t1::download_t1_data(outdir = outdir)})
  infile = kirby21.t1::get_t1_filenames(
    id = "113", visit = 1,
    outdir = outdir)
}

We will read in the file using neurobase:

img = readnii(infile)
ortho2(img)

We will then run robex::robex to perform the skull stripping

if (!is.null(infile)) {
  if (file.exists(infile)) {
    result = robex(infile = infile)
    stopifnot(file.exists(result$outfile))
  }
}
print(result)

output = readnii(result$outfile)
ortho2(output)
double_ortho(img, output)
ortho2(robust_window(img), output > 0)

muschellij2/robex documentation built on April 4, 2021, 5:49 p.m.