Executes Robust Brain Extraction

robex(infile, outfile = tempfile(fileext = ".nii.gz"), verbose = TRUE,
  ...)

Arguments

infile	Input filename
outfile	Output skull-stripped file
verbose	print diagnostic messages
...	arguments to be passed to `system`

Value

List of result of system command, names of input and output file

Examples

result = robex(infile = "", outfile = "")
#> ./ROBEX  
#> Warning: ROBEX result indicated an error!  Please check resutls.
#> Warning: ROBEX result image not found!  Please check resutls.

if (requireNamespace("kirby21.t1", quietly = TRUE)) {
   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)
   }
   if (!is.null(infile)) {
     if (file.exists(infile)) {
       result = robex(infile = infile)
       stopifnot(file.exists(result$outfile))
     }
   }
}
#> cloning into '/tmp/Rtmput3AXv/file6dcb32b8d16/kirby21.t1'...
#> Receiving objects:   1% (2/117),    8 kb
#> Receiving objects:  11% (13/117),    8 kb
#> Receiving objects:  21% (25/117),    8 kb
#> Receiving objects:  31% (37/117),    8 kb
#> Receiving objects:  41% (48/117), 7510 kb
#> Receiving objects:  51% (60/117), 38690 kb
#> Receiving objects:  61% (72/117), 46544 kb
#> Receiving objects:  71% (84/117), 46544 kb
#> Receiving objects:  81% (95/117), 46544 kb
#> Receiving objects:  91% (107/117), 46544 kb
#> Receiving objects: 100% (117/117), 46544 kb, done.
#> Warning: path[1]="/tmp/Rtmput3AXv/file6dcb1428708d.nii.gz": No such file or directory
#> ./ROBEX '/tmp/Rtmput3AXv/visit_1/113/113-01-T1.nii.gz' '/tmp/Rtmput3AXv/file6dcb1428708d.nii.gz'