Use FSL's Brain Extraction Tool (BET)

Source: R/fsl_bet.R, R/fslhd.R

This function calls bet to extract a brain from an image, usually for skull stripping.

fsl_bet(..., outfile = tempfile(fileext = ".nii.gz"), retimg = FALSE)

fslbet(
  infile,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  opts = "",
  betcmd = c("bet2", "bet"),
  verbose = TRUE,
  ...
)

Arguments

...

additional arguments passed to readnii.
outfile

(character) output filename
retimg

(logical) return image of class nifti
infile

(character) input filename
reorient

(logical) If retimg, should file be reoriented when read in? Passed to readnii.
intern

(logical) pass to system
opts

(character) additional options to bet
betcmd

(character) Use bet or bet2 function
verbose

(logical) print out command before running

Value

character or logical depending on intern

Note

Functions with underscores have different defaults and will return an output filename, so to be used for piping