fslr (version 1.3)

fslbet: Use FSL's Brain Extraction Tool (BET)

Description

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

Usage

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

Arguments

infile

(character) input filename

outfile

(character) output filename

retimg

(logical) return image of class nifti

reorient

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

intern

(logical) pass to system

opts

(character) additional options to FLIRT

betcmd

(character) Use bet or bet2 function

verbose

(logical) print out command before running

...

additional arguments passed to readNIfTI.

Value

• character or logical depending on intern