Bias Field Correct then Skull Strip

This function wraps fslbet and bias_correct, performing bias correction first

bias_ss(
  filename,
  maskfile = NULL,
  outfile = tempfile(fileext = ".nii.gz"),
  skull_strip = TRUE,
  bet.opts = "",
  betcmd = "bet",
  correct = TRUE,
  correction = "N3",
  shrinkfactor = "4",
  retimg = TRUE,
  reorient = FALSE,
  verbose = TRUE,
  ...
)

Arguments

filename	filename to be processed
maskfile	filename of masked to be passed in, otherwise bet is performed
outfile	output filename with extension (e.g. .nii.gz)s
skull_strip	should skull stripping be done
bet.opts	options for fslbet
betcmd	bet command to be used see fslbet
correct	should n3 correction be done stripping be done
correction	correction method used see bias_correct
shrinkfactor	correction method used see n3BiasFieldCorrection
retimg	(logical) return image of class nifti
reorient	(logical) If retimg, should file be reoriented when read in? Passed to readnii.
verbose	Diagnostic output
...	passed to bias_correct

Value

Filename of output file or object of class nifti

See also

ss_bias