fsl_deface {fslr}

Tool to deface a structural T1w image.

Description

Tool to deface a structural T1w image.

Usage

fsl_deface(
  file,
  outfile = NULL,
  retimg = TRUE,
  opts = "",
  deface_cropped = FALSE,
  bet_fractional_intensity = NULL,
  bias_correct = FALSE,
  shift_xyz = NULL,
  cog_xyz = NULL,
  reorient = FALSE,
  intern = FALSE,
  verbose = TRUE,
  ...
)

Arguments

file

(character) input image to estimate edge strength

outfile

(character) resultant image name (optional)

retimg

(logical) return image of class nifti

opts

(character) operations to be passed to fsl_deface

deface_cropped

apply the defacing to the cropped image instead of the original image

bet_fractional_intensity

fractional intensity for bet (0->1); default=0.5;

bias_correct

Bias-correct the input image (with fast);

shift_xyz

Shift, in mm, x-, y- and z-directions, to shift face mask by;

cog_xyz

centre-of-gravity for bet (voxels, not mm);

reorient

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

intern

(logical) to be passed to system

verbose

print diagnostic messages

...

additional arguments passed to fslcmd.

Examples

if (have_fsl()) {
  file = mni_fname(mm = 1, brain = FALSE)
  out = fsl_deface(file, retimg = FALSE)
}