fsl_deface: Tool to deface a structural T1w image.

In muschellij2/fslr: Wrapper Functions for 'FSL' ('FMRIB' Software Library) from Functional MRI of the Brain ('FMRIB')

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)
}

muschellij2/fslr documentation built on Aug. 31, 2022, 8:47 p.m.