Within Visit Registration

Source: R/preprocess_mri_within.R

This function performs skull stripping of the first image, within-visit registration using a rigid-body transformation, inhomogeneity correction, and potentially re-correcting after skull stripping.

preprocess_mri_within(
  files,
  outfiles = NULL,
  correct = TRUE,
  correction = "N4",
  retimg = FALSE,
  reorient = FALSE,
  typeofTransform = "Rigid",
  interpolator = "LanczosWindowedSinc",
  skull_strip = FALSE,
  bet.opts = "-B -f 0.1 -v",
  betcmd = "bet",
  maskfile = NULL,
  correct_after_mask = FALSE,
  verbose = TRUE,
  ...
)

Arguments

files

filenames (or nifti objects) of images to be processed. Will register to the first scan
outfiles

(character) name of output files, with extension
correct

do Bias field correction
correction

(character) N3 or N4 correction?
retimg

(logical) return list of images of class nifti
reorient

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

type of transformed used, passed to antsRegistration
interpolator

Interpolation to be performed, passed to antsRegistration
skull_strip

do Skull stripping with FSL BET
bet.opts

Options to pass to fslbet
betcmd

Command to pass to fslbet
maskfile

Filename (or nifti object) of mask for image to be registered to
correct_after_mask

Should the inhomogeneity correction be run after masking. If correct = FALSE, then
verbose

Diagnostic messages
...

arguments to bias_correct or within_visit_registration

Value

List of outfiles, maskfile, and output from registration.