preprocess_mri_within: Within Visit Registration

In neuroconductor/extrantsr: Extra Functions to Build on the 'ANTsR' Package

Description

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.

Usage

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.

neuroconductor/extrantsr documentation built on Sept. 28, 2020, 11:31 a.m.