Registration Wrapper function — registration • extrantsr

This function performs registration using ANTsR, carries out the transformation on other images, and can back-transform image in registered space to the native space of the original image. Returns the transforms

registration(
  filename,
  skull_strip = FALSE,
  correct = FALSE,
  correction = "N4",
  retimg = TRUE,
  outfile = NULL,
  template.file = file.path(fsldir(), "data", "standard", "MNI152_T1_1mm_brain.nii.gz"),
  interpolator = "Linear",
  other_interpolator = interpolator,
  other.files = NULL,
  other.outfiles = NULL,
  other.init = NULL,
  invert_interpolator = interpolator,
  invert.native.fname = NULL,
  invert.file = NULL,
  typeofTransform = "SyN",
  remove.warp = FALSE,
  outprefix = NULL,
  bet.opts = "-B -f 0.1 -v",
  betcmd = "bet",
  copy_origin = TRUE,
  verbose = TRUE,
  reproducible = TRUE,
  seed = 1,
  force_registration = TRUE,
  ...
)

Arguments

filename	filename of image to be registered
skull_strip	do skull stripping with FSL BET
correct	do bias correction on the filename
correction	N3 or N4 correction, see `bias_correct`
retimg	return a nifti object from function
outfile	output filename should have .nii or .nii.gz extension
template.file	Filename of image to warp to
interpolator	interpolation done for `antsApplyTransforms`
other_interpolator	interpolation done for `antsApplyTransforms` for `other.files`
other.files	Filenames of other iamges to be transformed with the T1
other.outfiles	Output filenames of `other.files` to be written
other.init	Initial transformation lists (same length as `other.files`) to use in before the estimated transformation for one interpolation
invert_interpolator	interpolation done for `antsApplyTransforms` for `invert.file`
invert.native.fname	filename of output native file, must have same length as `invert.file` or be `NULL`.
invert.file	Filename of image to invert to native space
typeofTransform	type of transformed used, passed to `antsRegistration`
remove.warp	(logical) Should warping images be deleted?
outprefix	Character path of where the warp files should be stored. Required if `remove.warp = FALSE`
bet.opts	Options passed to `fslbet`
betcmd	BET command used, passed to `fslbet`
copy_origin	Copy image origin from t1, using `antsCopyOrigin`
verbose	Print diagnostic messages
reproducible	Sets the seed and `Sys.setenv(ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS = 1)`. See https://github.com/ANTsX/ANTs/wiki/antsRegistration-reproducibility-issues for discussion.
seed	will execute `Sys.setenv(ANTS_RANDOM_SEED = seed)` before running to attempt a more reproducible result. If `NULL`, will not set anything, but `reproducible` must be `FALSE`.
force_registration	If `TRUE`, then registration will be run even if transforms exist.
...	arguments to `antsRegistration`

Value

List of the output filenames and transformations