registration: Registration Wrapper function
In neuroconductor/extrantsr: Extra Functions to Build on the 'ANTsR' Package

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,
  ...
)

`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`