reg_flip: Flip Image with Registration
In neuroconductor/extrantsr: Extra Functions to Build on the 'ANTsR' Package

This function performs registration to a template using ANTsR and will run fslswapdim

reg_flip(
  t1,
  register = TRUE,
  native = TRUE,
  template.file = file.path(fsldir(), "data", "standard", paste0("MNI152_T1_1mm",
    ifelse(is.null(mask), "", "_brain"), ".nii.gz")),
  typeofTransform = c("Rigid", "Affine"),
  interpolator = "LanczosWindowedSinc",
  t1.outfile = NULL,
  other.files = NULL,
  other.outfiles = NULL,
  mask = NULL,
  mask.outfile = NULL,
  verbose = TRUE,
  a = "-x",
  b = "y",
  c = "z",
  reproducible = TRUE,
  seed = 1,
  ...
)

`t1`	filename (or nifti objects) of T1 image
`register`	Register image to template file
`native`	If images are registered, should the native space normalized image be returned?
`template.file`	Filename of template to warp to
`typeofTransform`	type of transformed used, passed to `antsRegistration`
`interpolator`	Interpolation to be performed, passed to `antsRegistration`
`t1.outfile`	Output filename of normalized T1 image
`other.files`	Character filenames or list of nifti objects to normalize. In the same space as T1.
`other.outfiles`	Character filenames for output normalized files.
`mask`	File or nifti image of brain mask
`mask.outfile`	Character filename for output brain mask.
`verbose`	Print Diagnostic Messages
`a`	Option for x domain in `fslswapdim`
`b`	Option for y domain in `fslswapdim`
`c`	Option for z domain in `fslswapdim`
`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`.
`...`	arguments to `fslswapdim`