Flip Image with Registration

Source: R/reg_flip.R

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,
  ...
)

Arguments

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

Value

List of nifti objects or character filenames