oasis: OASIS Processing Pipeline
In muschellij2/extrantsr: Extra Functions to Build on the 'ANTsR' Package

This function performs registration to a T1 template using ANTsR transformation

oasis(
  filename,
  skull_strip = TRUE,
  skull_stripfile = NULL,
  correct = TRUE,
  normalize = TRUE,
  normalize_file = NULL,
  retimg = TRUE,
  outfile = NULL,
  template.file = file.path(fsldir(), "data", "standard", "MNI152_T1_1mm_brain.nii.gz"),
  interpolator = "LanczosWindowedSinc",
  other.files = NULL,
  other.outfiles = NULL,
  typeofTransform = "Rigid",
  remove.warp = TRUE,
  outprefix = NULL,
  bet.opts = "-B -f 0.1 -v",
  betcmd = "bet",
  reproducible = TRUE,
  seed = 1,
  ...
)

`filename`	filename of T1 image
`skull_strip`	do skull stripping with FSL BET
`skull_stripfile`	Output skull strip filename
`correct`	do N3 Bias correction
`normalize`	Normalize data using `whitestripe`
`normalize_file`	`whitestripe` image mask
`retimg`	return a nifti object from function
`outfile`	output filename should have .nii or .nii.gz extension
`template.file`	Filename of template to warp to
`interpolator`	interpolation done for `antsApplyTransforms`
`other.files`	Filenames of other iamges to be transformed with the T1
`other.outfiles`	Output filenames of `other.files` to be written
`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`
`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 `whitestripe`