reg_whitestripe: WhiteStripe Normalization

In neuroconductor-releases/extrantsr: Extra Functions to Build on the 'ANTsR' Package

Description

This function performs registration to a T1 template using ANTsR and SyN transformation

Usage

reg_whitestripe(t1 = NULL, t2 = NULL, 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", type = c("T1", "T2", "hybrid"),
  t1.outfile = NULL, t2.outfile = NULL, other.files = NULL,
  other.outfiles = NULL, ws.outfile = NULL, mask = NULL,
  mask.outfile = NULL, verbose = TRUE, reproducible = TRUE,
  seed = 1, ...)

Arguments

t1	filename (or nifti objects) of T1 image
t2	filename (or nifti objects) of T2 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
type	Type of whitestripe normalization done
t1.outfile	Output filename of normalized T1 image
t2.outfile	Output filename of normalized T2 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.
ws.outfile	Character filename for output whitestripe mask.
mask	File or nifti image of brain mask
mask.outfile	Character filename for output brain mask.
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.
...	arguments to whitestripe or whitestripe_hybrid

Value

List of nifti objects or character filenames

neuroconductor-releases/extrantsr documentation built on Dec. 10, 2019, 12:07 a.m.