Registration to a Template

Source: R/T1_Registration_function.R

This function performs registration to a template using ANTsR and SyN transformation, carry out the transformation on other images, and can back-transform atlases in template space to the native space of the iimage

ants_regwrite(
  filename,
  skull_strip = FALSE,
  correct = FALSE,
  correction = "N3",
  retimg = TRUE,
  outfile = NULL,
  template.file = file.path(fsldir(), "data", "standard", "MNI152_T1_1mm_brain.nii.gz"),
  interpolator = "Linear",
  other.files = NULL,
  other.outfiles = NULL,
  native.cereb = FALSE,
  native.fname = NULL,
  atlas.file = NULL,
  typeofTransform = "SyN",
  remove.warp = TRUE,
  outprefix = NULL,
  bet.opts = "-B -f 0.1 -v",
  betcmd = "bet",
  verbose = TRUE,
  reproducible = TRUE,
  seed = 1,
  ...
)

Arguments

filename

filename of T1 image
skull_strip

do skull stripping with FSL BET
correct

do Bias correction
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 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
native.cereb

Logical indicating if native cerebellum should be created to native.fname
native.fname

filename of native cerebellum file
atlas.file

Filename of atlas used for warping labels
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
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 antsRegistration

Value

NULL or object of class nifti for transformed T1 image