ants_regwrite: Registration to a Template

Description Usage Arguments Value

View source: R/T1_Registration_function.R

Description

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

Usage

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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


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