brain_extract: Wrapper for ANTs brain extraction

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

Description

This function wraps abpN4 and abpBrainExtraction for nifti images with additional checks

Usage

brain_extract(img, template, template.mask, typeofTransform = c("SyNabp",
  "SyN"), correct = TRUE, reproducible = TRUE, seed = 1, ...)

Arguments

img	Image for brain extraction, nifti, character or antsImage
template	Template image with mask, nifti, character or antsImage
template.mask	Template brain mask
typeofTransform	registration type: 'SyNabp' (better, slower), 'SyN' (fast)
correct	Should abpN4 be performed first?
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.
...	additional arguments passed to abpBrainExtraction

Value

A list of the brain image, brain mask, k-means segmentation, and transformations.

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