brain_extract: Wrapper for ANTs brain extraction

Description Usage Arguments Value

View source: R/brain_extract.R

Description

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

Usage

1
2
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/extrantsr documentation built on Feb. 10, 2020, 5:11 p.m.