robust_brain_mask: Robust Brain Mask from Template

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

Description

Masks the brain from scan using a rigid body transformation of the template mask to the native brain space and then inflating the mask to adjust for mis-registration.

Usage

robust_brain_mask(file, template.file, template.mask = NULL,
  nvoxels = 7, ret_mask = FALSE, typeofTransform = "Rigid",
  verbose = TRUE, ...)

Arguments

file	File for masking - either filename or class nifti
template.file	Template to warp to original image space
template.mask	Mask of template to use as rough brain mask. If template.file is specified, but template.mask is not, then fslbin(file=template.file) is performed.
nvoxels	Number of voxels in nxnxn direction to inflate, see fslmaths.help for -kernel boxv n -dilM.
ret_mask	Return mask of robust brain
typeofTransform	Transformation for template to image, passed to ants_regwrite.
verbose	Print diagnostic progress
...	Arguments passed to ants_regwrite

Value

Object of class nifti or vector of indices

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