Robust Brain Mask from Template

Source: R/robust_brain_mask.R

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.

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