Remove Neck Twice from a Scan

Source: R/remove_neck.R

Wrapper for running remove_neck twice, as some images require this if large number of slices of the neck or upper shoulders were scanned

double_remove_neck(
  file,
  template.file,
  template.mask,
  typeofTransform = "Rigid",
  rep.value = 0,
  swapdim = TRUE,
  verbose = TRUE,
  ret_mask = FALSE,
  ...
)

Arguments

file

File for neck removal - 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.
typeofTransform

Transformation for template to image, passed to ants_regwrite.
rep.value

Value to replace neck slices with
swapdim

Should the dimensions be swapped before registration, and then reset after
verbose

Print out diagnostic messages
ret_mask

Should the mask be returned vs. the image?
...

Additional arguments passed to remove_neck

Value

Object of class nifti