remove_neck: Remove Neck from Image

In muschellij2/extrantsr: Extra Functions to Build on the 'ANTsR' Package

Remove Neck from Image

Description

Removes the neck from axially acquired scan so skull stripping can be done.

Usage

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

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.
ret_mask	Return mask of slices to keep
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
...	Additional arguments passed to ants_regwrite

Value

Object of class nifti or vector of indices

Examples

if (fslr::have.fsl()){
  print(fslr::fsl_version())
  in_ci <- function() {
    nzchar(Sys.getenv("CI"))
  }
  if (in_ci()) {
    destfile = tempfile(fileext = ".nii.gz")
    dl = download.file(paste0(
      "https://github.com/muschellij2/",
      "Neurohacking/files/3454385/113-01-MPRAGE2.nii.gz"),
      destfile = destfile)
    tfile = fslr::mni_fname(brain = TRUE)
    if (file.exists(tfile)) {
      res = remove_neck(
        destfile, 
        template.file = tfile,
        template.mask = fslr::mni_fname(brain = TRUE, mask = TRUE)
      )
    }
  }
}

muschellij2/extrantsr documentation built on June 3, 2024, 7:04 p.m.