Remove Neck from Image — remove

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

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)
      )
    }
  }
}