ear_mask: Create Mask of the Ears

In neuroconductor/ichseg: Intracerebral Hemorrhage Segmentation of X-Ray Computed Tomography (CT) Images

Description

Creates a rough mask of the ear from a head scan

Usage

ct_ear_mask(
  file,
  skull_strip = TRUE,
  mask = NULL,
  robust = TRUE,
  template.file = system.file("scct_unsmooth_SS_0.01.nii.gz", package = "ichseg"),
  template.ear_mask = NULL,
  template.left_ear_inds = list(170:180, 60:110, 1:60),
  template.right_ear_inds = list(1:10, 60:110, 1:60),
  extend_left = TRUE,
  extend_right = TRUE,
  typeofTransform = "Affine",
  swapdim = TRUE,
  verbose = TRUE,
  ...
)

mri_ear_mask(
  ...,
  skull_strip = TRUE,
  mask = NULL,
  robust = FALSE,
  template.file = mni_fname(brain = skull_strip)
)

Arguments

file	File for face masking - either filename or class nifti
skull_strip	Should the data require skull stripping if no mask is provided?
mask	file or nifti to mask the file
robust	If mask = NULL, then robust is passed to CT_Skull_Stripper
template.file	Template to warp to original image space
template.ear_mask	Mask of template to use as rough ear mask. If template.file is not specified, template.left_ear_inds and template.right_ear_inds must be
template.left_ear_inds	List of length 3 for indices of template.file to indicate the left-ear mask.
template.right_ear_inds	List of length 3 for indices of template.file to indicate the right-ear mask.
extend_left	after transformation, should the mask be extended to the left of the image to ensure all left ear has been removed?
extend_right	after transformation, should the mask be extended to the right of the image to ensure all right ear has been removed?
typeofTransform	Transformation for template to image, passed to ants_regwrite.
swapdim	Should the dimensions be swapped before registration, and then reset after
verbose	Print out diagnostic messages
...	arguments passed to CT_Skull_Stripper

Value

Object of class nifti

Examples

## Not run: 
file = "~/Desktop/Desktop/scratch/100-318_20070723_0957_CT_3_CT_Head-.nii.gz"
mask = NULL
robust = FALSE
ears = ct_ear_mask(
   file = file,
   robust = FALSE
 )
 img = readnii(file)
 rimg = randomize_mask(img, mask = ears)

## End(Not run)

neuroconductor/ichseg documentation built on Sept. 29, 2020, 2:31 p.m.