face_mask: Create Mask of the Face

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

Description

Creates a rough mask of the face from a head scan

Usage

ct_face_mask(
  file,
  skull_strip = TRUE,
  mask = NULL,
  robust = TRUE,
  template.file = system.file(ifelse(skull_strip, "scct_unsmooth_SS_0.01.nii.gz",
    "scct_unsmooth.nii.gz"), package = "ichseg"),
  template.face_mask = NULL,
  template.face_mask_inds = list(50:130, 170:217, 1:15),
  extend_mask = TRUE,
  typeofTransform = "Affine",
  swapdim = TRUE,
  verbose = TRUE,
  ...
)

mri_face_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.face_mask	Mask of template to use as rough face mask. If template.file is not specified, template.face_mask_inds must be
template.face_mask_inds	List of length 3 for indices of template.file to indicate the mask.
extend_mask	after transformation, should the mask be extended to the front of the image to ensure all face 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
face = ct_face_mask(
   file = file,
   robust = FALSE
   )
 img = readnii(file)
 rimg = randomize_mask(img, mask = face)

## End(Not run)

## Not run: 
library(fslr)
library(extrantsr)
mri = "~/Desktop/Desktop/scratch/SUBJ0001-01-MPRAGE.nii.gz"

template.file = mni_fname(brain = TRUE)
tmask = mni_fname(brain = TRUE, mask = TRUE)

template.face_mask_inds = list(50:130, 170:217, 1:15)
brain = fslbet_robust(mri,
remove.neck = TRUE,
remover = "double_remove_neck",
template.file = template.file,
template.mask = tmask)
mask = brain > 0
img = brain
template.face_mask = NULL
verbose = TRUE
face = mri_face_mask(
   file = img,
   mask = mask,
   template.file = template.file
   )

## End(Not run)

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