--- a
+++ b/man/face_mask.Rd
@@ -0,0 +1,110 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/face_mask.R
+\name{ct_face_mask}
+\alias{ct_face_mask}
+\alias{ct_face_mask,mri_face_mask}
+\alias{mri_face_mask}
+\title{Create Mask of the Face}
+\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{
+\item{file}{File for face masking - either filename or class nifti}
+
+\item{skull_strip}{Should the data require skull stripping if
+no mask is provided?}
+
+\item{mask}{file or \code{nifti} to mask the \code{file}}
+
+\item{robust}{If \code{mask = NULL}, then \code{robust} is
+passed to \code{\link{CT_Skull_Stripper}}}
+
+\item{template.file}{Template to warp to original image space}
+
+\item{template.face_mask}{Mask of template to use as rough face mask.  If
+\code{template.file} is not specified, \code{template.face_mask_inds}
+must be}
+
+\item{template.face_mask_inds}{List of length 3 for indices of
+\code{template.file} to indicate the mask.}
+
+\item{extend_mask}{after transformation, should the mask be extended to the
+front of the image to ensure all face has been removed?}
+
+\item{typeofTransform}{Transformation for template to image, passed to
+\code{\link{ants_regwrite}}.}
+
+\item{swapdim}{Should the dimensions be swapped before registration,
+and then reset after}
+
+\item{verbose}{Print out diagnostic messages}
+
+\item{...}{arguments passed to \code{\link{CT_Skull_Stripper}}}
+}
+\value{
+Object of class nifti
+}
+\description{
+Creates a rough mask of the face from a head scan
+}
+\examples{
+\dontrun{
+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)
+}
+
+\dontrun{
+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
+   )
+}
+
+}