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+++ b/man/CT_Skull_Strip_robust.Rd
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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/CT_Skull_Strip_robust.R
+\name{CT_Skull_Strip_robust}
+\alias{CT_Skull_Strip_robust}
+\alias{CT_Skull_Strip_register}
+\alias{CT_Skull_Strip_smooth}
+\title{Robust CT Skull Stripping}
+\usage{
+CT_Skull_Strip_robust(
+  img,
+  outfile = NULL,
+  keepmask = TRUE,
+  maskfile = NULL,
+  retimg = TRUE,
+  reorient = FALSE,
+  int = "0.01",
+  lthresh = 0,
+  uthresh = 100,
+  nvoxels = 5,
+  remove.neck = TRUE,
+  remover = c("remove_neck", "double_remove_neck"),
+  smooth.factor = 2,
+  recog = TRUE,
+  verbose = TRUE,
+  opts = NULL,
+  mask_to_background = FALSE,
+  template.file = system.file("scct_unsmooth_SS_0.01.nii.gz", package = "ichseg"),
+  template.mask = system.file("scct_unsmooth_SS_0.01_Mask.nii.gz", package = "ichseg"),
+  ...
+)
+
+CT_Skull_Strip_register(
+  img,
+  outfile = NULL,
+  keepmask = TRUE,
+  maskfile = NULL,
+  retimg = TRUE,
+  reorient = FALSE,
+  lthresh = 0,
+  uthresh = 100,
+  remove.neck = TRUE,
+  remover = c("remove_neck", "double_remove_neck"),
+  verbose = TRUE,
+  mask_to_background = FALSE,
+  ...
+)
+
+CT_Skull_Strip_smooth(
+  img,
+  ...,
+  smooth_before_threshold = TRUE,
+  smooth.factor = 1,
+  remove.neck = TRUE,
+  remover = c("remove_neck", "double_remove_neck"),
+  recog = FALSE,
+  nvoxels = 0,
+  add_1024 = FALSE
+)
+}
+\arguments{
+\item{img}{(character) File to be skull stripped or object of class
+nifti}
+
+\item{outfile}{(character) output filename}
+
+\item{keepmask}{(logical) Should we keep the mask?}
+
+\item{maskfile}{(character) Filename for mask
+(if \code{keepmask = TRUE}).
+If \code{NULL}, then will do \code{paste0(outfile, "_Mask")}.}
+
+\item{retimg}{(logical) return image of class nifti}
+
+\item{reorient}{(logical) If retimg, should file be
+reoriented when read in?
+Passed to \code{\link{readNIfTI}}.}
+
+\item{int}{Fractional Intensity passed to
+\code{\link{CT_Skull_Strip}} and
+subsequently \code{\link{fslbet}}.}
+
+\item{lthresh}{(default: 0) Lower value to threshold CT
+\code{\link{fslthresh}}}
+
+\item{uthresh}{(default: 100) Upper value to threshold CT
+\code{\link{fslthresh}}}
+
+\item{nvoxels}{Number of voxels to dilate/erode.
+See \code{\link{dil_ero}}.
+If \code{nvoxels = 0}, then no smoothing is done.}
+
+\item{remove.neck}{Run \code{\link{remove_neck}} to register
+the template to a
+thresholded image to remove neck slices.}
+
+\item{remover}{if \code{remove.neck = TRUE}, then which function
+would you like to use to remove the neck}
+
+\item{smooth.factor}{Smoothing factor for \code{\link{fslbet}}.
+See \code{-w}
+option in \code{fslbet.help()}.}
+
+\item{recog}{Re-estimate the center of gravity (COG) and
+skull strip.}
+
+\item{verbose}{(logical) Should diagnostic output be printed?}
+
+\item{opts}{Not used}
+
+\item{mask_to_background}{When masking, should the values outside the
+mask be set to 0 (default) or -1024 (when TRUE)}
+
+\item{template.file}{Template to warp to original image
+space, passed to
+\code{\link{remove_neck}}}
+
+\item{template.mask}{Mask of template to use as rough
+brain mask, passed
+to \code{\link{remove_neck}}}
+
+\item{...}{additional arguments passed to
+\code{\link{CT_Skull_Strip}} or
+\code{\link{remove_neck}}.}
+
+\item{smooth_before_threshold}{Should the image be smoothed before
+thresholding?  This can be useful for bone-window scans.}
+
+\item{add_1024}{Adding 1024 to the image *before* running the skull
+stripping.  The values are subtracted after.  This has interplay with
+\code{mask_to_background}}
+}
+\value{
+Skull-stripped \code{nifti} object
+}
+\description{
+Skull Stripping (using FSL's BET) a CT file
+using \code{fslr}
+functions and robustified by registration
+}
+\note{
+This function first thresholds an image, runs a rigid
+registration
+(default in \code{\link{remove_neck}}) to drop any slices
+below the transformed
+skull stripped template to remove neck slices.  The neck-removed
+image is
+then skull stripped using defaults in \code{\link{CT_Skull_Strip}}.
+ A new
+center of gravity is estiamted using \code{\link{cog}}, then the
+image is
+skull stripped again using the new cog and the smoothness factor
+(passed to \code{-w} argument in BET). After the skull stripped
+mask is
+created, the image is dilated and eroded using
+\code{\link{dil_ero}} to
+fill holes using a box kernel with the number of voxels
+\code{nvoxels} in
+all 3 directions.
+
+\code{CT_Skull_Strip_register} removes the neck, registers the
+image to the template, using a rigid-body transformation,
+runs the skull stripper to get a mask, then transforms the mask
+back to native space.
+}