--- a
+++ b/man/CT_Skull_Strip.Rd
@@ -0,0 +1,90 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/CT_Skull_Strip.R
+\name{CT_Skull_Strip}
+\alias{CT_Skull_Strip}
+\title{CT Skull Stripping within R}
+\usage{
+CT_Skull_Strip(
+  img,
+  outfile = NULL,
+  keepmask = TRUE,
+  maskfile = NULL,
+  inskull_mesh = FALSE,
+  retimg = TRUE,
+  reorient = FALSE,
+  intern = TRUE,
+  betcmd = "bet2",
+  opts = "-f 0.01 -v",
+  presmooth = TRUE,
+  remask = TRUE,
+  refill = FALSE,
+  refill.thresh = 0.75,
+  sigma = 1,
+  lthresh = 0,
+  uthresh = 100,
+  smooth_before_threshold = FALSE,
+  verbose = TRUE,
+  ...
+)
+}
+\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{inskull_mesh}{(logical) Create inskull_mesh file from bet?
+(Warning - will take longer)
+This an exterior surface of the brain. (experimental)
+Also, if \code{outfile} is \code{NULL}, then this will be created in
+a temporary directory and not be retrieved.}
+
+\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{intern}{(logical) pass to \code{\link{system}}}
+
+\item{betcmd}{(character) bet command to be used, see \code{\link{fslbet}}}
+
+\item{opts}{(character) additional options to \code{\link{fslbet}}}
+
+\item{presmooth}{(logical) indicator if pre-smoothing should be
+done before BET}
+
+\item{remask}{(logical) Mask the smoothed image with HU mask from initial
+step?}
+
+\item{refill}{(logical) indicator to post-smooth mask and then fill}
+
+\item{refill.thresh}{(numeric) Value to threshold post-smoothed mask}
+
+\item{sigma}{(integer) size of Gaussian kernel passed to
+\code{\link{fslsmooth}} if \code{presmooth} is \code{TRUE}}
+
+\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{smooth_before_threshold}{Should the image be smoothed before
+thresholding?  This can be useful for bone-window scans.}
+
+\item{verbose}{(logical) Should diagnostic output be printed?}
+
+\item{...}{additional arguments passed to \code{\link{fslbet}}.}
+}
+\value{
+character or logical depending on intern
+}
+\description{
+Skull Stripping (using FSL's BET) a CT file using \code{fslr}
+functions
+}