+They can be read from and written to the disk. They are stored as ASCII
+files for easy cross-platform support and editing.
+
+\section{Global Menu Commands}
+These global commands are present on the menus of all windows.
+
+\subsection{File - Create Phantom}\label{IDH_DLG_PHANTOM}\index{Dialog!Create phantom}
+This command displays a dialog box showing the phantoms that are pre-programmed
+into \ctsim. After selecting one of these phantoms, the new window with that
+phantom will be generated. The pre-programmed phantoms are:
+
+\begin{twocollist}
+\twocolitem{\textbf{Herman}}{The Herman head phantom\cite{HERMAN80}}
+\twocolitem{\textbf{Shepp-Logan}}{The head phantom of Shepp \& Logan\cite{SHEPP74}}
+\twocolitem{\textbf{Unit pulse}}{A phantom that has a value of \texttt{1} for the
+center of the phantom and \texttt{0} everywhere else.}
+\end{twocollist}
+
+\subsection{File - Create Filter}\label{IDH_DLG_FILTER}\index{Dialog!Create filter}
+This command displays a dialog box showing the pre-programmed filters
+of \ctsim. This command will create a 2-dimensional image of the selected filter.
+The center of the filter is at the center of the image.
+
+These filters can be created in their natural frequency domain or in their inverse
+spatial domain.
+
+\begin{twocollist}
+\twocolitem{\textbf{Filter}}{Selects the filter to generate. The available filters are:
+
+\begin{itemize}\itemsep=0pt
+\item $|w|$ Bandlimit
+\item $|w|$ Hamming
+\item $|w|$ Hanning
+\item $|w|$ Cosine
+\item $|w|$ Sinc
+\item Shepp
+\item Bandlimit
+\item Sinc
+\item Hamming
+\item Hanning
+\item Cosine
+\item Triangle
+\end{itemize}
+}
+\twocolitem{\textbf{Domain}}{Selects either the \texttt{Frequency} or \texttt{Spatial} domain. The filters have the
+frequency domain as their natural domain. The spatial domain is obtained either analytically or performing
+an inverse Fourier transformation.}
+\twocolitem{\textbf{X Size}}{Number of columns in the output image.}
+\twocolitem{\textbf{Y Size}}{Number of rows in the output image.}
+\twocolitem{\textbf{Hamming Parameter}}{ This parameter adjusts the smoothing of the Hamming
+filter and can range from \texttt{0} to \texttt{1}.
+At a setting of \texttt{1}, the Hamming filter is the same as the bandlimit filter.
+At a setting of \texttt{0.54}, the Hamming filter is the same as the Hanning
+window.}
+\twocolitem{\textbf{Bandwidth}}{Sets the bandwidth of the filter.}
+\end{twocollist}
+\begin{twocollist}
+\twocolitem{\textbf{Axis (input) Scale}}{Sets the scale for the filter input. By default, the input to the filter is
+the distance in pixels from the center of the image. By changing this value, one can set a scale the input to the filter.
+For example, if the output image is \texttt{101} by \texttt{101} pixels and thus the center of the image is at \texttt{(50,50)}, then a pixel
+lying at point \texttt{100,50} would be 50 units from the center of the filter. By applying an \texttt{Axis scale} of
+\texttt{0.1}, then that point would be scaled to 5 units from the center of the filter.}
+\twocolitem{\textbf{Filter (output) Scale}}{Multiplies the output of the filter by this amount. By default, the filter has a maximum
+value of \texttt{1}.}
+\end{twocollist}
+
+\subsection{File - Preferences}\label{IDH_DLG_PREFERENCES}\index{Dialog!Preferences}
+This command displays a dialog box that allows users to control
+the behavior of \ctsim. These options are saved across \ctsim\ sessions.
+Under Microsoft Windows environments, they are stored in the registry.
+On UNIX and Linux environments, they are stored in the user's home
+directory with the filename of \texttt{.ctsim}.
+
+\begin{twocollist}
+\twocolitem{\textbf{Advanced options}}{This option is initially turned off in new installations.
+These advanced options are not required for normal simulations. When \texttt{Advanced
+Options} is set, \ctsim\ will display more options during scanning of phantoms and
+the reconstruction of projections.}
+
+\twocolitem{\textbf{Ask before closing new documents}}{This option is initially turned on in
+new installations. With this option set, \ctsim\ will ask before closing
+documents that have been modified or never saved on disk. By turning off
+this option, \ctsim\ will never ask if you want to save a file -- you'll
+be responsible for saving any files that you create.}
+
+\twocolitem{\textbf{Verbose logging}}{This option is initially turned off in
+new installations. With this option set, \ctsim\ will log more events than
+usual. There extra events are not important for viewing with typical operation of
+\ctsim.}
+
+\twocolitem{\textbf{Show startup tips}}{This option is initially turned on in
+new installations. With this option set, \ctsim\ will display
+helpful tips when \ctsim\ is started.}
+
+\end{twocollist}
+
+\subsection{File - Open}
+This command opens a file section dialog box. Of special consideration
+is the \texttt{File Type} combo box on the bottom of the dialog. You need
+to set the this combo box to the type of file that you wish to open.
+
+\subsection{File - Save}
+This command saves the contents of the active window. If the window hasn't
+been named, a dialog box will open asking for the file name to use.
+
+\subsection{File - Close}
+As one would expect, this closes the active window. If the contents of the window have not been
+saved and the \emph{Advanced Preferences} option \texttt{Ask before closing new documents}
+is turned on, then you will be prompted if decide if you want to save the contents of the window
+prior to closing.
+
+\subsection{File - Save As}
+Allows the saving of the contents of the active window to any file name.
+
+\subsection{Help - Contents}
+This command displays the online help.
+
+\subsection{Help - Tips}
+This command displays a dialog with tips on using \ctsim.
+
+\subsection{Help - Quick Start}
+This command displays a recommend approach to helping new users learn to use \ctsim.
+
+\subsection{Help - About}
+This command shows the version number and operating environment of \ctsim.
+