+\section{Global Menu Commands}
+These commands are present on the menus of all windows.
+
+\subsection{File - Create Phantom}\index{Create phantom dialog}
+This command brings up a dialog box showing the phantoms that are preprogrammed
+into \ctsim. After selecting one of these phantoms, the new window with that
+phantom will be generated. The preprogrammed 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}\index{Create filter dialog}
+This command brings up 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 spatial domain.
+\begin{twocollist}
+\twocolitem{\textbf{Filter}}{Selects the filter to generate.}
+\twocolitem{\textbf{Domain}}{Selects either the \texttt{Frequency} or \texttt{Spatial} domains. The filters have the
+frequency domain as their natural domain.}
+\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}}{Sets the parameter for the Hamming filter.}
+\twocolitem{\textbf{Bandwidth}}{Sets the bandwidth of the filter.}
+\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.}
+\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}\index{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 users home
+directory with the filename of \texttt{.ctsim}.
+
+\begin{twocollist}
+\twocolitem{\textbf{Advanced options}}{By default, this is 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 deleting new documents}}{By default, this is 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.}
+
+\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 \texttt{File Type} combo box to 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.
+
+\subsection{File - Save As}
+Allows the saving of the contents of a window to any filename.
+
+\subsection{Help - Contents}
+This command displays the online help.
+
+\subsection{Help - About}
+This command shows the version number of \ctsim.
+
+