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\documentclass[letterpaper,11pt]{report}
\usepackage{graphicx}
\usepackage{texhelp}
\usepackage{fancyhea}
\usepackage{mysober}
\usepackage{mytitle}
\usepackage{verbatim}
\usepackage{makeidx}
%\usepackage{times}
\usepackage{hyperref}
\input{psbox.tex}
\latexonly{\includeonly{ctsim-concepts,ctsim-install,ctsim-gui,ctsim-textui,ctsim-web,ctsim-algorithms,ctsim-sgp}}
\hyphenation{poly-gon-al multi-thread-ing}
\newcommand{\ctsim}{\texttt{CTSim}}
\newcommand{\ctsimtext}{\texttt{CTSimText}}
\newcommand{\usage}{\textbf{Usage}\par}
\newcommand{\commandref}[2]{\helpref{{\tt $\backslash$#1}}{#2}}%
\newcommand{\commandrefn}[2]{\helprefn{{\tt $\backslash$#1}}{#2}\index{#1}}%
\newcommand{\commandpageref}[2]{\latexignore{\helprefn{{\tt $\backslash$#1}}{#2}}\latexonly{{\tt $\backslash$#1} {\it page \pageref{#2}}}\index{#1}}
\newcommand{\indexit}[1]{#1\index{#1}}%
\newcommand{\inioption}[1]{{\bf {\tt #1}}\index{#1}}%
\newcommand{\manvernum}[0]{1.0}
\newcommand{\manver}[0]{v\manvernum}
\newcommand{\mandate}[0]{May 1, 2002}
\newcommand{\ctsimfooter}{\setfooter{\thepage}{}{}{\small Manual \manver}{\small \mandate}{\thepage}}
\newcommand{\doublehyphen}[1]{-\,-\texttt{#1}}
\newcommand{\ctsimvernum}[0]{3.5.0}
\newcommand{\ctsimver}[0]{CTSim \ctsimvernum}
\newcommand{\ctsimheadtitle}{\ctsimver\ Manual}
\latexignore{\newcommand{\sqrt}[2]{sqrt(#2)}}
\parskip=10pt%
\parindent=0pt%
%\backgroundcolour{255;255;255}\textcolour{0;0;0}% Has an effect in HTML only
\title{CTSim 3.5 User Manual}%
\author{Kevin M. Rosenberg, M.D.}%
\makeindex%
\textheight=9in
\textwidth=6.0in
\evensidemargin=0in
\oddsidemargin=0in
\begin{document}
\maketitle
\pagestyle{fancyplain}
\pagenumbering{roman}
\chapter*{Copyright notice}%
\setheader{{\it COPYRIGHT}}{}{}{\ctsimheadtitle}{}{{\it COPYRIGHT}}%
\ctsimfooter
Copyright (c) 1983-2002 Kevin M. Rosenberg, M.D.
Permission to use, copy, modify, and distribute this software and its
documentation for any purpose is hereby granted without fee, provided that the
above copyright notice, author statement and this permission notice appear in
all copies of this software and related documentation.
THE SOFTWARE IS PROVIDED ``AS-IS'' AND WITHOUT WARRANTY OF ANY KIND, EXPRESS,
IMPLIED OR OTHERWISE, INCLUDING WITHOUT LIMITATION, ANY WARRANTY OF
MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE.
IN NO EVENT SHALL KEVIN M. ROSENBERG BE LIABLE FOR ANY
SPECIAL, INCIDENTAL, INDIRECT OR CONSEQUENTIAL DAMAGES OF ANY KIND, OR
ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS,
WHETHER OR NOT ADVISED OF THE POSSIBILITY OF DAMAGE, AND ON ANY THEORY
OF LIABILITY, ARISING OUT OF OR IN CONNECTION WITH THE USE OR
PERFORMANCE OF THIS SOFTWARE.
\chapter*{Acknowledgements}
\setheader{{\it COPYRIGHT}}{}{}{\ctsimheadtitle}{}{{\it COPYRIGHT}}%
\setfooter{\thepage}{}{}{}{\manver}{\thepage}%
\textbf{Ian Kay, Ph.D.}\\ Special thanks to Dr. Kay for contributing
portions to this manual. Dr. Kay has assisted the development of
\ctsim\ with the addition of helical scanning, bug reports, and paches.
\textbf{Gabor T. Herman, Ph.D.}\\ Dr. Herman's publications on
computed tomography inspired the initial version \ctsim\ in
1983. Dr. Herman has graciously permitted use of his copyrighted head
phantom for use in \ctsim.
\setheader{{\it CONTENTS}}{}{}{\ctsimheadtitle}{}{{\it CONTENTS}}%
\ctsimfooter
\parskip=2pt
\tableofcontents%
\parskip=10pt
\chapter{Introduction}\label{IDH_INTRODUCTION}
\pagenumbering{arabic}
\setheader{{\it CHAPTER \thechapter}}{}{}{\ctsimheadtitle}{}{{\it CHAPTER \thechapter}}%
\ctsimfooter
\centerline{\image{3cm;3cm}{logo.eps}}
Computed tomography is a technique for estimating the interior of an
object from measurements of radiation collected around the object. This
radiation can be either projected through or emitted from the
object. \ctsim\ simulates the process of projecting X-rays
through a phantom object. \ctsim\ can then reconstruct the
interior of the object from those projections. \ctsim\ integrates
numerous visualization and analytic tools.
This manual begins with an introduction into the concepts of
\ctsim. Next, the graphical, command-line, and web shells are
presented. Finally, the installation of \ctsim\ is discussed.
I hope that you enjoy \ctsim!
\include{ctsim-concepts}
\include{ctsim-gui}
\include{ctsim-textui}
\include{ctsim-web}
\include{ctsim-install}
\appendix
\include{ctsim-algorithms}
\include{ctsim-sgp}
\newpage
\bibliographystyle{plain}
\bibliography{ctsim}
\addcontentsline{toc}{chapter}{Bibliography}
\setheader{{\it REFERENCES}}{}{}{\ctsimheadtitle}{}{{\it REFERENCES}}
\ctsimfooter
\newpage
\addcontentsline{toc}{chapter}{Index}
\setheader{{\it INDEX}}{}{}{\ctsimheadtitle}{}{{\it INDEX}} %
\ctsimfooter
\printindex
\end{document}
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