main.tex

%%%%%%%%%%%%%%%%
% Ph.D. thesis %
%%%%%%%%%%%%%%%%

%\documentclass[11pt,openright,twoside,letterpaper,onecolumn]{report} %% USE THIS FOR DOUBLE SIDED
\documentclass[11pt,openright,oneside,letterpaper,onecolumn]{report}  %% USE THIS FOR SINGLE SIDED
% \usepackage{textcomp}
% \usepackage{cprotect}
\newcommand{\sub}[1]{$_\text{#1}$}
\newcommand{\super}[1]{$^\text{#1}$}
\newcommand*{\thead}[1]{\multicolumn{1}{c}{#1}}
\usepackage{graphicx}
\usepackage{tabularx}
\usepackage{xcolor}
\usepackage{attrib}
\usepackage[colorinlistoftodos, disable]{todonotes}
% \usepackage[colorinlistoftodos]{todonotes}
\usepackage{listings}
\usepackage{color}
 
\definecolor{codegreen}{rgb}{0,0.6,0}
\definecolor{codegray}{rgb}{0.5,0.5,0.5}
\definecolor{codepurple}{rgb}{0.58,0,0.82}
\definecolor{backcolour}{rgb}{0.95,0.95,0.92}
 
\lstdefinestyle{mystyle}{
    backgroundcolor=\color{backcolour},   
    commentstyle=\color{codegreen},
    keywordstyle=\color{magenta},
    numberstyle=\tiny\color{codegray},
    stringstyle=\color{codepurple},
    basicstyle=\footnotesize,
    breakatwhitespace=false,         
    breaklines=true,                 
    captionpos=b,                    
    keepspaces=true,                 
    numbers=left,                    
    numbersep=5pt,                  
    showspaces=false,                
    showstringspaces=false,
    showtabs=false,                  
    tabsize=4
}
\lstset{style=mystyle}

\usepackage{acronym}
\input{acronyms}

\newcommand{\df}{}
\def\df/{\emph{Df(16)A\super{+/-}}}
\newcommand{\scz}{}
\def\scz/{schizophrenia}
\newcommand{\Scz}{}
\def\Scz/{Schizophrenia}

\graphicspath{{./figures/}}
\DeclareGraphicsExtensions{.pdf,.png,.jpg}

\input{header}

% \usepackage[
% labelfont=sf,
% hypcap=false,
% format=hang,
% margin=1cm,
% justification=RaggedRight,
% calcwidth=0.8\linewidth
% ]{caption}

\usepackage{caption}
\captionsetup{font={small,onehalfspacing},labelfont=bf}

\usepackage{wrapfig}
\usepackage{natbib}

\usepackage{amsmath}
\usepackage{amssymb}
\DeclareMathOperator\erf{erf}

\usepackage{hyperref}
 
\begin{document}

% For the first pages we do not have numbering 
\pagestyle{empty}

\thesistitlepage
\thesiscopyrightpage

\thesisabstract

\listoftodos

% In the "roman-numbered" section of the thesis, we have numbers at the bottom
% and we have to reduce the textheight of the text to make space for the number

\pagenumbering{roman}
\pagestyle{plain}

\setlength{\footskip}{0.5in}

\setcounter{tocdepth}{3}
\renewcommand{\contentsname}{Table of Contents}
\tableofcontents
\cleardoublepage

\listoffigures
\addcontentsline{toc}{chapter}{\listfigurename}
\cleardoublepage

\listoftables
\addcontentsline{toc}{chapter}{\listtablename}
\cleardoublepage

%%%
%%% Acknowledgments
%%%
\input{acknowledgments}
\cleardoublepage

%%%
%%% Dedication page
%%%
\thispagestyle{plain}
\strut \vfill
\centerline{\LARGE 
To Kate.
}
\todo[inline, color=green]{Write dedication}
\vfill \strut
\cleardoublepage

% \draft   % Generates a draft version in single-space

%%%
%%% BODY
%%%
\pagestyle{headings}
\pagenumbering{arabic}

%
% In the "arabic" section of the thesis, we do not have numbers at  the
% bottom and we want to use the full length of the page to avoid vbox
% underfulls. We use the fancyheaders package to adapt the headers
% according to the  Columbia requirements.
%
% \setlength{\textheight}{8.5in}
% \setlength{\footskip}{0in}

% We change the pagestyle 
\fancypagestyle{plain} {%
\setlength{\textheight}{9.0in}
\setlength{\headheight}{0pt}  % 14pt
\setlength{\headsep}{0pt}  % 22pt
% \fancyhf{}
\fancyhead[LE,RO]{}
\fancyhead[RE,LO]{}
% \fancyhead[LE,RO]{\thepage}
% \fancyhead[RE,LO]{\itshape \leftmark}
\renewcommand{\headrulewidth}{0pt}
}

\pagestyle{plain}
\pagenumbering{arabic}

\part{Introduction}
\input{intro-HPC}
\input{intro-SCZ}
\input{intro-techniques}

\part{Projects}
\input{chapter-df}
\input{chapter-sima}
\input{chapter-applications}

\part{Conclusions}
\input{conclusions}

%%%
%%% Appendices
%%%
% \part{Appendices}
% \appendix
% \input{sample-appendix}
% \input{sample-appendix}

%%%
%%% Bibliography
%%%
% \part{Bibliography}
\addcontentsline{toc}{chapter}{Bibliography}
\singlespacing
\bibliographystyle{neuron} 
\bibliography{library}

\end{document}