%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% This is the official Latex template prepared by the Vanderbilt University Graduate School for submission of dissertations. It is based on a template originally prepared by Eli Hooten and updated by Haley Adams.

% Using the template is no guarantee that you pass format review with your first submission, but it should save you significant amount of time.

% This template is correct as of March 2021.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\listfiles
\documentclass[10pt]{report}  %%% Changed from 12pt.

\usepackage[intoc]{nomencl}

\textwidth=6in \oddsidemargin=0.5in \topmargin=-0.5in
\textheight=9in  % 9in must include page numbers
\textfloatsep = 0.4in \addtocontents{toc}{\vspace{0.4in} \hfill
Page\endgraf} \addtocontents{lof}{\vspace{0.2in} \hspace{0.13in} \
Figure\hfill Page\endgraf} \addtocontents{lot}{\vspace{0.2in}
\hspace{0.13in} \ Table\hfill Page\endgraf}

% We've already imported some of the most commonly used packages for inserting formulas, images, tables, and references. If you need more, you can find a list of Latex packages here: https://www.ctan.org/pkg/ 

\usepackage{textcomp}
\usepackage{array}
\usepackage{listings}
\usepackage{setspace}
\usepackage{mathptmx}
\usepackage[table, svgnames]{xcolor}
\usepackage{colortbl}
\usepackage{graphicx}
\usepackage{ccaption}
\usepackage{amssymb, amsmath}
\usepackage{subfig}
\usepackage{epsfig}
\usepackage{times}
\usepackage{float}
\usepackage{rotating}
\usepackage{makeidx}
\usepackage{url}
\usepackage{multirow}
\usepackage{booktabs}
\usepackage{tabularx}

\usepackage{placeins}

\usepackage[subfigure, titles]{tocloft}
\usepackage{acronym}
\usepackage{datetime}

%%another algorithm package
\usepackage{algorithm}
\usepackage{algorithmic}

\renewcommand{\nomname}{LIST OF ABBREVIATIONS}
\makenomenclature

\graphicspath{{Figures/}}
\DeclareGraphicsExtensions{.pdf,.jpeg,.png,.PNG, .eps, .tiff}

\urlstyle{same}

\usepackage{makecell}
\usepackage{titletoc}
\usepackage{sfchap}
\usepackage{sfsection}
%\usepackage[authoryear]{natbib}
\usepackage{natbib}
\usepackage{appendix}
\usepackage[nottoc]{tocbibind}
\setcounter{secnumdepth}{7}
\setcounter{tocdepth}{7}

\usepackage{hyperref}
\hypersetup{
	pdftitle={A LaTeX Format for Theses and Dissertations},
	pdfauthor={Eli Hooten},
	bookmarksnumbered, %Determined if chapter numbers are included in the bookmark list
	pdfstartview={FitH},
	pdfborder={0 0 0},
	plainpages=false
}%
\usepackage[all]{hypcap}

% Stats table label
\newcommand{\statslabel}[2]{\multirowcell{#1}[-1.6mm][c]{#2}}

% Below heading rule.
\newcommand{\otoprule}{\midrule[\heavyrulewidth]}

% Prevent double spaced equations
\newenvironment{tightequation}{\singlespace\begin{equation}}{\end{equation}}

% Extra junk to pretty up the table of contents
\setlength{\cftsecnumwidth}{2.8em}
\setlength{\cftsubsecnumwidth}{3.7em}
\setlength{\cftsubsubsecnumwidth}{4.6em}
\setlength{\cftparanumwidth}{5.5em}
\setlength{\cftsubparanumwidth}{6.5em}
\setlength{\cfttabnumwidth}{3.5em}
\setlength{\cftfignumwidth}{3.5em} 

\renewcommand{\contentsname}{TABLE OF CONTENTS}
\renewcommand{\listfigurename}{LIST OF FIGURES}
\renewcommand{\listtablename}{LIST OF TABLES}
\renewcommand{\bibname}{ \texorpdfstring{{References\vspace{10mm}}}{References}   }
%
\renewcommand{\chaptermark}[1]{%
  \markboth{\MakeUppercase{%
      \chaptername}\ \thechapter.%
    \ #1}{}}
    
    
\interfootnotelinepenalty=10000 %prevents the splitting of long footnotes across multiple pages. Use with caution. 

\begin{document}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Prevent the warning: pdfTeX warning (ext4): destination with the same identifier (name{page.1}) has been already used, duplicate ignored
%%	This setting will make a difference to the output because the page number is suppressed for the title page
\pagenumbering{alph}

\input{Sections/Title}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\doublespacing
\pagenumbering{roman} \setcounter{page}{2}

% These 3 sections are optional 
\singlespacing
\input{Sections/Copyright}
\input{Sections/Dedication}
\input{Sections/Acknowledgments}


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\singlespacing
\tableofcontents

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\begingroup
\setlength{\parskip}{1\baselineskip}
\listoftables
\newpage
\listoffigures
\newpage
%\printnomenclature %list of abbreviations is optional
%\newpage
\endgroup

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\normalsize
\doublespacing
\pagenumbering{arabic}
\setcounter{page}{1}

\input{Sections/Chapter1-intro}
\input{Sections/Chapter2-pnas}
\input{Sections/Chapter3-naturecomms}
\input{Sections/Chapter4-elife}
\input{Sections/Chapter5-neuroimage}
\input{Sections/Chapter6-discussion}


\singlespacing
\bibliographystyle{apalike}
\bibliography{references}
\end{document}
