Main.tex

% UCL Thesis LaTeX Template
% 
% This is a template/skeleton for PhD/MPhil/MRes theses.
%
% It uses a rather split-up file structure because this tends to
%  work well for large, complex documents.
% We suggest using one file per chapter, but you may wish to use more
%  or fewer separate files than that.
% We've also separated out various bits of configuration into their
%  own files, to keep everything neat.
% Note that the \input command just streams in whatever file you give
%  it, while the \include command adds a page break, and does some
%  extra organisation to make compilation faster. Note that you can't
%  use \include inside an \include-d file.
% We suggest using \input for settings and configuration files that
%  you always want to use, and \include for each section of content.
% If you do that, it also means you can use the \includeonly statement
%  to only compile up the section you're currently interested in.
% You might also want to put figures into their own files to be \input.

% For more information on \input and \include, see:
%  http://tex.stackexchange.com/questions/246/when-should-i-use-input-vs-include


% Formatting rules for theses are here: 
%  http://www.ucl.ac.uk/current-students/research_degrees/thesis_formatting
% Binding and submitting guidelines are here:
%  http://www.ucl.ac.uk/current-students/research_degrees/thesis_binding_submission

% This package goes first and foremost, because it checks all 
%  your syntax for mistakes and some old-fashioned LaTeX commands.
% Note that normally you should load your documentclass before 
%  packages, because some packages change behaviour based on
%  your document settings.
% Also, for those confused by the RequirePackage here vs usepackage
%  elsewhere, usepackage cannot be used before the documentclass
%  command, while RequirePackage can. That's the only functional
%  difference.
\RequirePackage[l2tabu, orthodox]{nag}

% ------ Main document class specification ------
% The draft option here prevents images being inserted,
%  and adds chunky black bars to boxes that are exceeding 
%  the page width (to show that they are).
% The oneside option can optionally be replaced by twoside if
%  you intend to print double-sided. Note that this is
%  *specifically permitted* by the UCL thesis formatting
%  guidelines.
%
% Valid options in terms of type are:
%  phd
%  mres
%  mphil
\documentclass[12pt, phd, a4paper, oneside]{ucl_thesis}

\usepackage{titlesec}

\titleformat{\paragraph}
{\normalfont\normalsize\bfseries}{\theparagraph}{1em}{}
\titlespacing*{\paragraph}
{0pt}{3.25ex plus 1ex minus .2ex}{1.5ex plus .2ex}

% Package configuration:
%  LaTeX uses "packages" to add extra commands and features.
%  There are quite a few useful ones, so we've put them in a 
%   separate file.
\input{MainPackages}

% \usepackage{fontspec}
% \setmainfont[Ligatures=TeX]{LexendDeca-Regular.ttf}

\usepackage{pdflscape}

% Sets up links within your document, for e.g. contents page entries
%  and references, and also PDF metadata.
% You should edit this!
\input{LinksAndMetadata}

% And then some settings in separate files.
\input{FloatSettings} % For things like figures and tables
%\input{BibSettings}   % For bibliographies

% Title Settings
\setcounter{secnumdepth}{4}
\setcounter{tocdepth}{4}

\usepackage[top=6.0cm, bottom=1.25cm, left=6.5cm, right=0.5cm, headheight=2.0cm, headsep=0.0cm]{geometry}

\usepackage[activate={true, nocompatibility}, final, tracking=true, kerning=true, spacing=false, factor=1100, stretch=10, shrink=10]{microtype}
\microtypecontext{spacing=nonfrench}

\input{glossary}

\makeglossaries

\usepackage{fancyref}
\usepackage{fancyhdr}
\usepackage{ragged2e}
\fancyhead{}
\lhead{\parbox[t]{0.5\textwidth}{\footnotesize\RaggedRight\nouppercase{\rightmark}\strut}}
\rhead{\parbox[t]{0.5\textwidth}{\footnotesize\RaggedLeft\nouppercase{\leftmark}\strut}}
\pagestyle{fancy}

\newcommand{\rmd}
{%
    \mathrm{d}%
}

\newcommand{\rmD}
{%
    \mathrm{D}%
}

\newcommand{\rmI}
{%
    \mathrm{I}%
}

\usepackage[binary-units]{siunitx}

\usepackage[ruled, linesnumbered]{algorithm2e}
\DontPrintSemicolon

\usepackage[utf8]{inputenc}
\usepackage[british]{babel}
\usepackage{csquotes}

\headsep=1cm

\addbibresource{./bibtex/bib/Biblio.bib}

\begin{document}
    %\nobibliography*
    % This is a dumb trick that works with the bibentry package to let
    %  you put bibliography entries where ever you like.
    % I used this to put references to papers a chapter's work was 
    %  published in at the end of that chapter.
    % For more information, see: http://stefaanlippens.net/bibentry
    
    % If you haven't finished making your full BibTex file yet, you
    %  might find this useful -- it'll just replace all your
    %  citations with little superscript notes.
    % Uncomment to use.
    %\renewcommand{\cite}[1]{\emph{\textsuperscript{[#1]}}}
    
    % At last, content! Remember filenames are case-sensitive and 
    %  *must not* include spaces.
    
    \glsresetall
    \include{Preamble}
    \glsresetall
    
    \include{Chapter1Introduction}
    \include{Chapter2Background}
    \include{Chapter3MotionCorrectionOne}
    \include{Chapter4MotionCorrectionTwo}
    \include{Chapter5DataDrivenSurrogateSignalExtraction}
    \include{Chapter6DiscussionAndConclusion}
    \include{Appendices} 
    % You could separate these out into different files if you have
    %  particularly large appendices.
    
    % This line manually adds the Bibliography to the table of contents.
    % The fact that \include is the last thing before this ensures that it
    % is on a clear page, and adding it like this means that it doesn't
    % get a chapter or appendix number.
    \addcontentsline{toc}{chapter}{Bibliography}
    
    % Actually generates your bibliography.
    \printbibliography
    % All done. \o/
\end{document}