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main.tex
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\documentclass[
% draft, % comment for final version (both ELECTRONIC and HARDBOUND): uncomment to skip loading figures
a4paper,
12pt, % should be 11pt or 12pt
dvipsnames, % for extra color options
twoside, % uncomment for final version (both ELECTRONIC and HARDBOUND): different left and right side pages
openright % uncomment for final version (both ELECTRONIC and HARDBOUND): start new chapters on right hand side page
]{report}
%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%
\input{misc/headings} % for fancy layout
\input{misc/preamble}
\input{misc/glossaries}
%%%%%%%%%%%%%%%%%%%%%%%%%%%
\newcommand\optionalindent{} % for fancy layout
%%
\begin{document}
\pagenumbering{roman}
%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%
% \includepdf{misc/deposit_and_copying_declaration.pdf} % uncomment only for HARDBOUND version
% \clearpage
\input{misc/title_page}
\thispagestyle{empty}
\input{misc/declaration}
\clearpage
\thispagestyle{empty}
\input{misc/abstract}
\input{misc/acknowledgements}
%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%
\tableofcontents
%%
\clearpage
\listoffigures
%%
\clearpage
\thispagestyle{empty}
\listoftables
%%
\clearpage
\thispagestyle{empty}
% \printglossary[type=\acronymtype,title=List of Abbreviations]
\printnoidxglossaries
%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%
\renewcommand\optionalindent{\tabto{1.2cm}} % for fancy layout
\newpage
\pagenumbering{arabic}
\pagestyle{fancy} % add fancy headers and footers
%%
\input{ch/1_Introduction/0_Introduction}
\input{ch/1_Introduction/1_Functional_connectivity}
\input{ch/1_Introduction/2_Functional_networks}
\input{ch/1_Introduction/3_TVFC}
\input{ch/1_Introduction/4_The_trouble_with_estimating_TVFC}
\input{ch/1_Introduction/5_Functional_connectivity_and_depression}
\input{ch/1_Introduction/6_Outline_and_contributions_of_thesis}
%%
\input{ch/2_Robust_estimation_of_TVFC/0_Introduction}
\input{ch/2_Robust_estimation_of_TVFC/1_Established_methods_and_baselines}
\input{ch/2_Robust_estimation_of_TVFC/2_Cross-validated_sliding-windows}
\input{ch/2_Robust_estimation_of_TVFC/3_The_Wishart_process}
\input{ch/2_Robust_estimation_of_TVFC/4_Extracting_TVFC-based_features_and_biomarkers}
\input{ch/2_Robust_estimation_of_TVFC/5_The_benchmarking_framework}
\input{ch/2_Robust_estimation_of_TVFC/6_Discussion}
%%
\input{ch/3_Benchmarking_TVFC_estimation/0_Introduction}
\input{ch/3_Benchmarking_TVFC_estimation/1_Material_and_methods}
\input{ch/3_Benchmarking_TVFC_estimation/2_Results}
\input{ch/3_Benchmarking_TVFC_estimation/3_Discussion}
%%
\input{ch/4_TVFC_and_depression/0_Introduction}
\input{ch/4_TVFC_and_depression/1_Data_cohorts_and_parcellations}
\input{ch/4_TVFC_and_depression/2_Material_and_methods}
\input{ch/4_TVFC_and_depression/3_Results}
\input{ch/4_TVFC_and_depression/4_Discussion}
%%
\input{ch/5_Discussion/0_Introduction}
\input{ch/5_Discussion/1_Summary_of_presented_work}
\input{ch/5_Discussion/2_Future_work}
\input{ch/5_Discussion/3_Concluding_remarks}
%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%
\clearpage
\todototoc
\listoftodos[Notes]
%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%
\clearpage
\appendix
%%
\input{appendix/03_extra_benchmarking_results}
\input{appendix/04_ukb_with_other_methods}
%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%
\clearpage
\renewcommand\optionalindent{} % for fancy layout
\renewcommand{\bibname}{References} % changes the default name `Bibliography` -> `References'
\printbibliography[heading=bibintoc]
%%%%%%%%%%%%%%%%%%%%%%%%%%%
\end{document}