main.tex

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% Classicthesis Typographic Thesis
% LaTeX Template
% Version 1.3 (15/2/14)
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% This template has been downloaded from:
% http://www.LaTeXTemplates.com
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% Original author:
% André Miede (http://www.miede.de)
%
% License:
% CC BY-NC-SA 3.0 (http://creativecommons.org/licenses/by-nc-sa/3.0/)
%
% General Tips:
% 1) Make sure to edit the classicthesis-config.file
% 2) New enumeration (A., B., C., etc in small caps): \begin{aenumerate} \end{aenumerate}
% 3) For margin notes: \marginpar or \graffito{}
% 4) Do not use bold fonts in this style, it is designed around them
% 5) Use tables as in the examples
% 6) See classicthesis-preamble.sty for useful commands
%
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%	PACKAGES AND OTHER DOCUMENT CONFIGURATIONS
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\documentclass[
		twoside,openright,titlepage,numbers=noenddot,headinclude,%1headlines,
                footinclude=true,cleardoublepage=empty,
                BCOR=5mm,paper=a4,fontsize=10pt, % Binding correction, paper type and font size
                ngerman,american, % Languages
                ]{scrreprt} 
                
% Includes the file which contains all the document configurations and packages - make sure to edit this file
\input{cfg.tex}
                
\begin{document}

\frenchspacing % Reduces space after periods to make text more compact

\raggedbottom % Makes all pages the height of the text on that page

\selectlanguage{american} % Select your default language - e.g. american or ngerman

%\renewcommand*{\bibname}{new name} % Uncomment to change the name of the bibliography
%\setbibpreamble{} % Uncomment to include a preamble to the bibliography - some text before the reference list starts

\pagenumbering{roman} % Roman page numbering prior to the start of the thesis content (i, ii, iii, etc)

\pagestyle{plain} % Suppress headers for the pre-content pages

%----------------------------------------------------------------------------------------
%	PRE-CONTENT THESIS PAGES
%----------------------------------------------------------------------------------------
\begin{titlepage}
% \begin{center}
  \large
  % \begingroup
  \noindent {\LARGE{\color{pantone328}\spacedallcaps{\myTitle}}} \\ %\bigskip % Thesis title
  \emph{\Large \mySubtitle} \\ \medskip % Thesis subtitle

  % \spacedlowsmallcaps
  \noindent {\Large \myName}\\[5pt] % Your name
  \emph{\myInst} \\
  \emph{\myInstDeptLong}\\[1pt] %\bigskip

  \noindent
  \emph{IMPRS for Cognitive and Systems Neuroscience} \\
  \emph{School of Neural Information Processing }\\[20pt] %\bigskip

  \noindent
  For the full version of this PhD thesis please refer to the original reference \cite{safaviBrainComplexSystem2022}:\\[5pt]

  \fullcite{safaviBrainComplexSystem2022}
  % \endgroup
  % \end{center}
\end{titlepage}
\newpage
\include{FrontBackMatter/TitlepageGTCformat_JRFVversion} % Main title - page GTC format


\cleardoublepage\include{FrontBackMatter/phdCommittee} % Supervisors + 2nd Reader and their affilations

\cleardoublepage\include{FrontBackMatter/Declaration} % Declaration

\include{FrontBackMatter/Titleback_ccByv3} % Back of the title page


\cleardoublepage\include{FrontBackMatter/Dedication} % Dedication page
\cleardoublepage\include{FrontBackMatter/entrance} % The poem 
\include{FrontBackMatter/entrance_credit}                 % credit of the poem

\pagestyle{scrheadings} % Show chapter titles as \cleardoublepage\include{FrontBackMatter/Contents} % Contents, list of figures/tables/listings and acronyms
% \include{Chapters/Chapter00} % Preface


\cleardoublepage\include{FrontBackMatter/Acknowledgments} % Acknowledgements page

\cleardoublepage\include{FrontBackMatter/Contents} % Contents, list of figures/tables/listings and acronyms
\cleardoublepage\include{FrontBackMatter/preface} % Acknowledgements page
\cleardoublepage\include{FrontBackMatter/Abstract} % Acknowledgements page
\cleardoublepage

\pagenumbering{arabic} % Arabic page numbering for thesis content (2, 2, 3, etc)
%\setcounter{page}{90} % Uncomment to manually start the page counter at an arbitrary value (for example if you wish to count the pre-content pages in the page count)

\cleardoublepage % Avoids problems with pdfbookmark

%----------------------------------------------------------------------------------------
%	THESIS CONTENT - CHAPTERS
%----------------------------------------------------------------------------------------


% ------------------------------------------------
% Synopsis


\input{chapters/ch1prem_synopsis.tex}
\part{Synopsis} % First part of the thesis
\label{part:synopsis}
% \include{chapters/p1ch1_complexBrain} % Chapter 2
\input{chapters/p1ch1_complexBrain.tex} % Chapter 2
\input{chapters/p1ch2_approachNDA.tex} % Chapter 3
\input{chapters/p1ch2_approachNT.tex} % Chapter 3
\input{chapters/p1ch4_approachCognition.tex} % Chapter 4

   
\cleardoublepage % Empty page before the start of the next part
% brain as a complex system
% 

% ------------------------------------------------
% Manuscripts

\input{chapters/ch2prem_manuscripts.tex}
\part{Manuscripts Information}
\label{part:manuscr-inform}
% order of appearnace
\input{chapters/p2ch5_safavi_arxiv2020.tex}     % 1
\input{chapters/p2ch6_safavi_biorxiv2020.tex}   % 2
\input{chapters/p2ch7_besserve_ned2020.tex}     % 3
\input{chapters/p2ch8_safavi_inprogress2020.tex} % 4
\input{chapters/p2ch1_safavi_front2014.tex}      % 5
\input{chapters/p2ch2_safavi_pnas2018.tex}       % 6
\input{chapters/p2ch3_kapoor_biorxiv2020.tex}    % 7
\input{chapters/p2ch4_dwarakanath_biorxiv2020.tex} % 8

\cleardoublepage % Empty page before the start of the next part


% ------------------------------------------------
% Outlook

\input{chapters/ch2prem_outlook.tex}
\part{Outlook}\label{part:outlook}
\input{chapters/p3ch1_complexAdaptiveBrain.tex}

%----------------------------------------------------------------------------------------
%	THESIS CONTENT - APPENDICES
%----------------------------------------------------------------------------------------

 
\appendix

%----------------------------------------------------------------------------------------
%	POST-CONTENT THESIS PAGES
%----------------------------------------------------------------------------------------

\cleardoublepage\include{FrontBackMatter/Lists} % List of Figures etc.
\cleardoublepage\include{FrontBackMatter/Bibliography} % Bibliography

% ********************************************************************
% Backmatter
%*******************************************************
\cleardoublepage
\input{chapters/prem_manuscript.tex}
\part{Manuscripts}\label{part:manuscripts}

%----------------------------------------------------------------------------------------
%	MANUSCRIPTS
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\input{chapters/app_manuscriptPDFs.tex}

%----------------------------------------------------------------------------------------
%	COLOPHON
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\cleardoublepage\include{FrontBackMatter/Colophon} % Colophon


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\end{document}

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