My PhD Dissertation

Model based analysis of multimodal neuroimaging: from neural masses to spectral graph theory.

The PDF file viewable at main/dissertation.pdf.

Students are welcomed to look at each tex file and use the main documents as a template for their own thesis. Hopefully this saves you from hours of formatting and reading some awful formatting requirements document.

How to compile:

For beginners that's never touched LaTeX before, you will need:

• LaTeX compilers like pdflatex and bibtex to turn text files into a beautiful PDF. MacOS users familiar with the commandline should have brew setup and follow this to install the necessary compilers. More details can be found at https://www.latex-project.org/get/.

• A plain text editor of any sort, there are ones made for LaTeX specifically.

  • I personally used texmaker, remember to go to Preferences and edit Quick Build to pdflatex + bib(la)tex + pdflatex + View PDF for a smooth experience. Change the font size and other preferences while you are at it for your comfort.
  • For coders, use VSCode with the LaTeX Workshop extension, it's quite lightweight and you can add a bunch of other text editing extensions for quite a good experience.
  • Here's quite a large list of other options: https://tex.stackexchange.com/questions/339/latex-editors-ides

You will only build the main/dissertation.tex file. It includes everything you will need. For experienced git users, feel free to clone this repository and start your own project by copying over main/{dissertation.tex,hangcaption.sty,cornell.cls} to your repo. Then create a blank References.bib and copy over from a citation manager your desired references in bibtex format.

Notice all files are placed with relative paths (ex: ../chapter1/introduction from main/dissertation.tex for chapter1/introduction). So follow the folder structure or modify the paths to match your own.

Add-On's to make your life easier AND to accomodate dumb formatting requirements that nobody wants to read:

• \usepackage{subfiles} to separate chapters into digestable files.
• \usepackage{indentfirst} indents first paragraph after \section tags
• \usepackage[all]{nowidow} to eliminate widow/orphan sentences.
• \usepackage[justification=centerlast]{caption} to uniformly justify figure captions.
• begin{tabular*}{\textwidth} to fit fat tables to text width with the tabular* environment instead of the simpler tabular environment.
• For long figures or captions that span more than one page:
  • First delcare a new command to label the figure as Continued: \DeclareCaptionLabelFormat{adja-page}{\hrulefill\\#1 #2 \emph{(Continued)}}
  • For the large figure, declare 2 figure environments, and use \ContinuedFloat and \captionsetup{labelformat=adja-page} for continuation.
  • Make sure the figure caption is alone with no other text with \clearpage before and after inserting the caption.
  • The second figure environment's caption should be \caption[]{} to avoid an empty caption being added to the figures list.

These changes are already implemented in main/dissertation.tex, do not edit the preamble unless you know what you are doing, and you are certain your edits will still follow formatting guidelines.

For LaTeX newcomers that's never created documents in plain text before, google overleaf how to x for simple guidelines on how to do certain things if following my .tex files are not instructive.

How to create slides with jupyter:

Install rise. This only works with jupyter notebook right now, and is not compatible with jupyter lab.

License:

This work is licensed under the Creative Commons Attribution 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ or send a letter to Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.