A primer book on neuroimaging methods for cognitive neuroscience. This work is licensed under a

Creative Commons Attribution 4.0 International License, except for specific images (license for each image is detailed in the corresponding image caption). See the content of the book for a detailed list of contributions for each chapter.

Usage

building the book

If you want to contribute changes and check how the book renders, you need to:

• clone this repository.
• Run pip install -r methods_cogneuro_book/requirements.txt (it is recommended to run this instruction in a virtual environment).
• (Recommended) Clean the environment jb clean methods-cogneuro-book/
• Build the book jb build methods-cogneuro-book/

A static html version of the book will be generated in methods-cogneuro-book/_build/html/.

Hosting the book

The html version of the book is hosted on the gh-pages branch of this repo. Navigate to your local build and run,

• ghp-import -n -p -f methods-cogneuro-book/_build/html

This will automatically push your build to the gh-pages branch. More information on this hosting process can be found here.

Generating pdf

The support for pdf generation is experimental with jupyter book, and the output is not perfect. Currently the process looks like:

• install the depencies described in the section "Building a pdf with latex" in the jb docs.
• build latex with individual pages: jb build methods-cogneuro-book/ --builder pdflatex --individualpages. This produces warnings (skip them) and errors. If you ever get stuck in the terminal, leaving the weird latex compilation environment is achieved by pressing X (you're welcome).
• install xetex sudo apt-get install texlive-xetex
• go in the build directory cd methods-cogneuro-book/_build/latex
• edit manually the tex file of the chapter. Replace all \chapter by \section and add a proper \chapter at the beginning. You can also search Content and replace by Table des matières. I have tried to switch the whole doc in French but without success so far.
• before adding the chapter title, add the following lines: \setcounter{chapter}{n} \addtocounter{chapter}{-1}, where n is the number of the chapter.
• Compile a chapter, e.g. xelatex cartes_cerebrales.tex
• the resulting pdf is mega-huge. So shrink it with gs -sDEVICE=pdfwrite -dCompatibilityLevel=1.4 -dNOPAUSE -dQUIET -dBATCH -sOutputFile=notes_cours_cartes_cerebrales.pdf -dPDFSETTINGS=/ebook cartes_cerebrales.pdf
• Voilà 🎉 🎉 🎉

Contributors

We welcome and recognize all contributions. You can see a list of current contributors in the contributors tab.

Credits

This project is created using the excellent open source Jupyter Book project and the executablebooks/cookiecutter-jupyter-book template. Further credits for the book can be found in the book itself.