About this course

These two neuroimaging courses were created for the Research Master Psychology at the University of Amsterdam. The fMRI-introduction course is an eight-week course, which contains seven weeks of extensive tutorials (and a final exam in the eighth week). The fMRI-pattern-analysis is a four-week course, with three weeks of tutorials (and a final project in the last week).

The week-by-week contents of the course roughtly match the sections on this website (see left sidebar). Our students spend about 20 hours per week on this course, but you may of course do the tutorials in any order and pace you want!

Tutorials

This website contains information and tutorials about fMRI analyses. Each topic/tutorial has its own page. Tutorials are designed with a (T) in the menu on the left. The tutorials were written in Jupyter notebooks, which are embedded as static HTML files on the website. You can, of course, just read through these pages, but Jupyter notebooks really shine when used interactively, which allows you to add, change, run the Python code embedded in these notebooks.

To use these notebooks interactively, you can click on the “rocket” button at the top right of the page (see below; note that this button doesn’t do anything). This reveals two options: Binder and JupyterHub. Both allow you to run the notebooks interactively, but the latter is only available to students of the Research Master Psychology.

Many of the notebooks contain exercises (“ToDos” and “ToThinks”), which are included to make you think about the material and understand the concepts by implementing them in code. For many of the code exercises, the notebook contains “test cells” which you can run to see whether your implementation is correct. Note that the solutions for these exercises are not available (because the exercises are graded in our own on-site course).

Availability of materials

All material from this course is open-source and available under the BSD 3-clause license. This allows redistribution and use, with or without modification, as long as proper attribution is given (see below). We would love it when others would use this material!

Mistakes, errors, bugs

Although the course materials are tested regularly, they likely still contain mistakes, (spelling) errors, and bugs. You can raise an issue or suggest and edit by clicking on the Github button (see below) on the top of each page.

For more information about contributing, check out this page.

Acknowledgements

The course material was developed by Lukas Snoek with help from Noor Seijdel, Jessica Loke, and Carolin Streitberger. The course structure was inherited from a previous Matlab-based course designed by H. Steven Scholte.

The exercises in Jupyter notebook tutorials were created using the nbgrader package [Ham16]. This website was created using the awesome Jupyter book package.

Attribution

Snoek, L. (2021). NI-edu (Version 0.1.0) [Computer software]. https://doi.org/10.5281/zenodo.5658183