fMRI connectivity

fMRI connectivity

"An introduction to fMRI data: the captured signal, the main steps of preprocessing and how functional connectivity is calculated."


The estimated time to complete this training module is 4h.

The prerequisites to take this module are:

If you have any questions regarding the module content please ask them in the relevant module channel on the school Discord server. If you do not have access to the server and would like to join, please send us an email at school.brainhack [at] gmail [dot] com

Follow up with your local TA(s) to validate you completed the exercises correctly.


This module was presented by Pierre Bellec during the QLSC 612 course in 2020. The video of the presentation is available below:

The slides are available here.

You can find the Jupyter notebook for this module here


  • Watch the video presentation by Pierre Bellec and go over the slides.
  • Download the jupyter notebook using the link above or the following command
  • Run the notebook and complete the 3 exercises at the end.
  • Follow up with your local TA(s) to validate you completed the exercise correctly.
  • πŸŽ‰ πŸŽ‰ πŸŽ‰ you completed this training module! πŸŽ‰ πŸŽ‰ πŸŽ‰

More resources

Here are Pierre Bellec’s slides for a course on brain parcellation. They contain snippets of examples of nilearn code to load datasets, plot brains, compute and plot connectomes.

The chapter on Functional Connectivity from the course MΓ©thods en neurosciences cognitives is here (in French only).

The video on resting state mentioned by Pierre in his presentation is here.

Additional Nilearn tutorials on functional connectivity can be found here.

If you want to know more about fMRIprep, Basile Pinsard made a presentation on this topic for BrainHack school 2019: