The brain imaging data standards and applications

The brain imaging data standards and applications

"Learning the basics of the brain imaging data structure, the pybids interface to interact with a BIDS-compliant dataset as well as the BIDS apps - a collection of software designed to operate on BIDS datasets."


The estimated time to complete this training module is 2h.

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 [dot] brainhack [at] gmail [dot] com.


This module was presented by Christopher J. Markiewicz during the QLSC 612 course in 2020.

The slides are available here.

The video of his presentation is available below:


  • Download a few subjects (n=3) from the dataset DS000228 on openneuro. Hint: the dataset is available with datalad from this git repository.

  • Check that the resulting folder is a bids-compliant dataset using the bids validator (using a web browser or a local npm install). Did you get any warnings? Explain what they are and whether they are a concern.

  • Install pybids. Use pybids to get a list of all BOLD nii.gz files for subject pixar003. In which folder did you find them? is it logical? You may want to have a look at the BIDS documentation to familiarize yourself with the BIDS standard.

  • Using pybids, get a list of the flip angles in DS000228.

  • Clone a Midnight Brain Scan dataset from this git repository. Use pybids to load the participant.tsv file as a pandas dataframe in python.

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

  • 🎉 🎉 🎉 you completed this training module! 🎉 🎉 🎉

More resources

If you want to learn more about BIDS and pybids, check: