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:


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 Pierre Bellec to validate you completed the exercise correctly.
  • 🎉 🎉 🎉 you completed this training module! 🎉 🎉 🎉

More resources

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