Brain Imaging Data Structure (BIDS)

Starts at:

Thursday, 14:30

Slides

Objectives

💡 You understand what BIDS (Brain Imaging Data Structure) is and why it’s important for neuroimaging.
💡 You can explain the core principles of BIDS and how it solves common data organization problems.
💡 You can organize neuroimaging data according to BIDS directory structure standards.
💡 You understand the role of JSON metadata files and TSV data files in BIDS datasets.
💡 You know how to validate BIDS datasets using the BIDS validator.
💡 You understand the benefits of using BIDS for collaboration, reproducibility, and data sharing.

Exercises

Exercise 1: Explore BIDS datasets on OpenNeuro

Objective: Familiarize yourself with BIDS-formatted datasets and understand how standardized organization facilitates data sharing and reuse.

Instructions:

  1. Navigate to OpenNeuro:

  2. Select and explore a dataset:

    • Choose one dataset that interests you (e.g., neuroimaging study related to your research area)
    • Click on the dataset to view its details

  3. Examine the BIDS structure:

    • Click “Browse” or “Files” to view the dataset’s file structure
    • Explore the following directories (if present):
      • Root level files (dataset_description.json, README, participants.tsv)
      • Subject folders (sub-01, sub-02, etc.)
      • Session folders (if applicable: ses-01, ses-baseline, etc.)
      • Modality folders (anat, func, dwi, fmap, etc.)

  4. Explore the dataset:

    • What type of neuroimaging data does it contain?
    • How many subjects are included?
    • What file naming patterns do you observe?
    • Are there any derivative datasets associated with it?

  5. Compare with raw data organization:

    • Think about how this standardized structure compares to typical “raw” data organization
    • What advantages does this standardization provide for:
      • Data sharing?
      • Automated processing?
      • Reproducibility?

Discussion points:

  • How does the BIDS structure make it easier to understand the dataset without detailed documentation?
  • What challenges might researchers face when converting their data to BIDS format?

Exercise 2: Hands-on BIDS practice

Objective: Learn how to create a BIDS dataset using heudiconv and use BIDS validation.

Access the hands-on tutorial: https://lennartwittkuhn.com/rdm-bids/

Slides

To export the slides to PDF, do the following:

  1. Toggle into Print View using the E key (or using the Navigation Menu).
  2. Open the in-browser print dialog (CTRL/CMD+P).
  3. Change the Destination setting to Save as PDF.
  4. Change the Layout to Landscape.
  5. Change the Margins to None.
  6. Enable the Background graphics option.
  7. Click Save.

Note: This feature has been confirmed to work in Google Chrome, Chromium as well as in Firefox.

These instructions were copied from the Quarto documentation (MIT License) and slightly modified.

Resources