Brain Imaging Data Structure (BIDS)

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

NoteExercise 1: Explore BIDS datasets on OpenNeuro

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:

   • Visit https://openneuro.org/
   • Browse the available datasets on the homepage

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?

NoteExercise 2: Hands-on BIDS practice

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

NoteHow can I download the slides as a PDF file?

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.

Here’s what the Chrome print dialog would look like with these settings enabled:

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