Introduction to the Brain Imaging Data Structure

BIDS BIDS Spec HeuDiConv PyDeface MRIQC

Overview

Topics

• 💡 Introduction to the Brain Imaging Data Structure (BIDS)
• 💡 Transform your DICOM MRI data to BIDS using HeuDiConv
• 💡 Pseudonymize your MRI data by removing facial structure from MRI images using PyDeface
• 💡 Inspect the quality of your MRI data using MRIQC
• 💡 Preprocess fMRI data using fMRIPrep

The Brain Imaging Data Structure (BIDS) is a simple and intuitive way to organize and describe data. HeuDiConv is a flexible DICOM converter for organizing brain imaging data into structured directory layouts. PyDeface is a tool to remove facial structure from MRI images. MRIQC extracts image quality metrics from structural (T1w and T2w) and functional MRI (magnetic resonance imaging) data. fMRIPrep is a functional magnetic resonance imaging (fMRI) data preprocessing pipeline.

Target audience

Students or researchers at any level.

Prerequisites

Beneficial, but not required:

• Basic Python or Bash skills
• Bring your own MRI dataset
• Optional: Access to a high-performance computing (HPC) cluster

Key learning objectives

At the end of this training, participants will be able to

1. Understand the organization and benefits of BIDS
2. Transform their MRI DICOM data to BIDS
3. Remove facial features from MRI images using PyDeface
4. Evaluate the quality of MRI data using MRIQC
5. Optional: Preprocess their fMRI data using fMRIPrep

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Images: BIDS Logo on Wikimedia Commons. License: Creative Commons Attribution 4.0 International; Illustration of a BIDS structured dataset. License: Creative Commons Attribution 4.0 International.

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