The previous module, MRI scans, ensured that you were familiar with the types of MRI scan you might use, and how to describe and view those scans. With that background, you are now ready to learn about why and how you should convert those scans from DICOM to NIfTI images following the BIDS specification.

Goals This module explains the benefits of BIDS and provides practice converting DICOM data to BIDS using different tools. This will prepare you for the rest of the class where processing is done on BIDS datasets.

Module Description BIDS (Brain Imaging Data Structure) is a best practice convention for naming and organizing your NIfTI data. I explain why you should care about BIDS, and what you need to learn to take advantage of the rich BIDS infrastructure for organizing neuroimaging data. Crucially, you need to convert your DICOM data, so I introduce you to current options including dcm2niix, ezBIDS, BIDScoin, and Heudiconv. You'll get practice with three of these: dcm2niix, ezBIDS, and Heudiconv (I chose these three because each is very different, and I have had the most success with these). You will explore the resulting data structure and naming conventions so you are aware of issues impacting the creation of a BIDS-compliant dataset. I'll introduce you to the official and evolving BIDS specification. BIDS also requires that each NIfTI image be accompanied by a JSON (Javascript Object Notation) sidecar file that contains metadata related to that image, so you will spend time learning to understand and manipulate the structure and contents of those JSON files.

The BIDS and JSON module consists of 13 assignments: 11 lessons (including 4 practices and 2 reading assignments), and 2 quizzes. The readings include the paper that introduced BIDS to the world, and a subsequent paper focused on containerized BIDS apps, and a nice overview of DICOM to BIDS conversion issues.

Note

It takes a while to get used to the rules for naming and organizing BIDS files, but you'll get lots of exposure to BIDS naming in the next several lessons.

BIDS 1 (10 pts): Overview