Viewing BIDS Metadata in Flywheel
Introduction
Brain Imaging Data Structure (BIDS) is a codified way of organizing neuroimaging and behavioral experimental data for the purpose of sharing. More can be found on their website bids.neuroimaging.io. The goal of BIDS integration in the Flywheel product is to allow users to work with their data as they would normally with as little overhead as possible, and ultimately be able to export their data in BIDS structure for sharing.
See "Flywheel + BIDS: how to start". This article gives an overview of where BIDS metadata appears in Flywheel.
Prefer videos?We also have a collection of webinars on using BIDS and Flywheel.
Instruction Steps
Viewing Metadata in Flywheel
Curation is the process of producing metadata on an existing Flywheel project so the project can then be exported in the BIDS format. BIDS metadata is stored in the open-ended info.BIDS attribute that is associated on every project, session, acquisition, analysis, and file object in the Flywheel system. This metadata is used in the BIDS view in the acquisitions section of the UI, as well as for the final export of a project to BIDS.
info.BIDS
There are two prominent places where BIDS metadata is stored:
- Project metadata: The BIDS project metadata becomes the top-level
dataset_description.json. - File metadata: The file metadata is used to build the file folder, path and filename fields which describe where the file will be placed when exported to BIDS.
Project BIDS Metadata
Here is an example of project metadata:
File BIDS Metadata
Here is an example of the file metadata:
How is this metadata used to export a project in BIDS format?
The only fields that are looked at when exporting BIDS are Path (the subfolder where the file is stored) and Filename (the name of the file when exported). The **Folder ** field is used when grouping Acquisitions in the BIDS view.
For this particular file, the Filename and Path is built automatically using other fields in the metadata (and in the project/session/subject’s metadata). This is a demonstration of how fields from subject and session can be used when constructing the filename.
- Filename here is resolved as:
sub-<subject.code>_ses<session.label>_<modality>.nii.gz - Path is resolved as:
sub-<subject.code>/ses-<session.label>/<Folder>
This is a demonstration of how fields from subject and session can be used when constructing the filename.
BIDS Interface Support
Info Editor
Info editing allows for quick and easy editing of information on any of: projects, sessions, subjects, acquisitions, analyses and files, including, but not limited to, BIDS metadata.
BIDS View
The BIDS View is available on the acquisitions tab for projects that have either been imported, or curated for BIDS. The BIDS View is a toggle that switches the file layout to indicate what the folder structure would be if the session were exported as BIDS.
