BIDS Introduction
BIDS stands for Brain Imaging Data Structure. More can be found on their website bids.neuroimaging.io. BIDS is a codified way of organizing Neuroimaging and Behavioral experimental data for the purpose of sharing. The goal of BIDS integration in the Flywheel product is to allow users to work with their data as they would normally in a Flywheel project with as little overhead as possible, and ultimately be able to export their data in BIDS structure for sharing.
Researchers will also be able to import BIDS projects into Flywheel in order to be able to take advantage of the Flywheel infrastructure.
In order to accomplish these goals, data import and export tools have been created, along with a gear that can be run to convert a project to BIDS and rerun to update BIDS File paths and names. In addition, User Interface enhancements have been made to support the BIDS project organization, including the ability to edit info (metadata) for Projects, Sessions, Subjects, Acquisitions, Files, and Analyses, and the ability to view a session in its BIDS structure.
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We also have a collection of webinars on using BIDS and Flywheel.
BIDS Layout
In general, the BIDS project layout is organized as:
project/sub-<subject>[/ses-<session>]/<data_type>/
Files under the data folder also have special formatted filenames which can include fields such as modality, task and run index to name a few. Files can also include json sidecars, which includes additional metadata about the file (most commonly dicom headers). Json sidecar files have the same base name, with a .json extension. More detailed information about the specification can be found at https://bids-specification.readthedocs.io/en/stable/
BIDS in Flywheel
“Curation” is the process of producing metadata on an existing Flywheel project such that 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: at the project level and at the file level. The project level metadata ultimately gets output as the top-level `dataset_description.json` file. The file level 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:
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.
