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.
This article gives an overview of the BIDS specification and where BIDS metadata appears in Flywheel.
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We also have a collection of webinars on using BIDS and Flywheel.
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 the BIDS documentation
Here is an example subject (with a single session) layout from the BIDS spec that includes sidecars:
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sub-control01
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anat
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sub-control01_T1w.nii.gz -
sub-control01_T1w.json -
sub-control01_T2w.nii.gz -
sub-control01_T2w.json
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func
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sub-control01_task-nback_bold.nii.gz -
sub-control01_task-nback_bold.json -
sub-control01_task-nback_events.tsv -
sub-control01_task-nback_physio.tsv.gz -
sub-control01_task-nback_physio.json -
sub-control01_task-nback_sbref.nii.gz
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dwi
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sub-control01_dwi.nii.gz -
sub-control01_dwi.bval -
sub-control01_dwi.bvec
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fmap
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sub-control01_phasediff.nii.gz -
sub-control01_phasediff.json -
sub-control01_magnitude1.nii.gz
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code
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deface.py
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derivates
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README
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participants.tsv -
dataset_description.json -
README -
CHANGES
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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.
There are two prominent places where BIDS metadata is stored:
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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.
Here is an example of the file metadata:
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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.
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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.
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.
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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.
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Click Next to learn more about BIDS templates, which is how Flywheel uploads and curates data in to the BIDS format.