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Flywheel’s Comprehensive Support for BIDS

Author Staff

The Brain Imaging Data Structure (BIDS), is becoming a widely used standard in neuroimaging research collaboration. BIDS is a guide for how to organize neuroimaging and behavioral data and associated analytic applications.  Until BIDS, there has been no standard, making research collaboration difficult.  The BIDS initiative, led by Dr. Russell Poldrack and Dr. Chris Gorgolewski at the Stanford Center for Reproducible Neuroscience, addresses this need and opens the door for better collaboration. 

Flywheel, like BIDS, is about enabling researchers to collaborate with one another.  Flywheel is a comprehensive software platform for computational research and collaboration, while BIDS is a standard structure for sharing data and applications in neuroimaging.  The two are highly complementary.  Flywheel offers comprehensive support for BIDS including:

  • BIDS Conversion and Curation
  • BIDS Import
  • BIDS View
  • BIDS App Gears
  • BIDS Export

Let’s take a closer look at how Flywheel and BIDS differ when it comes to organizing data.  Flywheel’s default method for organizing files is to group them as individual time sequenced acquisitions, representing each unique measurement or scan as they come off the instrument.  Flywheel adds value by capturing the metadata and classifying each file to further identify its specific type (e.g., anatomical, functional). In contrast, BIDS groups files into folders by their class.  For example, the anat folder contains anatomical data, while the func folder holds functional data.  BIDS also specifies a file naming convention that incorporates multiple attributes of the scan into the filename, including the subject, session, type of scan, etc.  

Flywheel can accommodate alternate views and organization of data, such as BIDS, using its extensible metadata capability.  To implement BIDS support, the Flywheel system adds BIDS-specific metadata such as BIDS folder and BIDS filename to the appropriate objects within the Flywheel hierarchy.

One key challenge many researchers face is converting original DICOM scans into a BIDS dataset. Flywheel’s BIDS Curator Gear automates this process.  The BIDS Curator Gear uses a configurable template and Flywheel metadata to create and populate the necessary attributes for BIDS.  The BIDS Curator also leverages Flywheel’s ability to automate DICOM to NIfTI conversion to create the NIfTI files and metadata sidecars required by BIDS.  If some of the required attributes are missing in the existing metadata, that’s where the info editor comes in.  The info editor is a metadata editor for any custom metadata within Flywheel, including BIDS attributes.  With the info editor you can view attributes created by the BIDS Curator and edit any missing or incorrect attributes.

If you are a Flywheel Lab Edition user, you can easily import existing BIDS datasets into Flywheel using BIDS Import.  The BIDS Import tool uploads your existing BIDS dataset into Flywheel and retains all BIDS attributes as metadata.  This will allow you to reliably reproduce the dataset for subsequent export or use in BIDS App Gears.

With the BIDS metadata available in a Flywheel session, you can view your data in BIDS format using the BIDS View.  You can conveniently toggle back and forth between the standard Flywheel view and a BIDS view of your data.  The BIDS View will visually flag any invalid items to simplify finding items that need review and correction.

Flywheel’s BIDS capabilities also include support for BIDS Apps.  BIDS Apps are enabled as standard Flywheel Gears with the ability to prepare the input dataset in BIDS format.  Your BIDS App Gears can incorporate existing BIDS Apps or new custom applications in BIDS App format.  The Flywheel Gear Exchange currently includes a few popular BIDS App Gears, such as MRIQC and FMRIPREP.  

Finally, Flywheel allows you to download your entire project in BIDS format.  BIDS Export retains all of your BIDS attributes and structure, whether it was created using BIDS Import or BIDS Curator.  BIDS Export also performs a full BIDS validation to ensure compliance with the BIDS standard.  

Flywheel's BIDS capabilities make it a great platform for those who want to incorporate the BIDS standards naturally into their research workflow, while saving a significant amount of time.