BIDSonym

Description

A BIDS App for the de-identification of neuroimaging data. BIDSonym gathers all T1w images from a BIDS dataset and applies one of several popular de-identification algorithms. It currently supports:

MRI deface, Pydeface, Quickshear and mridefacer.

Additionally, the user can choose to evaluate the sidecar JSON files regarding potentially sensitive information, like for example participant names and define a list of fields which information should be deleted.

Using BIDSonym can help you make collected neuroimaging data available for others without violating subjects’ privacy or anonymity (depending on the regulations of the country you’re in).

BIDSonym Documentation

• Installation
  • Docker
  • Singularity
    • Preparing a Singularity image (Singularity version >= 2.5)
    • Preparing a Singularity image (Singularity version < 2.5)
    • Running a Singularity Image
  • Bare metal version (Python 3.6+)
    • External Dependencies
    • Previous image versions on OSF
• Usage
  • Execution and the BIDS format
  • Command-Line Arguments
    • Positional Arguments
    • Named Arguments
    • Example Call(s)
  • Support and communication
  • Not running on a local machine? - Data transfer
• Processing details
• Outputs of BIDSonym
  • Visual QA
  • Imaging data
    • copied non-defaced images
    • defaced images
  • Sidecar JSON and metadata .tsv files
    • metadata .tsv files
    • copied non-de-identified sidecar JSON files
    • de-identified sidecar JSON files
• An usage example
• Contributing to BIDSonym
  • Issue labels
  • Making a change
  • Notes for New Code
    • Catching exceptions
    • Testing
    • Recognizing contributions
• Credits
  • Maintainer
  • Contributors
• Citing BIDSonym
• Release History
  • v0.0.5 (2021-08-28)
  • v0.0.4 (2021-01-16)
  • v0.0.3 (2021-01-16)
  • v0.0.2 (2020-08-12)
  • v0.0.1 (2020-08-12)
• What’s new
  • Changes