Tools

This section describes core tools and standards produced by ReproNim. For a more comprehensive catalog of resources related to reproducible neuroimaging, please see the ReproInventory project.

Core Tools

• DataLad: Software for data versioning and distribution.
• HeuDiConv: A DICOM to BIDS converter.
• Neurobagel: A set of tools to query and share clinical and brain imaging data.
• Neurodocker: A tool to generate custom Dockerfiles and Singularity recipes to containerize neuroimaging tools.
• Nipoppy: A command line tool to manage a complete neuroimaging processing workflow.
• PyNIDM: A command line tool for working with NIDM data.
• ReproSchema: A tool for defining, sharing, and reusing structured research protocols, enabling versioning and interoperability across studies.

Core Standards

• The Brain Imaging Data Structure (BIDS): A standard for organizing neuroimaging data and metadata on disk.
• The Neuroimaging Data Model (NIDM): A Semantic Web extension for neuroimaging concepts.

Best Practices

• ReproIn: Scripts and configuration files for DICOM to BIDS conversion.