Tools

This section describes core tools and standards produced by ReproNim. Each tool page has a description of the tool, the principles and actions to which it applies and provides information on how to access the tool along with links to help materials, useful references and tutorials.

For a general orientation to ReproNim resources, we suggest reviewing the Getting started with ReproNim and Resources overviews.

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.

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.

Infrastructure

• ReproLake: A public triplestore of neuroimaging metadata.

Best Practices

• ReproIn: Convention and helpers for naming and organization of MRI sequences for turnkey DICOM to BIDS conversion.