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

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.

Additional Associated Tools

In addition to our Core Tools, ReproNim has developed an extensive set of additional tools that serve more specialized purposes. These include:

  • con/duct - A helper to run a command, capture stdout/stderr and execution metadata
  • ReproMan - Simplify creation and management of computing environments in Neuroimaging
  • Open Brain Consent - Make open data sharing a no-brainer for ethics committees
  • repromon - A service to monitor data acquisition etc to alert if anything goes wrong
  • testkraken - Generalized regression testing of scientific workflows
  • reprostim - Automated capture of audio-visual stimuli into BIDS datasets
  • reproflow - Materials for ReproFlow: ReproNim tools to establish scalable and automated MRI and behavioral data acquisition and QC
  • reprozip - ReproZip is a tool that simplifies the process of creating reproducible experiments from command-line executions, a frequently-used common denominator in computational science.

NIDM Converters

The following tools support conversion of the outputs of specific tools into the NIDM representation.

  • FreeSurfer
    • segstats_jsonld - Script to Export Freesurfer-based Parcellation/Segmentation Stats and Provenance as JSON-LD and NIDM
  • FSL
    • fsl_seg_to_nidm - Converts structural segmentation outputs from FSL’s FIRST and FAST tool to NIDM
  • ANTS