Welcome to junifer’s documentation!

junifer (JUelich NeuroImaging FEature extractoR) is a data handling and feature extraction library targeted towards neuroimaging data specifically functional MRI data.

It is currently being developed and maintained at the Applied Machine Learning (AML) group at Forschungszentrum Juelich, Germany. Although the library is designed for people working at Institute of Neuroscience and Medicine - Brain and Behaviour (INM-7), it is designed to be as modular as possible thus enabling others to extend it easily.

Contents:

• 1. Installing junifer
  • 1.1. Using a package manager
  • 1.2. From the source
• 2. Installing external dependencies
  • 2.1. AFNI
  • 2.2. FSL
  • 2.3. ANTs
  • 2.4. FreeSurfer
• 3. First steps with junifer
• 4. Understanding junifer
  • 4.1. The junifer Pipeline
  • 4.2. The Data Object
  • 4.3. Data Grabber
  • 4.4. Data Reader
  • 4.5. Preprocess
  • 4.6. Marker
  • 4.7. Storage
• 5. Using junifer
  • 5.1. Code-less Configuration
  • 5.2. Running Jobs
  • 5.3. Collecting Results
  • 5.4. Analysing Results
  • 5.5. Queueing Jobs (HPC, HTC)
  • 5.6. Configuring Pipeline Behaviour
  • 5.7. Dumping Pipeline Data
  • 5.8. Using Common Components
• 6. Built-in Pipeline Components
  • 6.1. Data Grabber
  • 6.2. Preprocessor
  • 6.3. Marker
  • 6.4. Parcellation
  • 6.5. Coordinates
  • 6.6. Mask
  • 6.7. Maps
• 7. Extending junifer
  • 7.1. Creating a junifer extension
  • 7.2. Creating Data Grabbers
  • 7.3. Creating Markers
  • 7.4. Creating Preprocessors
  • 7.5. Specifying Dependencies
  • 7.6. Adding Parcellations
  • 7.7. Adding Coordinates
  • 7.8. Adding Masks
  • 7.9. Adding Maps
  • 7.10. Creating a junifer plugin
  • 7.11. Creating a Data Registry
  • 7.12. Adding Data Types
  • 7.13. Adding Data Dump Assets
• 8. Examples
• 9. API Reference
  • 9.1. Pipeline Elements
  • 9.2. Utilities
  • 9.3. Configs
  • 9.4. External
• 10. Getting Help
• 11. Contributing
  • 11.1. Setting up the local development environment
  • 11.2. GitHub Pull Request guidelines
  • 11.3. Running unit tests
  • 11.4. Adding and building documentation
  • 11.5. Writing Examples
• 12. Maintaining
  • 12.1. Versioning
  • 12.2. Releasing a new version
• 13. FAQs
  • 13.1. How do I contribute to junifer?
  • 13.2. How do I set up VSCode for contribution?
• 14. What’s new
  • 14.1. Junifer 0.0.7.dev401 (2025-11-18)
  • 14.2. Junifer 0.0.6 (2025-03-24)
  • 14.3. Junifer 0.0.5 (2024-07-22)
  • 14.4. Junifer 0.0.4 (2024-04-05)
  • 14.5. Junifer 0.0.3 (2023-07-21)
  • 14.6. Junifer 0.0.2 (2023-03-31)
  • 14.7. Junifer 0.0.1 (2022-12-20)

Indices and tables

• Index

• Module Index

• Search Page

Funding

We thank the Helmholtz Imaging Platform, SMHB and eBRAIN Health (HORIZON-INFRA-2021-TECH-01) for supporting development of junifer. (The funding sources had no role in the design, implementation and evaluation of the pipeline.)