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junifer documentation

Contents:

  • 1. Installing junifer
  • 2. Installing external dependencies
  • 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
    • 5.8.1. Masks
  • 6. Built-in Pipeline Components
  • 7. Extending junifer
    • 7.1. Creating a junifer extension
    • 7.2. Logging in a junifer extension
    • 7.3. Creating Data Grabbers
    • 7.4. Creating Markers
    • 7.5. Creating Preprocessors
    • 7.6. Specifying Dependencies
    • 7.7. Adding Parcellations
    • 7.8. Adding Coordinates
    • 7.9. Adding Masks
    • 7.10. Adding Maps
    • 7.11. Creating a junifer plugin
    • 7.12. Creating a Data Registry
    • 7.13. Adding Data Types
    • 7.14. Adding Confounds Format
    • 7.15. Adding Data Dump Assets
  • 8. Examples
    • 8.1. UKB VBM GMD Extraction
    • 8.2. Generic BIDS DataGrabber for datalad.
    • 8.3. UCLA CNP VBM GMD Extraction
    • 8.4. Extracting root sum of squares from edge-wise timeseries.
    • 8.5. Compute Parcel Aggregation.
    • 8.6. HCP FC Extraction
    • 8.7. Run junifer and julearn.
  • 9. API Reference
    • 9.1.1. Data Grabbers
    • 9.1.2. DataReaders
    • 9.1.3. Pre-processing
    • 9.1.4. Markers
    • 9.1.5. Storage
    • 9.2.1. Data
    • 9.2.2. Stats
    • 9.2.3. Pipeline
    • 9.2.4. API Functions
    • 9.2.5. CLI Functions
    • 9.2.6. Utils
    • 9.2.7. Testing
    • 9.2.8. On-the-fly
    • 9.3.1. Configs
    • 9.4.1. Nilearn
  • 10. Getting Help
  • 11. Contributing
  • 12. Maintaining
  • 13. Implementation details
  • 14. FAQs
  • 15. What’s new
v0.0.8
  • v0.0.8 (latest)
  • v0.0.7
  • v0.0.6
  • v0.0.5
  • v0.0.4
  • v0.0.3
  • v0.0.2
  • v0.0.1
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✓ Latest release — You are viewing the documentation for the latest stable release of junifer (v0.0.8).