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uniharmony 0.0.4.dev9 documentation

  • ▶️ Getting Started
  • 🛠️ Utilities
    • Multisite Data Simulation
    • MAREoS Benchmark Datasets
    • ON-Harmony Dataset
    • Datalad Integration
    • Site-Stratified Metrics
  • 🧮 Methods
    • 🤺 ComBat-based Harmonization
      • ComBat and neuroComBat
      • ComBat-GAM
      • CovBat
      • Neuroharmony
      • LongComBat
      • DeepComBat
      • PrettYharmonize
    • 📈 Interpolation-based Harmonization
      • Inter-Site Matched Interpolation (ISMI)
      • Intra-Site Interpolation (ISI)
    • 🔬 IQM-based Harmonization
      • BARTharm
  • 🎛️ Examples
    • Basic examples
      • Characterise a multisite problem
      • Explore EoS with dimensionality reduction techniques
      • Compute metrics by site
      • Characterise a multisite problem with MAREoS
      • Discover biases in metrics by site
      • Impact of Effects of Site in ML
    • Multisite Data
      • Load ON-Harmony dataset
      • Load MAREoS dataset
      • Generate imbalance multisite data
      • Multisite data generation
    • ComBat Methods
      • Analysing NeuroComBat behaviour with imbalance across sites
      • Binary classification with NeuroComBat
      • Analysing ComBatGAM behaviour with imbalance across sites
      • Binary classification with ComBatGAM
      • Using NeuroComBat with MAREoS dataset
      • Using ComBatGAM with MAREoS dataset
    • Interpolation Methods
      • Binary classification using ISI
      • IntraSiteInterpolation advance usage
      • Multiclass classification using ISI
      • Multisite Harmonization using Inter-Site Matched Interpolation (ISMI)
    • Optimal Transport based Domain Adaptation
      • Binary classification using OTDA
  • 🗺️ API Reference
    • uniharmony
      • verbosity
      • verbosity_context
    • uniharmony.datasets
      • make_multisite_classification
      • load_MAREoS
      • load_ONharmony
      • download_bids_dataset
      • clean_tmp
      • list_available_files
    • uniharmony.metrics
      • report_metrics_by_site
    • uniharmony.combat
      • NeuroComBat
      • ComBatGAM
    • uniharmony.interpolation
      • InterSiteMatchedInterpolation
      • IntraSiteInterpolation
    • uniharmony.ot
      • OptimalTransportDomainAdaptation
  • 📂 CHANGELOG
  • .md

🛠️ Utilities

🛠️ Utilities#

  • Multisite Data Simulation
    • Overview
    • Usage
    • Behind the Scenes
    • Flexible Configuration
  • MAREoS Benchmark Datasets
    • Overview
    • Usage
    • Dataset Structure and Experimental Design
      • Effect
      • Effect Type
      • Replication Examples
    • Dataset Specifications
    • Scientific Rationale
    • Citation
  • ON-Harmony Dataset
    • Overview
    • Usage
    • Examples
      • Download all files for a subject and a session
      • Direct Download (No hidden cache)
      • Download diffusion MRI
    • Advanced Usage
      • Working with ON-Harmony Session Names
    • Citation
  • Datalad Integration
    • Overview
      • Key Features
    • Core Concepts
      • Hidden vs. Direct Mode
        • Hidden Mode (hidden=True, default)
        • Direct Mode (hidden=False)
    • Usage
      • Downloading Data
        • download_bids_dataset()
      • Dataset Management
        • clean_tmp()
      • Utility Functions
        • list_available_files()
    • Troubleshooting
      • Disk space running out
      • Clone fails with SSL error
  • Site-Stratified Metrics
    • Features
    • Quick Start
      • Auto-Binarization
      • How It Works

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Multisite Data Simulation

By uniharmony Contributors

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