neurodatahub-cli 1.0.3

A command-line interface for downloading neuroimaging datasets and brain atlases

NeuroDataHub CLI

A command-line interface for downloading neuroimaging datasets and brain atlases with ease! Access 39 popular neuroimaging datasets from various sources (INDI, OpenNeuro, ReproBrainChart, IDA-LONI) and 10 curated brain atlases for network analysis.

🌐 Homepage: https://blackpearl006.github.io/NeuroDataHub/ 📦 Repository: https://github.com/blackpearl006/neurodatahub-cli

Features

• 🗂️ 39 Datasets: Access popular neuroimaging datasets from multiple sources (87% with metadata)
• 🧠 10 Brain Atlases: Curated atlases from BrainGraph (AAL90, Glasser360, Power264, etc.)
• 🔍 Smart Search: Find datasets by name, description, or category
• 🚀 Multiple Backends: Supports AWS CLI, aria2c, DataLad, and more
• 🔐 Authentication Support: Handles various authentication workflows
• 📊 Rich UI: Beautiful tables, progress bars, and interactive prompts
• ⚡ Resume Support: Interrupted downloads can be resumed
• 🛡️ Dependency Checking: Validates required tools with helpful installation guidance
• 🎯 Filtering: Filter datasets by category, authentication requirements, size, etc.
• 📁 Organized Output: Separate anat/ and metadata/ folders for datasets

Quick Start

Installation

# Via pip
pip install neurodatahub-cli

# Via conda (coming soon - Windows compatibility in progress)
# conda install -c conda-forge neurodatahub-cli

Basic Usage

# List all available datasets
neurodatahub --list

# Search for specific datasets
neurodatahub search "brain development"

# Get detailed info about a dataset
neurodatahub info HBN

# Download a dataset
neurodatahub --pull HBN --path ./data/HBN

# Check system dependencies
neurodatahub check

Brain Atlas Commands

# List all available atlases
neurodatahub atlas list

# Filter atlases by type
neurodatahub atlas list --type functional

# Get detailed atlas information
neurodatahub atlas info HCP_MMP_GLASSER_360

# Download a specific atlas
neurodatahub atlas download AAL90 --path ./atlases

# Download all atlases
neurodatahub atlas download-all --path ./all_atlases

# Show attribution information
neurodatahub atlas attribution

Dataset Categories

INDI Datasets (No Authentication Required)

Access datasets from the International Neuroimaging Data-sharing Initiative:

• HBN - Healthy Brain Network (2TB)
• CORR - Consortium for Reliability and Reproducibility (500GB)
• ADHD200 - ADHD diagnosis dataset (200GB)
• NKI - Nathan Kline Institute Rockland Sample (800GB)
• And many more...

OpenNeuro Datasets (No Authentication Required)

Open platform datasets:

• AOMIC variants - Amsterdam Open MRI Collection
• Pixar - fMRI responses to movie clips
• MPI - Max Planck Institute datasets
• Dense sampling - High-resolution single subjects

Independent Datasets

• IXI - Imperial College London brain MRI (12GB)
• OASIS-1/2 - Cross-sectional and longitudinal aging studies
• HCP - Human Connectome Project (requires authentication)
• CamCAN - Cambridge aging study (requires authentication)

ReproBrainChart (RBC) Datasets

Git/DataLad-based datasets:

• PNC - Philadelphia Neurodevelopmental Cohort
• BHRC - Brain Health Registry Cohort
• CCNP - Chinese Color Nest Project

IDA-LONI Datasets (Interactive Authentication)

Datasets requiring complex authentication workflows:

• ADNI - Alzheimer's Disease Neuroimaging Initiative
• PPMI - Parkinson's Progression Markers Initiative
• AIBL - Australian Imaging Biomarkers study
• MCSA - Mayo Clinic Study of Aging

Installation & Dependencies

System Dependencies

Different datasets require different tools. The CLI will guide you through installation:

# AWS CLI (for INDI and OpenNeuro datasets)
pip install awscli
# or
conda install -c conda-forge awscli

# aria2c (for fast parallel downloads)
brew install aria2          # macOS
apt-get install aria2       # Ubuntu/Debian
conda install -c conda-forge aria2

# DataLad (for RBC datasets)
pip install datalad

# Firefox (for interactive authentication)
# Download from https://www.mozilla.org/firefox/

Check Dependencies

neurodatahub check

This will show you which tools are installed and provide installation guidance for missing dependencies.

Command Reference

Core Commands

List Datasets

# List all datasets
neurodatahub --list
neurodatahub list

# Filter by category
neurodatahub --list --category indi
neurodatahub list --category openneuro

# Show only datasets requiring authentication
neurodatahub --list --auth-only
neurodatahub list --auth-required

# Show only datasets NOT requiring authentication  
neurodatahub --list --no-auth-only
neurodatahub list --no-auth

# Show detailed information
neurodatahub --list --detailed

Download Datasets

# Basic download
neurodatahub --pull HBN --path ./data/HBN
neurodatahub pull HBN ./data/HBN

# Dry run (see what would be downloaded)
neurodatahub pull HBN ./data/HBN --dry-run

# Skip confirmation prompts
neurodatahub pull HBN ./data/HBN --force

Information Commands

# Dataset information
neurodatahub info HBN

# Search datasets
neurodatahub search "alzheimer"
neurodatahub search "resting state"

# Show categories
neurodatahub categories

# Show datasets in specific category
neurodatahub categories --category ida

# Show statistics
neurodatahub stats

# Check system dependencies
neurodatahub check

# Show version
neurodatahub version

Authentication Workflows

No Authentication Required

Most INDI and OpenNeuro datasets can be downloaded immediately:

neurodatahub pull HBN ./data/HBN

AWS Credentials Required (HCP)

For datasets like HCP that require AWS credentials:

# The CLI will guide you through AWS setup
neurodatahub pull HCP_1200 ./data/HCP

# Or set up manually:
aws configure

IDA-LONI Interactive Workflow

For complex datasets like ADNI, PPMI, etc., the CLI provides an interactive checklist:

neurodatahub pull ADNI ./data/ADNI

This will walk you through:

1. ✅ IDA-LONI account registration
2. ✅ Data Use Agreement (DUA) approval
3. ✅ Image collection creation
4. ✅ Advanced Downloader link generation
5. ✅ IP address verification
6. 📥 Automated download execution

Examples

Download Multiple Datasets

# Download several INDI datasets
for dataset in HBN CORR ADHD200; do
  neurodatahub pull $dataset ./data/$dataset
done

Search and Filter Workflow

# Find brain development datasets
neurodatahub search "development"

# Show only small datasets without authentication
neurodatahub list --no-auth | grep -E "(MB|GB)" | head -5

# List all OpenNeuro datasets
neurodatahub list --category openneuro

Check Before Downloading

# Preview what will be downloaded
neurodatahub pull HBN ./data/HBN --dry-run

# Check system readiness
neurodatahub check

# Get dataset details
neurodatahub info HBN

Troubleshooting

Common Issues

Download Failed - Missing Dependencies

# Check what's missing
neurodatahub check

# Install missing tools as suggested
pip install awscli
brew install aria2

Authentication Issues

# For AWS datasets, check credentials
aws configure list

# For IDA-LONI datasets, verify:
# - Account registration
# - DUA approval
# - Same IP for link generation and download

Network/Resume Issues

# Most downloads can be resumed by re-running the command
neurodatahub pull HBN ./data/HBN

# For aria2c downloads, use native resume:
aria2c --continue=true [URL]

Getting Help

1. Built-in Help

   neurodatahub --help
   neurodatahub pull --help
   

2. Check Dependencies

   neurodatahub check
   

3. Dataset Information

   neurodatahub info DATASET_ID
   

4. GitHub Issues: https://github.com/blackpearl006/neurodatahub-cli/issues

Contributing

We welcome contributions! Please see our Contributing Guidelines for details.

Development Setup

git clone https://github.com/blackpearl006/neurodatahub-cli.git
cd neurodatahub-cli
pip install -e ".[dev]"

Running Tests

pytest tests/

License

MIT License - see LICENSE file for details.

Citation

If you use NeuroDataHub CLI in your research, please cite:

@software{neurodatahub_cli,
  title={NeuroDataHub},
  author={Ninad Aithal},
  year={2025},
  url={https://github.com/blackpearl006/neurodatahub-cli},
  version={0.1.0}
}

Acknowledgments

• Thanks to all dataset providers for making their data openly available
• INDI consortium for pioneering open neuroimaging data sharing
• OpenNeuro platform for standardized dataset hosting
• ReproBrainChart project for reproducible brain charting
• IDA-LONI for comprehensive neuroimaging data archives

Links

• 🌐 Homepage: https://blackpearl006.github.io/NeuroDataHub/
• 📦 PyPI: https://pypi.org/project/neurodatahub-cli/
• 📚 Documentation: https://blackpearl006.github.io/NeuroDataHub/docs/
• 🐛 Issues: https://github.com/blackpearl006/neurodatahub-cli/issues
• 💬 Discussions: https://github.com/blackpearl006/neurodatahub-cli/discussions

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Made with ❤️ for the neuroimaging community