neurodatahub-cli 1.1.0

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

Privacy & Telemetry

NeuroDataHub CLI includes an opt-in telemetry and feedback system to help us understand usage patterns and improve the tool. Your privacy is our top priority.

What We Collect (Only if You Opt In)

✅ Anonymized usage data:

• Dataset download success/failure counts
• OS platform, Python version, CLI version
• Optional user-provided notes via --note flag

❌ What we DON'T collect:

• No IP addresses, usernames, or emails
• No local file paths or hostnames
• No persistent user identifiers
• No AWS credentials or authentication tokens
• No dataset contents

Telemetry Consent

On your first successful download, you'll be prompted to enable telemetry:

neurodatahub pull HBN ./data/HBN

# After download completes:
# "Enable telemetry? [Y/n]:"

Choose Y to help us improve or n to disable. Your choice is saved locally.

Feedback System

You can provide feedback manually at any time:

neurodatahub feedback
# or
neurodatahub --feedback

Feedback is also prompted automatically at milestones (runs 1, 3, 10, 30, 50, then every 50).

Opting Out

To disable telemetry, edit ~/.neurodatahub/state.json:

{
  "telemetry_consent_given": false,
  "telemetry_consent_asked": true
}

Or delete the file to be prompted again.

Learn More

For complete privacy details, see TELEMETRY.md.

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