NYUAD XNAT User Documentation

Welcome to the NYUAD XNAT User Documentation. This guide is designed to help you effectively use xnat with a focus on practical, hands-on workflows.

Getting Started

• What is NYUAD XNAT?
• Getting Started with XNAT Documentation

Working with XNAT

• Accessing XNAT
• Data Upload Procedures
• Understanding the Prearchive
• Transferring Data Between Projects
• Resolving UID Errors During Archiving
• Install XNAT Desktop Client
• Enabling Pipelines for Your Project
• Running Pipelines on XNAT
• Running Pipelines Across Multiple Subjects

Understanding MRI Data

• Understanding Data Structure
• BIDS Format

XNAT Pipelines

• XNAT Pipelines Overview
• dcm2niix
• dcm2bids
• dcm2hcp (Under Development)
• MRIQC
• ari-validator
• fMRIPrep
• TractoFlow
• HCP (Under Development)

Data Download Methods

• Download via Browser
• Download via Desktop Client
• Download via Python
• Download via MATLAB

Support

• Frequently Asked Questions
• Troubleshooting Guide
• Data Loss and Recovery
• Contributing to this Documentation
• Contact Information

Coming Soon

• XNAT Navigation Basics
• Project Management