Getting Started with XNAT Documentation

Welcome to the NYUAD XNAT User Documentation. This guide is designed to help you use XNAT through practical, hands-on workflows.

Documentation Structure

This documentation focuses on the core activities most users need:

XNAT Documentation Structure
1. Understanding MRI Data

Data formats and their relationships (DICOM → NIfTI → BIDS/HCP)

2. Running Pipelines on XNAT

Available tools for data conversion, quality control, and preprocessing

3. Downloading Data from XNAT

Multiple approaches: browser, desktop client, and automated scripts

Additional Resources: This documentation also includes account setup, data upload, prearchive review, project management, and support guidance.

How to Use This Documentation

If you’re new to XNAT:

  1. Read What is NYUAD XNAT? to understand what XNAT is and how we use it at NYUAD

  2. Start with Accessing XNAT to set up your account

  3. Read Understanding Data Structure to understand data formats

  4. Review Data Upload Procedures before adding new data

  5. Browse XNAT Pipelines Overview to see available tools

If you’re experienced:

  • Jump directly to the pipeline documentation for specific tools

  • Use the download methods section for efficient data retrieval

  • Use Troubleshooting Guide when a workflow fails or produces unexpected output