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:

.. image:: ../_static/1.1.docStructure.png 
   :alt: XNAT Documentation Structure
   :align: center
   :width: 900px

**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 :doc:`what_is_xnat` to understand what XNAT is and how we use it at NYUAD
2. Start with :doc:`../working_with_xnat/access` to set up your account
3. Read :doc:`../understanding_data/overview` to understand data formats  
4. Review :doc:`../working_with_xnat/uploading` before adding new data
5. Browse :doc:`../processing_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 :doc:`../support/troubleshooting` when a workflow fails or produces unexpected output