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.

   
.. toctree::
   :maxdepth: 1
   :caption: Getting Started

   getting_started/what_is_xnat
   getting_started/overview

.. toctree::
   :maxdepth: 1
   :caption: Working with XNAT

   working_with_xnat/access
   working_with_xnat/uploading
   working_with_xnat/prearchive
   working_with_xnat/transferring_data
   working_with_xnat/uid_errors_archiving
   working_with_xnat/install_desktop_client
   working_with_xnat/enabling_pipelines
   working_with_xnat/running_pipelines
   working_with_xnat/parallel_processing

.. toctree::
   :maxdepth: 1
   :caption: Understanding MRI Data

   understanding_data/overview
   understanding_data/bids

.. toctree::
   :maxdepth: 1
   :caption: XNAT Pipelines

   processing_pipelines/overview
   processing_pipelines/dcm2niix
   processing_pipelines/dcm2bids
   processing_pipelines/dcm2hcp
   processing_pipelines/mriqc
   processing_pipelines/ari-validator
   processing_pipelines/fmriprep
   processing_pipelines/tractoflow
   processing_pipelines/hcp-pipeline

.. toctree::
   :maxdepth: 1
   :caption: Data Download Methods

   data_download/browser
   data_download/desktop_client
   data_download/python_scripts
   data_download/matlab_scripts

.. toctree::
   :maxdepth: 1
   :caption: Support

   support/faq
   support/troubleshooting
   support/data_loss_recovery
   support/contributing
   support/contact

.. toctree::
   :maxdepth: 1
   :caption: Coming Soon

   working_with_xnat/navigation
   working_with_xnat/project_management