Welcome to the Online XNAT Workshop. Completing this online training is an acceptable substitute for the in-person XNAT Workshop. By watching all the workshop videos below and completing the associated quiz you will have completed the mandatory training component for enabling your user account. XNAT administrators will automatically be notified when you have completed the quiz.

The workshop videos can be viewed at your own speed and the quiz can be taken after the completion of all videos.

By the end of this tutorial you should know how to navigate XNAT, the XNAT data model, how to upload and download data, the user permission roles, proper naming convention, how to set up pre-processing scripts.
If you would like to know more about XNAT beyond the scope of this tutorial, you can check out the official XNAT documentation here.

Resources:

Get the course slides: Here
Start the Quiz: Here
Need Help? Contact: xnat.neuro@camh.ca

IMPORTANT NOTE: the following videos reference neurowiki.camh.ca as a resource for information on naming convention and xnat procedures. The neurowiki is now deprecated. All information that was found on neurowiki can now be found here on confluence by searching in the left panel.

Course Outline

Course Introduction

Link to Course Introduction video

What you'll learn:

Workshop Requirements
Course Rubric

Neuroinformatics Platform Overview

Link to Neuroinformatics Platform Overview video

What you'll learn:

What is XNAT
What is the Neuroinformatics Platform

Getting Started with the Neuroinformatics Platform

Link to Neuroinformatics Platform Overview video

What you'll learn:

How to get started with the Neuroinformatics Platform
How to create a New User Account
How to create a New Project
XNAT permission model
How to share data between Projects
The Neuroinformatics Platform Naming Convention

Resources:

Introduction to XNAT

Link to Introduction to XNAT video

What you'll learn:

The XNAT Data Model
Navigating XNAT
Archive vs. Prearchive
Viewing data
Moidifying data

Working with MR/PET Data

Link to Working with MR/PET Data video

What you'll learn:

Uploading data manually
How to setup automated uploads
Anonymization
Downloading data

Working with EEG Data

Link to Working with EEG Data video

What you'll learn:

Uploading data manually
How to setup automated uploads
Downloading data

Pipelines

Standard Pipelines

These pipelines will run on your data without any additional configuration steps. Raw data will not be altered and is still available.

Link to Standard Pipelines video
What you'll learn:

Pipelines that will run automatically on your data:
- Name Checker (All data)
- fBIRN QC (Only fMRI)
- Manual QC (Optional, only MR)

Optional Pipelines

The following pipelines must be configured before they will run. The Next 4 subsections are optional learning (not mandatory for the quiz) but are recommended. If you only want to learn the absolute minimum for the quiz, you can jump ahead to this section Pipeline Next Steps