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elcome 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@camh.ca

Course Outline

Course Introduction

Link to Course Introduction video

What you'll learn:

• Workshop Requirements
• Course Rubric

Neuroinformatics Platform Overview

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What you'll learn:

• What is XNAT
• What is the Neuroinformatics Platform

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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:

• New User Request Form
• New Project Request Form

Introduction to XNAT

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What you'll learn:

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

Working with MR/PET Data

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What you'll learn:

• Uploading data manually
• How to setup automated uploads
• Anonymization
• Downloading data

Working with EEG Data

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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

MR Protocol QC

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• How to configure MR Protocol QC

Resources:

• Download example schematron
• Link to schematron standard

Dicom to Nifti Conversion

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What you'll learn:

• How to configure dicom to nifti conversion

Resources:

• Link to description of Rordenlab's dcm2niix script

EEG Pre-Process

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What you'll learn:

• How to configure EEG pre-processing conversion

Resources:

• Link to Redcap Pipeline Configuration form
• Link to description of MNE python package used to pre-process the data

EEG Protocol QC

Link to EEG Protocol QC video

What you'll learn:

• How to configure EEG Protocol QC pipeline

Resources:

• Link to Redcap Pipeline Config form

Pipeline Next Steps

Link to Pipeline Next Steps video

What you'll learn:

• How to request new pipelines
• Additional upcoming XNAT pipelines and features

Spotfire Introduction

Link to Spotfire Introduction video

What you'll learn:

• What is Spotfire
• How can it be used for your project

Take the Quiz

Now that you've completed all the video tutorials take the quiz!

• Take the Quizz

Congratulations!

You've completed the XNAT online workshop. You can now create a Neuroinformatics Platform user account and project.