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
- 1 Course Introduction
- 2 Neuroinformatics Platform Overview
- 3 Getting Started with the Neuroinformatics Platform
- 4 Introduction to XNAT
- 5 Working with MR/PET Data
- 6 Working with EEG Data
- 7 Pipelines
- 7.1 Standard Pipelines
- 7.2 Optional Pipelines
- 7.2.1 MR Protocol QC
- 7.2.2 Dicom to Nifti Conversion
- 7.2.3 EEG Pre-Process
- 7.2.4 EEG Protocol QC
- 7.3 Pipeline Next Steps
- 8 Take the Quiz
- 9 Congratulations!
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
MR Protocol QC
Link to MR Protocol QC video
What you'll learn:
- How to configure MR Protocol QC
Resources:
Dicom to Nifti Conversion
What you'll learn:
- How to configure dicom to nifti conversion
Resources:
- Link to description of Rordenlab's dcm2niix script
EEG Pre-Process
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
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!
Congratulations!
You've completed the XNAT online workshop. You can now create a Neuroinformatics Platform user account and project.
Contact: