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Welcome to the Krembil Center for NeuroInformatics XNAT page.

This page is meant to be a guide for new KCNI XNAT users as well as a reference for experienced XNAT users.

In this XNAT section, you'll find:

  • Introduction
  • Next Steps for New Users
  • Account Request Instructions
  • Links to External Resources

What is XNAT?

The eXtensible Neuroimaging Archive Toolkit (XNAT) is an open-source imaging informatics platform used by CAMH's Neuroinformatics Platform. It facilitates common data management, data storage, provenance tracking, image processing utilities, and quality assurance tasks for imaging and associated data. Essentially, it provides a project hub for managing your imageing data. Furthermore, as part of the Neuroinfoimatics platform, the data stored in XNAT can be federated with data from other domains like genetic data or clinical assessments and is then made available in a centralized location as described here. It's a great resource for any projects at CAMH that acquire neuroimaging data like MRI, PET, CT or EEG.

Who Uses XNAT?

Our instance of XNAT is hosted at CAMH and is freely available for use by all CAMH members and collaborators. Typically, a Principal Investigator (PI) will coordinate with the neuroinformatics team at the KCNI to set up a study on XNAT; instructions for this process can be found in the [[#New Project Request]] section 6455465 section. Meanwhile, all collaborators including students, research assistants and colleagues who would like access to the XNAT study will submit a user account request form for approval by the PI and the KCNI team. Instructions for this process can be found in the [[#New User Request]] section 6455465 section.
It's important to note that all users, including PI's will have to attend an [[XNATOnlineWorkshop| an XNAT Workshop]] (now online) for guidance on how to use XNAT and CAMH best practices before their user accounts will be approved by the KCNI team.

Next Steps

For prospective XNAT users, your next steps are:

Training

Mandatory XNAT Training for New Users can now be done online [[XNATOnlineWorkshop| online XNAT Workshop]]. Please complete the short quiz after completing the videos.

New User Request

You can request a New Neuroinformatics/XNAT User Account once you have succesfully completed the training and quiz. To do so, complete

To request a new user account:

[https://edc.camhx.ca/redcap/surveys/?s=8C74RY7MR8 Here].
  • . (If you know the project to which you would like access and the project has already been created on XNAT, please have the REB number and XNAT Project code ready as you will need it to complete the form.)
  • Once completed, a confirmation email will be sent to your PI and XNAT admin to approve your access.
  • Following approval, you will receive an email inviting you to create your account on XNAT.

If you are a ''' staff or student at CAMH''':

  •  You can login at [https://at xnat.camh.ca/xnat] using / using your CAMH email username and password. (warning) (NOTE: You must use firstname_lastname for username and your password must be your CAMH password)
  • It will then prompt you to register a new account; fill-in with your information. (warning) (NOTE: The registration panel will autofill and remove the underscore in your username, please replace it so that your username is firstname_lastname before finalizing your registration)
  • An email will be sent to XNAT admin to Enable your account.
  • Once Enabled (usually within less than 24hrs), you will be notified via email and your account creation is complete.
  • At the XNAT login page make sure the login drop down box is set to "CAMH". This should be the default.
  • You can now access your projects on XNAT.

If you ''' do not have a CAMH email''':

  • Go to [https://xnat.camh.ca/xnat], you will need to first select "database" from the dropdown menu on the login page.
  • Create a username and password, preferably your username will be firstname_lastname.
  • Click ~register~ register. You will then be prompted for more information, fill in this information and click ~register~ register.
  • You will then be sent an verification email, and be prompted to return to the XNAT login page.
  • Click the link the in the verification email, XNAT Admin will be notified and will enable your account.
  • Once enabled, you will be notified via email.
  • To access data, go to XNAT and on the login page select "database" from the Login dropdown menu above the username entry field. (Note: this is not selected by default. This must be selected everytime at login.)
  • Eenter your credentials, you will then be able to login to XNAT to access your project using your new credentials.

New Project Request

If you would like to create a new project on the Neuroinformatics Platform, you can request a New Neuroinformatics/XNAT Project completing the following steps:

  • Completing the Project Request Form.
  • Once completed, an email will automatically be sent to the specified PI for approval, followed by Neuroinformatics Platform Admin.
  • Once the PI approval email is received, the project will be created.
  • You will then receive an email notification from the Neuroinformatics Platform team to request a meeting to discuss any specific needs your project might have as well as any specific project initialization steps that need to be taken. This might include sharing credentials to set up automated image uploads to XNAT or processing pipeline parameters.

Useful Links