Xnat:Quick Start Guide
To upload data to XNAT for the first time, several steps are required (also see image):
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All of these points are explained below. Furthermore, the different possible access rights for users and projects are listed in the last section.
Create account
Both services have a separate procedure for the registration of new users.
- For BIGR-XNAT: You can create an account on the registration page: https://bigr-xnat.erasmusmc.nl/app/template/Register.vm. Your account has to be approved by the administrator before it can be used.
- For BMIA-XNAT: You can create an account on the registration page: https://xnat.bmia.nl/app/template/Register.vm. Your account has to be approved by the TraIT servicedesk. Note that access to this service is in principle restricted to participants of CTMM projects.
More detailed information about registration, including screenshots, can be found in the Account Management section of the XNAT Documentation. Everything below Enhanced Authentication Options on that page is not relevant for our services.
Create project
After the account is approved, you can create a new project or request access to an existing one.
- To create a new project, select in the top menu the option New. A new menu should appear below it. Select 'Project' in that new menu. After filling in the details, a new project is created. Also see section 1 of Creating and Managing Projects chapter of the XNAT manual.
- To request access for a project, select the project on the homepage or via the left menu -> Other projects if the project is not listed on the home page. See Access rights below which role you should request for which actions. Each project has a principal investigator which should grant access for the request.
Upload and archive data
To store medical images in XNAT e.g. MRI, CT, PET, different upload techniques are available.
- Using the web interface
- Using the DICOM interface (for radiology workstation)
- Using the Pyxnat programmable interface.
Each of these techniques are explained in their corresponding pages (you click on the link).
When creating a new project in XNAT, the accessability can be configured as: public, protected and private.
- Public: anyone can see the data, but cannot not upload/delete data
- Protected: shown on the home page, but have to request access
- Private: not shown on the home page, have to request access
You can invite users to a project with the following steps (also see image):
- Select the project
- Go to the access tab in the center menu
- Select the user with the button 'Show list'
- Select the user with the appropriate role (see below)
- After confirmation the added user will receive an e-mail notification
When adding a new user to a project, his or her role can be configured as: owner, member, collaborator.
- Owner: can do any action for a project.
- Member: can do any action for a project, except deleting data.
- Collaborator: can read/download data.
See XNAT User Roles and Permissions and XNAT Central FAQ for more information.
