As the Principal Investigator (PI) of an approved UKBiobank (UKB) project you would have received an email containing a 32-character MD5 Checksum and a 64-character Password that can be used to access the subject information requested in your study. To access the images you must do five things:
- Download and convert your subject data to a CSV file
- Create an authentication file
- Create a project on the biobank node
- Add your key to the newly created project
- Upload the CSV file to the project
This page details each of the steps in turn.
Download and convert your subject data to a CSV file
To download your dataset, you must first login to the UK Biobank Showcase via the Access Management System, then select the Downloads option. Your dataset is stored in the dataset tab. Instructions for how to do this can be found on the UK Biobank web site.
This process is a one-off process and is required to be performed by one of the study members only. The UKB XNAT Node requires the output to be generated to a .CSV file so ensure to follow the correct instructions on the UKB web site. Once the .CSV file for the study has been created it can be uploaded into a project created on the UKB XNAT Node.
Create the authentication file
Some data is provided separately from the standard dataset. These are usually the Showcase fields that are large, complex objects and cannot be presented as a single row of data per participant. These files need to be accessed separately.
To access the image data repository, it is necessary to prove your identity to the system. This is done by supplying an Authentication File which contains your Application ID together with the first 24-characters of the 64-character decryption Password (provided to you via email).
The authentication file can be created in a standard text editor, for instance MS-Notepad on a Windows system or nano/emacs on a Linux system. It should contain two lines of text, the first containing the Application ID and the second the truncated password.
For example, if the Application ID is 123 and the decryption key is a1b2c3d4a1b2c3d4a1b2c3d4e5f6a44b343d334eef232ce3d3298ba847d2983c3cc23490 then the file contents would be:
The authentication file should be named “.ukbkey”.
This authentication file is then uploaded into the XNAT project and used by XNAT in the background when an authorised user is accessing an imaging resource via the UKB XNAT Node.
Setup and configure your UKB project
Once logged in to the UKB XNAT Node the following project listing page will be displayed and to create a new project click on the “New” menu item and select “Project”.
There are 3 mandatory fields to populate when creating the project. It is also important to define the accessibility of the project before pressing the “Submit” button. There are 3 different levels of accessibility, see below.
Private – Only you and study members will be able to access study data.
Protected – All users will be able to see your study title and description, but only collaborators you approve will be able to analyse and download data.
Public – All users will be able to access study data for analysis and download.
Add your key to the newly created project
Once the project has been created, navigate to the BioBank tab and upload the recently created token file (authentication file) by selecting the correct file and then click on the “Upload Token” button.
Upload the CSV file to the project
At this point it is possible to upload the data sheet previously created (.csv file) containing the subject information required to enable XNAT to access the associated image files for the subjects. To upload the subject information, select the file from the file system and click on the “Upload CSV” button.
Once all subjects have been loaded into XNAT from the spreadsheet, press the “Reload” button to verify that all subjects have been loaded, the system is ready to access image data from the UK Biobank image store.