UKBiobank calculator

The UK Biobank holds a lot of neuroimaging data (17K imaging subjects at the time of writing this post) and continues to scan subjects (see http://imaging.ukbiobank.ac.uk/ for more details). The DPUK Biobank node is intended to make it easier for dementia researchers to work with those data. You can create a spreadsheet of the subjects that you’re interested in from your biobank project (perhaps subjects over 60 with a family history of dementia/alzheimers/cognitive impairment) and upload that spreadsheet to the node to access the imaging data. If you wish to do this there are several questions that are worth asking:

  1. how long will it take for my upload spreadsheet to be processed?
  2. how much space will I need to store the images of interest?
  3. how long will it take to download the images?

We cant answer these questions categorically for you, as there are several possible confounding factors, but we can give you a ballpark to help your planning:

Spreadsheet upload

The spreadsheet upload is described in the projects page.  It takes approx 1.5 seconds to process each subject in the spreadsheet, but it’s not a process that needs to be watched.  You’ll receive an email when the upload’s finished.  Our test project included 8.5K subjects.  It took the node 3.5 hours to load the data from this spreadsheet.

Space requirement

There are six types of file and for each type you can access dicom or nifti files.   In our sampling of the codebase we’ve noticed the following size breakdowns:

SequenceDicom: Zipped size (MB)Dicom: Unzipped size (MB)Nifti: size (MB)
Functional brain images - task239363447
Multiband diffusion brain images123276501
Susceptibility weighted brain images588160428
T1 structural brain images379347
Functional brain images352535672
T2 FLAIR structural brain images29865
Total136829571700

So as a rough rule of thumb you’ll need 2GB for each subject to download the nifti images (e.g. 2TB for 1000 subjects) and 3GB for each subject to download and unzip the dicom images.

Download time

For downloading all of the dicoms we allow approx 1 minute per subject.

Matt

Matt is a software developer and system administrator based in the Oxford Centre for Human Brain Activity at Oxford University's department of Psychiatry