An Improved Pipeline for Constructing UK Biobank Brain Imaging Confounds

Abstract UK Biobank (UKB) brain imaging data is a one-of-a-kind resource for studying the links between the brain and demographic-, lifestyle- and genetic data. When establishing such links, it is crucial to account for confounding effects caused by the acquisition of fMRI images, as well as demographic confounding factors. UKB brain imaging confounds are constructed through variable selection by the proportion of variance explained in the Imaging Derived Phenotypes (IDPs), from tens of thousands of possible confounds. The current implementation of this pipeline is very computationally intensive and has a large memory footprint, largely due to the varying patterns of missing data in IDPs. This makes it impractical for many users of UK Biobank brain imaging data. We propose a fast and memory efficient multivariate pipeline for constructing imaging confounds using mean imputation combined with a bias-corrected estimator of R2, the proportion of confound variance explained in an IDP. Building on this, we also improve the pipeline in order to better select confounds that explain unique variance in IDPs, and non-imaging variables of interest, so called nIDPs. The new implementation leads to a more compact set of confounds that explains roughly the same amount of variance, and runs in around 1 hour on a single CPU. Competing Interest Statement The authors have declared no competing interest. Funding Statement LR is supported by the EPSRC Centre for Doctoral Training in Health Data Science (EP/S02428X/1) The Wellcome Centre for Integrative Neuroimaging (WIN FMRIB) is supported by core funding from the Wellcome Trust (203139/Z/16/Z). SS: Wellcome Trust Collaborative Award 215573/Z/19/Z Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The UK Biobank has received ethical approval from the North West Multi-Center Research Ethics Committee (11/NW/0382). This research project received approval from the UKB under application number 8107. This research project has adhered to the Declaration of Helsinki. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Data Availability All data produced in the present work are contained in the manuscript