PT - JOURNAL ARTICLE AU - Jean-Philippe Fortin AU - Nicholas Cullen AU - Yvette I. Sheline AU - Warren D. Taylor AU - Irem Aselcioglu AU - Phil Adams AU - Crystal Cooper AU - Maurizio Fava AU - Patrick J. McGrath AU - Melvin McInnis AU - Ramin V. Parsey AU - Mary L. Phillips AU - Madhukar H. Trivedi AU - Myrna M. Weissman AU - Russell T. Shinohara TI - Harmonization of cortical thickness measurements across scanners and sites AID - 10.1101/148502 DP - 2017 Jan 01 TA - bioRxiv PG - 148502 4099 - http://biorxiv.org/content/early/2017/06/10/148502.short 4100 - http://biorxiv.org/content/early/2017/06/10/148502.full AB - With the proliferation of multi-site neuroimaging studies, there is a greater need for handling non-biological variance introduced by differences in MRI scanners and acquisition protocols. Such unwanted sources of variation, which we refer to as “scanner effects”, can hinder the detection of imaging features associated with clinical covariates of interest and cause spurious findings. In this paper, we investigate scanner effects in two large multi-site studies on cortical thickness measurements, across a total of 11 scanners. We propose a set of general tools for visualizing and identifying scanner effects that are generalizable to other modalities. We then propose to use ComBat, a technique adopted from the genomics literature and recently applied to diffusion tensor imaging data, to combine and harmonize cortical thickness values across scanners. We show that ComBat removes unwanted sources of scan variability while simultaneously increasing the power and reproducibility of subsequent statistical analyses. We also show that ComBat is useful for combining imaging data with the goal of studying life-span trajectories in the brain.AbbreviationsANTsAdvanced normalization toolsADAlzheimer’s diseaseADNIAlzheimer’s Disease Neuroimaging InitiativeANOVAAnalysis of varianceDTIDiffusion tensor imagingEBEmpirical BayesEMBARCEstablishing Moderators and Biosignatures of Antidepressant Response in Clinical careFAFractional anisotropyFWERFamily-wise error rateGPRGaussian process regressionHAMDHamilton Depression Rating ScaleIPWInverse probability weightingLDALinear discriminant analysisLLDLate-life depressionMASQMood and Anxiety Symptom QuestionnaireMCIMild cognitive impairmentMDMean diffusivityMVPAMultivariate pattern analysisOASISOpen Access Series of Imaging StudiesPCPrincipal componentPCAPrincipal component analysisQIDSQuick Inventory for Depression SymptomatologyRMSERoot-mean-square errorROIRegion of interestSTAISpielberger State-Trait Anxiety InventorySVMSupport vector machineSVRSupport vector regressionVDLCVascular disease: Longitudinal changes