Abstract
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.
Abbreviations
- ANTs
- Advanced normalization tools
- AD
- Alzheimer’s disease
- ADNI
- Alzheimer’s Disease Neuroimaging Initiative
- ANOVA
- Analysis of variance
- DTI
- Diffusion tensor imaging
- EB
- Empirical Bayes
- EMBARC
- Establishing Moderators and Biosignatures of Antidepressant Response in Clinical care
- FA
- Fractional anisotropy
- FWER
- Family-wise error rate
- GPR
- Gaussian process regression
- HAMD
- Hamilton Depression Rating Scale
- IPW
- Inverse probability weighting
- LDA
- Linear discriminant analysis
- LLD
- Late-life depression
- MASQ
- Mood and Anxiety Symptom Questionnaire
- MCI
- Mild cognitive impairment
- MD
- Mean diffusivity
- MVPA
- Multivariate pattern analysis
- OASIS
- Open Access Series of Imaging Studies
- PC
- Principal component
- PCA
- Principal component analysis
- QIDS
- Quick Inventory for Depression Symptomatology
- RMSE
- Root-mean-square error
- ROI
- Region of interest
- STAI
- Spielberger State-Trait Anxiety Inventory
- SVM
- Support vector machine
- SVR
- Support vector regression
- VDLC
- Vascular disease: Longitudinal changes