False discovery rate control in magnetic resonance imaging studies via Markov random fields
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Updated: Jan 28, 2026

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Published on: January 6, 2019
Abstract:
Magnetic resonance imaging (MRI) is widely used to study population effects of factors on brain morphometry. Inference from such studies often require the simultaneous testing of millions of statistical hypotheses. Such scale of inference is known to lead to large numbers of false positive results. Control of the false discovery rate (FDR) is commonly employed to mitigate against such outcomes. However, current methodologies in FDR control only account for the marginal significance of hypotheses, and are not able to explicitly account for spatial relationships, such as those between MRI voxels. In this article, we present novel methods that incorporate spatial dependencies into the process of controlling FDR through the use of Markov random fields. Our method is able to automatically estimate the relationships between spatially dependent hypotheses by means of maximum pseudo-likelihood estimation and the pseudo-likelihood information criterion. We show that our methods have desirable statistical properties with regards to FDR control and are able to outperform noncontexual methods in simulations of dependent hypothesis scenarios. Our method is applied to investigate the effects of aging on brain morphometry using data from the PATH study. Evidence of whole brain and component level effects that correspond to similar findings in the literature is found in our investigation.
Insights
This study introduces a new method using Markov random fields to control false discoveries in brain imaging studies. It improves statistical accuracy by accounting for spatial relationships between MRI voxels, outperforming existing methods.
Area of Science:
- Neuroimaging
- Statistical genetics
- Computational neuroscience
Background:
- Magnetic resonance imaging (MRI) studies population effects on brain morphometry, involving millions of statistical hypotheses.
- High-dimensional inference leads to numerous false positives, commonly managed by controlling the false discovery rate (FDR).
- Existing FDR methods ignore spatial relationships between MRI voxels, limiting their accuracy.
Purpose of the Study:
- To develop novel methods for controlling FDR that explicitly incorporate spatial dependencies between MRI voxels.
- To improve the statistical rigor of neuroimaging studies by accounting for contextual information.
Main Methods:
- Utilized Markov random fields to model spatial dependencies between statistical hypotheses in MRI data.
- Employed maximum pseudo-likelihood estimation and the pseudo-likelihood information criterion for relationship estimation.
- Simulated dependent hypothesis scenarios to evaluate method performance.
Main Results:
- The proposed methods demonstrate desirable statistical properties for FDR control.
- The novel approach outperformed non-contextual methods in simulations of spatially dependent hypotheses.
- Applied to the PATH study, the method identified age-related effects on brain morphometry at whole-brain and component levels.
Conclusions:
- Incorporating spatial dependencies via Markov random fields enhances FDR control in neuroimaging.
- The developed method offers a more accurate approach to analyzing large-scale neuroimaging data.
- Findings from the PATH study align with existing literature on aging and brain morphometry.
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