False positives in neuroimaging genetics using voxel-based morphometry data
Voxel-wise statistical inference is commonly used to identify significant experimental effects or group differences in both functional and structural studies of the living brain. Tests based on the size of spatially extended clusters of contiguous suprathreshold voxels are also widely used due to th...
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Published in | NeuroImage (Orlando, Fla.) Vol. 54; no. 2; pp. 992 - 1000 |
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Main Authors | , , |
Format | Journal Article |
Language | English |
Published |
United States
Elsevier Inc
15.01.2011
Elsevier Limited Academic Press |
Subjects | |
Online Access | Get full text |
ISSN | 1053-8119 1095-9572 1095-9572 |
DOI | 10.1016/j.neuroimage.2010.08.049 |
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Abstract | Voxel-wise statistical inference is commonly used to identify significant experimental effects or group differences in both functional and structural studies of the living brain. Tests based on the size of spatially extended clusters of contiguous suprathreshold voxels are also widely used due to their typically increased statistical power. In “imaging genetics”, such tests are used to identify regions of the brain that are associated with genetic variation. However, concerns have been raised about the adequate control of rejection rates in studies of this type. A previous study tested the effect of a set of ‘null’ SNPs on brain structure and function, and found that false positive rates were well-controlled. However, no similar analysis of false positive rates in an imaging genetic study using cluster size inference has yet been undertaken.
We measured false positive rates in an investigation of the effect of 700 pre-selected null SNPs on grey matter volume using voxel-based morphometry (VBM). As VBM data exhibit spatially-varying smoothness, we used both non-stationary and stationary cluster size tests in our analysis. Image and genotype data on 181 subjects with mild cognitive impairment were obtained from the Alzheimer's Disease Neuroimaging Initiative (ADNI). At a nominal significance level of 5%, false positive rates were found to be well-controlled (3.9–5.6%), using a relatively high cluster-forming threshold, αc=0.001, on images smoothed with a 12mm Gaussian kernel. Tests were however anticonservative at lower cluster-forming thresholds (αc=0.01, 0.05), and for images smoothed using a 6mm Gaussian kernel. Here false positive rates ranged from 9.8 to 67.6%. In a further analysis, false positive rates using simulated data were observed to be well-controlled across a wide range of conditions.
While motivated by imaging genetics, our findings apply to any VBM study, and suggest that parametric cluster size inference should only be used with high cluster-forming thresholds and smoothness. We would advocate the use of nonparametric methods in other cases.
►RFT nonstationary cluster size test on VBM is found to be invalid based on empirical null studies. ►Invalid inferences (inflated false positive risk) were found with 3 voxel smoothing. ►With 6 voxel smoothing, invalid inferences were found with 6 voxel smoothing and alpha=0.01 cluster-forming threshold. ►RFT nonstationary test only found to be valid with 6 voxel smoothing with alpha=0.001 cluster-forming threshold. ►Equivalent Gaussian data simulations produced valid inferences, suggesting VBM data violates RFT assumptions and motivates the use of nonparametric permutation methods. |
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AbstractList | Voxel-wise statistical inference is commonly used to identify significant experimental effects or group differences in both functional and structural studies of the living brain. Tests based on the size of spatially extended clusters of contiguous suprathreshold voxels are also widely used due to their typically increased statistical power. In “imaging genetics”, such tests are used to identify regions of the brain that are associated with genetic variation. However, concerns have been raised about the adequate control of rejection rates in studies of this type. A previous study tested the effect of a set of ‘null’ SNPs on brain structure and function, and found that false positive rates were well-controlled. However, no similar analysis of false positive rates in an imaging genetic study using cluster size inference has yet been undertaken.
We measured false positive rates in an investigation of the effect of 700 pre-selected null SNPs on grey matter volume using voxel-based morphometry (VBM). As VBM data exhibit spatially-varying smoothness, we used both non-stationary and stationary cluster size tests in our analysis. Image and genotype data on 181 subjects with mild cognitive impairment were obtained from the Alzheimer's Disease Neuroimaging Initiative (ADNI). At a nominal significance level of 5%, false positive rates were found to be well-controlled (3.9–5.6%), using a relatively high cluster-forming threshold, αc=0.001, on images smoothed with a 12mm Gaussian kernel. Tests were however anticonservative at lower cluster-forming thresholds (αc=0.01, 0.05), and for images smoothed using a 6mm Gaussian kernel. Here false positive rates ranged from 9.8 to 67.6%. In a further analysis, false positive rates using simulated data were observed to be well-controlled across a wide range of conditions.
While motivated by imaging genetics, our findings apply to any VBM study, and suggest that parametric cluster size inference should only be used with high cluster-forming thresholds and smoothness. We would advocate the use of nonparametric methods in other cases.
►RFT nonstationary cluster size test on VBM is found to be invalid based on empirical null studies. ►Invalid inferences (inflated false positive risk) were found with 3 voxel smoothing. ►With 6 voxel smoothing, invalid inferences were found with 6 voxel smoothing and alpha=0.01 cluster-forming threshold. ►RFT nonstationary test only found to be valid with 6 voxel smoothing with alpha=0.001 cluster-forming threshold. ►Equivalent Gaussian data simulations produced valid inferences, suggesting VBM data violates RFT assumptions and motivates the use of nonparametric permutation methods. Voxel-wise statistical inference is commonly used to identify significant experimental effects or group differences in both functional and structural studies of the living brain. Tests based on the size of spatially extended clusters of contiguous suprathreshold voxels are also widely used due to their typically increased statistical power. In "imaging genetics", such tests are used to identify regions of the brain that are associated with genetic variation. However, concerns have been raised about the adequate control of rejection rates in studies of this type. A previous study tested the effect of a set of 'null' SNPs on brain structure and function, and found that false positive rates were well-controlled. However, no similar analysis of false positive rates in an imaging genetic study using cluster size inference has yet been undertaken. We measured false positive rates in an investigation of the effect of 700 pre-selected null SNPs on grey matter volume using voxel-based morphometry (VBM). As VBM data exhibit spatially-varying smoothness, we used both non-stationary and stationary cluster size tests in our analysis. Image and genotype data on 181 subjects with mild cognitive impairment were obtained from the Alzheimer's Disease Neuroimaging Initiative (ADNI). At a nominal significance level of 5%, false positive rates were found to be well-controlled (3.9-5.6%), using a relatively high cluster-forming threshold, alpha sub(c) = 0.001, on images smoothed with a 12 mm Gaussian kernel. Tests were however anticonservative at lower cluster-forming thresholds ( alpha sub(c) = 0.01, 0.05), and for images smoothed using a 6 mm Gaussian kernel. Here false positive rates ranged from 9.8 to 67.6%. In a further analysis, false positive rates using simulated data were observed to be well-controlled across a wide range of conditions. While motivated by imaging genetics, our findings apply to any VBM study, and suggest that parametric cluster size inference should only be used with high cluster-forming thresholds and smoothness. We would advocate the use of nonparametric methods in other cases. Voxel-wise statistical inference is commonly used to identify significant experimental effects or group differences in both functional and structural studies of the living brain. Tests based on the size of spatially extended clusters of contiguous suprathreshold voxels are also widely used due to their typically increased statistical power. In "imaging genetics", such tests are used to identify regions of the brain that are associated with genetic variation. However, concerns have been raised about the adequate control of rejection rates in studies of this type. A previous study tested the effect of a set of 'null' SNPs on brain structure and function, and found that false positive rates were well-controlled. However, no similar analysis of false positive rates in an imaging genetic study using cluster size inference has yet been undertaken. We measured false positive rates in an investigation of the effect of 700 pre-selected null SNPs on grey matter volume using voxel-based morphometry (VBM). As VBM data exhibit spatially-varying smoothness, we used both non-stationary and stationary cluster size tests in our analysis. Image and genotype data on 181 subjects with mild cognitive impairment were obtained from the Alzheimer's Disease Neuroimaging Initiative (ADNI). At a nominal significance level of 5%, false positive rates were found to be well-controlled (3.9-5.6%), using a relatively high cluster-forming threshold, α(c)=0.001, on images smoothed with a 12 mm Gaussian kernel. Tests were however anticonservative at lower cluster-forming thresholds (α(c)=0.01, 0.05), and for images smoothed using a 6mm Gaussian kernel. Here false positive rates ranged from 9.8 to 67.6%. In a further analysis, false positive rates using simulated data were observed to be well-controlled across a wide range of conditions. While motivated by imaging genetics, our findings apply to any VBM study, and suggest that parametric cluster size inference should only be used with high cluster-forming thresholds and smoothness. We would advocate the use of nonparametric methods in other cases.Voxel-wise statistical inference is commonly used to identify significant experimental effects or group differences in both functional and structural studies of the living brain. Tests based on the size of spatially extended clusters of contiguous suprathreshold voxels are also widely used due to their typically increased statistical power. In "imaging genetics", such tests are used to identify regions of the brain that are associated with genetic variation. However, concerns have been raised about the adequate control of rejection rates in studies of this type. A previous study tested the effect of a set of 'null' SNPs on brain structure and function, and found that false positive rates were well-controlled. However, no similar analysis of false positive rates in an imaging genetic study using cluster size inference has yet been undertaken. We measured false positive rates in an investigation of the effect of 700 pre-selected null SNPs on grey matter volume using voxel-based morphometry (VBM). As VBM data exhibit spatially-varying smoothness, we used both non-stationary and stationary cluster size tests in our analysis. Image and genotype data on 181 subjects with mild cognitive impairment were obtained from the Alzheimer's Disease Neuroimaging Initiative (ADNI). At a nominal significance level of 5%, false positive rates were found to be well-controlled (3.9-5.6%), using a relatively high cluster-forming threshold, α(c)=0.001, on images smoothed with a 12 mm Gaussian kernel. Tests were however anticonservative at lower cluster-forming thresholds (α(c)=0.01, 0.05), and for images smoothed using a 6mm Gaussian kernel. Here false positive rates ranged from 9.8 to 67.6%. In a further analysis, false positive rates using simulated data were observed to be well-controlled across a wide range of conditions. While motivated by imaging genetics, our findings apply to any VBM study, and suggest that parametric cluster size inference should only be used with high cluster-forming thresholds and smoothness. We would advocate the use of nonparametric methods in other cases. Voxel-wise statistical inference is commonly used to identify significant experimental effects or group differences in both functional and structural studies of the living brain. Tests based on the size of spatially extended clusters of contiguous suprathreshold voxels are also widely used due to their typically increased statistical power. In "imaging genetics", such tests are used to identify regions of the brain that are associated with genetic variation. However, concerns have been raised about the adequate control of rejection rates in studies of this type. A previous study tested the effect of a set of 'null' SNPs on brain structure and function, and found that false positive rates were well-controlled. However, no similar analysis of false positive rates in an imaging genetic study using cluster size inference has yet been undertaken. We measured false positive rates in an investigation of the effect of 700 pre-selected null SNPs on grey matter volume using voxel-based morphometry (VBM). As VBM data exhibit spatially-varying smoothness, we used both non-stationary and stationary cluster size tests in our analysis. Image and genotype data on 181 subjects with mild cognitive impairment were obtained from the Alzheimer's Disease Neuroimaging Initiative (ADNI). At a nominal significance level of 5%, false positive rates were found to be well-controlled (3.9-5.6%), using a relatively high cluster-forming threshold, α(c)=0.001, on images smoothed with a 12 mm Gaussian kernel. Tests were however anticonservative at lower cluster-forming thresholds (α(c)=0.01, 0.05), and for images smoothed using a 6mm Gaussian kernel. Here false positive rates ranged from 9.8 to 67.6%. In a further analysis, false positive rates using simulated data were observed to be well-controlled across a wide range of conditions. While motivated by imaging genetics, our findings apply to any VBM study, and suggest that parametric cluster size inference should only be used with high cluster-forming thresholds and smoothness. We would advocate the use of nonparametric methods in other cases. Voxel-wise statistical inference is commonly used to identify significant experimental effects or group differences in both functional and structural studies of the living brain. Tests based on the size of spatially extended clusters of contiguous suprathreshold voxels are also widely used due to their typically increased statistical power. In “imaging genetics”, such tests are used to identify regions of the brain that are associated with genetic variation. However, concerns have been raised about the adequate control of rejection rates in studies of this type. A previous study tested the effect of a set of ‘null’ SNPs on brain structure and function, and found that false positive rates were well-controlled. However, no similar analysis of false positive rates in an imaging genetic study using cluster size inference has yet been undertaken.We measured false positive rates in an investigation of the effect of 700 pre-selected null SNPs on grey matter volume using voxel-based morphometry (VBM). As VBM data exhibit spatially-varying smoothness, we used both non-stationary and stationary cluster size tests in our analysis. Image and genotype data on 181 subjects with mild cognitive impairment were obtained from the Alzheimer's Disease Neuroimaging Initiative (ADNI). At a nominal significance level of 5%, false positive rates were found to be well-controlled (3.9–5.6%), using a relatively high cluster-forming threshold, αc=0.001, on images smoothed with a 12mm Gaussian kernel. Tests were however anticonservative at lower cluster-forming thresholds (αc=0.01, 0.05), and for images smoothed using a 6mm Gaussian kernel. Here false positive rates ranged from 9.8 to 67.6%. In a further analysis, false positive rates using simulated data were observed to be well-controlled across a wide range of conditions.While motivated by imaging genetics, our findings apply to any VBM study, and suggest that parametric cluster size inference should only be used with high cluster-forming thresholds and smoothness. We would advocate the use of nonparametric methods in other cases. Voxel-wise statistical inference is commonly used to identify significant experimental effects or group differences in both functional and structural studies of the living brain. Tests based on the size of spatially extended clusters of contiguous suprathreshold voxels are also widely used due to their typically increased statistical power. In “imaging genetics”, such tests are used to identify regions of the brain that are associated with genetic variation. However, concerns have been raised about the adequate control of rejection rates in studies of this type. A previous study tested the effect of a set of ‘null’ SNPs on brain structure and function, and found that false positive rates were well-controlled. However, no similar analysis of false positive rates in an imaging genetic study using cluster size inference has yet been undertaken. We measured false positive rates in an investigation of the effect of 700 pre-selected null SNPs on grey matter volume using voxel-based morphometry (VBM). As VBM data exhibit spatially-varying smoothness, we used both non-stationary and stationary cluster size tests in our analysis. Image and genotype data on 181 subjects with mild cognitive impairment were obtained from the Alzheimer's Disease Neuroimaging Initiative (ADNI). At a nominal significance level of 5%, false positive rates were found to be well-controlled (3.9–5.6%), using a relatively high cluster-forming threshold, α c = 0.001, on images smoothed with a 12 mm Gaussian kernel. Tests were however anticonservative at lower cluster-forming thresholds ( α c = 0.01, 0.05), and for images smoothed using a 6 mm Gaussian kernel. Here false positive rates ranged from 9.8 to 67.6%. In a further analysis, false positive rates using simulated data were observed to be well-controlled across a wide range of conditions. While motivated by imaging genetics, our findings apply to any VBM study, and suggest that parametric cluster size inference should only be used with high cluster-forming thresholds and smoothness. We would advocate the use of nonparametric methods in other cases. ►RFT nonstationary cluster size test on VBM is found to be invalid based on empirical null studies. ►Invalid inferences (inflated false positive risk) were found with 3 voxel smoothing. ►With 6 voxel smoothing, invalid inferences were found with 6 voxel smoothing and alpha=0.01 cluster-forming threshold. ►RFT nonstationary test only found to be valid with 6 voxel smoothing with alpha=0.001 cluster-forming threshold. ►Equivalent Gaussian data simulations produced valid inferences, suggesting VBM data violates RFT assumptions and motivates the use of nonparametric permutation methods. |
Author | Montana, Giovanni Silver, Matt Nichols, Thomas E. |
AuthorAffiliation | b Department of Statistics & Warwick Manufacturing Group, University of Warwick, UK a Statistics Section, Department of Mathematics, Imperial College London, UK |
AuthorAffiliation_xml | – name: a Statistics Section, Department of Mathematics, Imperial College London, UK – name: b Department of Statistics & Warwick Manufacturing Group, University of Warwick, UK |
Author_xml | – sequence: 1 givenname: Matt surname: Silver fullname: Silver, Matt organization: Statistics Section, Department of Mathematics, Imperial College London, UK – sequence: 2 givenname: Giovanni surname: Montana fullname: Montana, Giovanni organization: Statistics Section, Department of Mathematics, Imperial College London, UK – sequence: 3 givenname: Thomas E. surname: Nichols fullname: Nichols, Thomas E. email: t.e.nichols@warwick.ac.uk organization: Department of Statistics & Warwick Manufacturing Group, University of Warwick, UK |
BackLink | https://www.ncbi.nlm.nih.gov/pubmed/20849959$$D View this record in MEDLINE/PubMed |
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ContentType | Journal Article |
Copyright | 2010 Elsevier Inc. Copyright © 2010 Elsevier Inc. All rights reserved. 2010. Elsevier Inc. 2011 Elsevier Inc. 2010 Elsevier Inc. |
Copyright_xml | – notice: 2010 Elsevier Inc. – notice: Copyright © 2010 Elsevier Inc. All rights reserved. – notice: 2010. Elsevier Inc. – notice: 2011 Elsevier Inc. 2010 Elsevier Inc. |
CorporateAuthor | the Alzheimer's Disease Neuroimaging Initiative Alzheimer's Disease Neuroimaging Initiative |
CorporateAuthor_xml | – name: the Alzheimer's Disease Neuroimaging Initiative – name: Alzheimer's Disease Neuroimaging Initiative |
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Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23 Data used in the preparation of this article were obtained from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database (www.loni.ucla.edu/ADNI). As such, the investigators within the ADNI contributed to the design and implementation of ADNI and/or provided data but did not participate in analysis or writing of this report. A complete list of ADNI investigators is available at http://www.loni.ucla.edu/ADNI/Collaboration/ADNI_Manuscript_Citations.pdf. |
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SubjectTerms | Alzheimer's disease Brain Brain - pathology Brain - physiopathology Clusters Cognition Disorders - genetics Cognition Disorders - pathology Cognitive ability False Positive Reactions Functional anatomy Gaussian Genetic diversity Genetics Genotype Genotypes Humans Image processing Imaging Inference Magnetic Resonance Imaging Medical imaging Morphometry Neurodegenerative diseases Neuroimaging Neurosciences Polymorphism, Single Nucleotide Schizophrenia Single-nucleotide polymorphism Smoothness Statistical methods Statistics Structure-function relationships Studies Substantia grisea Thresholds |
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