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Xu H, Newlin NR, Kim ME, Gao C, Kanakaraj P, Krishnan AR, Remedios LW, Khairi NM, Pechman K, Archer D, Hohman TJ, Jefferson AL, Isgum I, Huo Y, Moyer D, Schilling KG, Landman BA. Evaluation of Mean Shift, ComBat, and CycleGAN for Harmonizing Brain Connectivity Matrices Across Sites. ARXIV 2024:arXiv:2401.06798v2. [PMID: 38344221 PMCID: PMC10854272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Connectivity matrices derived from diffusion MRI (dMRI) provide an interpretable and generalizable way of understanding the human brain connectome. However, dMRI suffers from inter-site and between-scanner variation, which impedes analysis across datasets to improve robustness and reproducibility of results. To evaluate different harmonization approaches on connectivity matrices, we compared graph measures derived from these matrices before and after applying three harmonization techniques: mean shift, ComBat, and CycleGAN. The sample comprises 168 age-matched, sex-matched normal subjects from two studies: the Vanderbilt Memory and Aging Project (VMAP) and the Biomarkers of Cognitive Decline Among Normal Individuals (BIOCARD). First, we plotted the graph measures and used coefficient of variation (CoV) and the Mann-Whitney U test to evaluate different methods' effectiveness in removing site effects on the matrices and the derived graph measures. ComBat effectively eliminated site effects for global efficiency and modularity and outperformed the other two methods. However, all methods exhibited poor performance when harmonizing average betweenness centrality. Second, we tested whether our harmonization methods preserved correlations between age and graph measures. All methods except for CycleGAN in one direction improved correlations between age and global efficiency and between age and modularity from insignificant to significant with p-values less than 0.05.
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Affiliation(s)
- Hanliang Xu
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Nancy R Newlin
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Michael E Kim
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Chenyu Gao
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA
| | | | - Aravind R Krishnan
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA
| | - Lucas W Remedios
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Nazirah Mohd Khairi
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA
| | - Kimberly Pechman
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Derek Archer
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Timothy J Hohman
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Angela L Jefferson
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ivana Isgum
- Department of Biomedical Engineering and Physics & Radiology and Nuclear Medicine, University Medical Center Amsterdam, University of Amsterdam, Amsterdam, the Netherlands
| | - Yuankai Huo
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA
| | - Daniel Moyer
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Kurt G Schilling
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN, USA
| | - Bennett A Landman
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN, USA
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
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de Brito Robalo BM, de Luca A, Chen C, Dewenter A, Duering M, Hilal S, Koek HL, Kopczak A, Lam BYK, Leemans A, Mok V, Onkenhout LP, van den Brink H, Biessels GJ. Improved sensitivity and precision in multicentre diffusion MRI network analysis using thresholding and harmonization. Neuroimage Clin 2022; 36:103217. [PMID: 36240537 PMCID: PMC9668636 DOI: 10.1016/j.nicl.2022.103217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 08/22/2022] [Accepted: 10/01/2022] [Indexed: 11/06/2022]
Abstract
PURPOSE To investigate if network thresholding and raw data harmonization improve consistency of diffusion MRI (dMRI)-based brain networks while also increasing precision and sensitivity to detect disease effects in multicentre datasets. METHODS Brain networks were reconstructed from dMRI of five samples with cerebral small vessel disease (SVD; 629 patients, 166 controls), as a clinically relevant exemplar condition for studies on network integrity. We evaluated consistency of network architecture in age-matched controls, by calculating cross-site differences in connection probability and fractional anisotropy (FA). Subsequently we evaluated precision and sensitivity to disease effects by identifying connections with low FA in sporadic SVD patients relative to controls, using more severely affected patients with a pure form of genetically defined SVD as reference. RESULTS In controls, thresholding and harmonization improved consistency of network architecture, minimizing cross-site differences in connection probability and FA. In patients relative to controls, thresholding improved precision to detect disrupted connections by removing false positive connections (precision, before: 0.09-0.19; after: 0.38-0.70). Before harmonization, sensitivity was low within individual sites, with few connections surviving multiple testing correction (k = 0-25 connections). Harmonization and pooling improved sensitivity (k = 38), while also achieving higher precision when combined with thresholding (0.97). CONCLUSION We demonstrated that network consistency, precision and sensitivity to detect disease effects in SVD are improved by thresholding and harmonization. We recommend introducing these techniques to leverage large existing multicentre datasets to better understand the impact of disease on brain networks.
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Affiliation(s)
- Bruno M. de Brito Robalo
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht, the Netherlands,Image Sciences Institute, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Alberto de Luca
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht, the Netherlands,Image Sciences Institute, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Christopher Chen
- Memory, Aging and Cognition Center, Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Anna Dewenter
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Germany
| | - Marco Duering
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Germany,Medical Image Analysis Center (MIAC AG) and Department of Biomedical Engineering, University of Basel, Basel, Switzerland
| | - Saima Hilal
- Memory, Aging and Cognition Center, Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore,Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore
| | - Huiberdina L. Koek
- Department of Geriatric Medicine, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Anna Kopczak
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Germany
| | - Bonnie Yin Ka Lam
- Division of Neurology, Department of Medicine and Therapeutics, Gerald Choa Neuroscience Centre, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region
| | - Alexander Leemans
- Image Sciences Institute, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Vincent Mok
- Division of Neurology, Department of Medicine and Therapeutics, Gerald Choa Neuroscience Centre, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region
| | - Laurien P. Onkenhout
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Hilde van den Brink
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Geert Jan Biessels
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht, the Netherlands,Corresponding author at: Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, P.O. Box 85500, 3508 GA Utrecht, the Netherlands.
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De Luca A, Kuijf H, Exalto L, Thiebaut de Schotten M, Biessels GJ. Multimodal tract-based MRI metrics outperform whole brain markers in determining cognitive impact of small vessel disease-related brain injury. Brain Struct Funct 2022; 227:2553-2567. [PMID: 35994115 PMCID: PMC9418106 DOI: 10.1007/s00429-022-02546-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 07/27/2022] [Indexed: 01/04/2023]
Abstract
In cerebral small vessel disease (cSVD), whole brain MRI markers of cSVD-related brain injury explain limited variance to support individualized prediction. Here, we investigate whether considering abnormalities in brain tracts by integrating multimodal metrics from diffusion MRI (dMRI) and structural MRI (sMRI), can better capture cognitive performance in cSVD patients than established approaches based on whole brain markers. We selected 102 patients (73.7 ± 10.2 years old, 59 males) with MRI-visible SVD lesions and both sMRI and dMRI. Conventional linear models using demographics and established whole brain markers were used as benchmark of predicting individual cognitive scores. Multi-modal metrics of 73 major brain tracts were derived from dMRI and sMRI, and used together with established markers as input of a feed-forward artificial neural network (ANN) to predict individual cognitive scores. A feature selection strategy was implemented to reduce the risk of overfitting. Prediction was performed with leave-one-out cross-validation and evaluated with the R2 of the correlation between measured and predicted cognitive scores. Linear models predicted memory and processing speed with R2 = 0.26 and R2 = 0.38, respectively. With ANN, feature selection resulted in 13 tract-specific metrics and 5 whole brain markers for predicting processing speed, and 28 tract-specific metrics and 4 whole brain markers for predicting memory. Leave-one-out ANN prediction with the selected features achieved R2 = 0.49 and R2 = 0.40 for processing speed and memory, respectively. Our results show proof-of-concept that combining tract-specific multimodal MRI metrics can improve the prediction of cognitive performance in cSVD by leveraging tract-specific multi-modal metrics.
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Affiliation(s)
- Alberto De Luca
- VCI Group, Neurology Department, UMC Utrecht Brain Center, UMC Utrecht, Utrecht, The Netherlands.
- Image Sciences Institute, Division Imaging and Oncology, UMC Utrecht, Utrecht, The Netherlands.
| | - Hugo Kuijf
- Image Sciences Institute, Division Imaging and Oncology, UMC Utrecht, Utrecht, The Netherlands
| | - Lieza Exalto
- VCI Group, Neurology Department, UMC Utrecht Brain Center, UMC Utrecht, Utrecht, The Netherlands
| | - Michel Thiebaut de Schotten
- Brain Connectivity and Behaviour Lab, Sorbonne University, Paris, France
- Institut des Maladies Neurodégénératives, Neurofunctional Imaging Group, University of Bordeaux, Bordeaux, France
| | - Geert-Jan Biessels
- VCI Group, Neurology Department, UMC Utrecht Brain Center, UMC Utrecht, Utrecht, The Netherlands
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De Luca A, Karayumak SC, Leemans A, Rathi Y, Swinnen S, Gooijers J, Clauwaert A, Bahr R, Sandmo SB, Sochen N, Kaufmann D, Muehlmann M, Biessels GJ, Koerte I, Pasternak O. Cross-site harmonization of multi-shell diffusion MRI measures based on rotational invariant spherical harmonics (RISH). Neuroimage 2022; 259:119439. [PMID: 35788044 DOI: 10.1016/j.neuroimage.2022.119439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 06/23/2022] [Accepted: 06/30/2022] [Indexed: 11/25/2022] Open
Abstract
Quantification methods based on the acquisition of diffusion magnetic resonance imaging (dMRI) with multiple diffusion weightings (e.g., multi-shell) are becoming increasingly applied to study the in-vivo brain. Compared to single-shell data for diffusion tensor imaging (DTI), multi-shell data allows to apply more complex models such as diffusion kurtosis imaging (DKI), which attempts to capture both diffusion hindrance and restriction effects, or biophysical models such as NODDI, which attempt to increase specificity by separating biophysical components. Because of the strong dependence of the dMRI signal on the measurement hardware, DKI and NODDI metrics show scanner and site differences, much like other dMRI metrics. These effects limit the implementation of multi-shell approaches in multicenter studies, which are needed to collect large sample sizes for robust analyses. Recently, a post-processing technique based on rotation invariant spherical harmonics (RISH) features was introduced to mitigate cross-scanner differences in DTI metrics. Unlike statistical harmonization methods, which require repeated application to every dMRI metric of choice, RISH harmonization is applied once on the raw data, and can be followed by any analysis. RISH features harmonization has been tested on DTI features but not its generalizability to harmonize multi-shell dMRI. In this work, we investigated whether performing the RISH features harmonization of multi-shell dMRI data removes cross-site differences in DKI and NODDI metrics while retaining longitudinal effects. To this end, 46 subjects underwent a longitudinal (up to 3 time points) two-shell dMRI protocol at 3 imaging sites. DKI and NODDI metrics were derived before and after harmonization and compared both at the whole brain level and at the voxel level. Then, the harmonization effects on cross-sectional and on longitudinal group differences were evaluated. RISH features averaged for each of the 3 sites exhibited prominent between-site differences in the frontal and posterior part of the brain. Statistically significant differences in fractional anisotropy, mean diffusivity and mean kurtosis were observed both at the whole brain and voxel level between all the acquisition sites before harmonization, but not after. The RISH method also proved effective to harmonize NODDI metrics, particularly in white matter. The RISH based harmonization maintained the magnitude and variance of longitudinal changes as compared to the non-harmonized data of all considered metrics. In conclusion, the application of RISH feature based harmonization to multi-shell dMRI data can be used to remove cross-site differences in DKI metrics and NODDI analyses, while retaining inherent relations between longitudinal acquisitions.
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Affiliation(s)
- Alberto De Luca
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht, The Netherlands; PROVIDI Lab, Image Sciences Institute, University Medical Center Utrecht, Utrecht, The Netherlands; Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia.
| | | | - Alexander Leemans
- PROVIDI Lab, Image Sciences Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Yogesh Rathi
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Stephan Swinnen
- Movement Control and Neuroplasticity Research Group, KU Leuven, Leuven, Belgium; KU Leuven Brain Institute (LBI), Leuven, Belgium
| | - Jolien Gooijers
- Movement Control and Neuroplasticity Research Group, KU Leuven, Leuven, Belgium; KU Leuven Brain Institute (LBI), Leuven, Belgium
| | - Amanda Clauwaert
- Movement Control and Neuroplasticity Research Group, KU Leuven, Leuven, Belgium; KU Leuven Brain Institute (LBI), Leuven, Belgium
| | - Roald Bahr
- Oslo Sports Trauma Research Center, Norwegian School of Sport Sciences, Oslo, Norway
| | - Stian Bahr Sandmo
- Oslo Sports Trauma Research Center, Norwegian School of Sport Sciences, Oslo, Norway
| | - Nir Sochen
- Department of Applied Mathematics, Tel Aviv University, Tel Aviv, Israel; Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - David Kaufmann
- Radiology Department, Charite University Hospital, Berlin, Germany
| | - Marc Muehlmann
- Department of Radiology, Ludwig-Maximilians-Universität, Munich, Germany
| | - Geert-Jan Biessels
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Inga Koerte
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA; cBRAIN, Department of Child and Adolescent Psychiatry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Ofer Pasternak
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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Egle M, Hilal S, Tuladhar AM, Pirpamer L, Bell S, Hofer E, Duering M, Wason J, Morris RG, Dichgans M, Schmidt R, Tozer DJ, Barrick TR, Chen C, de Leeuw FE, Markus HS. Determining the OPTIMAL DTI analysis method for application in cerebral small vessel disease. NEUROIMAGE: CLINICAL 2022; 35:103114. [PMID: 35908307 PMCID: PMC9421487 DOI: 10.1016/j.nicl.2022.103114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 05/24/2022] [Accepted: 07/10/2022] [Indexed: 11/23/2022] Open
Abstract
We were not able to identify a single optimal diffusion-weighted imaging analysis strategy across all 6 cohorts. Diffusion tensor imaging measures at baseline predicted dementia conversion in cerebral small vessel disease and mild cognitive impairment. Diffusion tensor imaging measures at baseline may be sensitive to differentiate between later vascular dementia vs Alzheimer’s disease dementia. Diffusion tensor imaging measures significantly changed over time in cohorts with cerebral small vessel disease and cohorts with mild cognitive impairment. Change in diffusion tensor imaging measures were only consistently associated with dementia conversion in severe SVD. The diffusion tensor imaging measures PSMD and DSEG required the lowest minimum sample sizes for a hypothetical clinical trial in patients with sporadic cerebral small vessel disease and mild cognitive impairment.
Background DTI is sensitive to white matter (WM) microstructural damage and has been suggested as a surrogate marker for phase 2 clinical trials in cerebral small vessel disease (SVD). The study’s objective is to establish the best way to analyse the diffusion-weighted imaging data in SVD for this purpose. The ideal method would be sensitive to change and predict dementia conversion, but also straightforward to implement and ideally automated. As part of the OPTIMAL collaboration, we evaluated five different DTI analysis strategies across six different cohorts with differing SVD severity. Methods Those 5 strategies were: (1) conventional mean diffusivity WM histogram measure (MD median), (2) a principal component-derived measure based on conventional WM histogram measures (PC1), (3) peak width skeletonized mean diffusivity (PSMD), (4) diffusion tensor image segmentation θ (DSEG θ) and (5) a WM measure of global network efficiency (Geff). The association between each measure and cognitive function was tested using a linear regression model adjusted by clinical markers. Changes in the imaging measures over time were determined. In three cohort studies, repeated imaging data together with data on incident dementia were available. The association between the baseline measure, change measure and incident dementia conversion was examined using Cox proportional-hazard regression or logistic regression models. Sample size estimates for a hypothetical clinical trial were furthermore computed for each DTI analysis strategy. Results There was a consistent cross-sectional association between the imaging measures and impaired cognitive function across all cohorts. All baseline measures predicted dementia conversion in severe SVD. In mild SVD, PC1, PSMD and Geff predicted dementia conversion. In MCI, all markers except Geff predicted dementia conversion. Baseline DTI was significantly different in patients converting to vascular dementia than to Alzheimer’ s disease. Significant change in all measures was associated with dementia conversion in severe but not in mild SVD. The automatic and semi-automatic measures PSMD and DSEG θ required the lowest minimum sample sizes for a hypothetical clinical trial in single-centre sporadic SVD cohorts. Conclusion DTI parameters obtained from all analysis methods predicted dementia, and there was no clear winner amongst the different analysis strategies. The fully automated analysis provided by PSMD offers advantages particularly for large datasets.
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Affiliation(s)
- Marco Egle
- Stroke Research Group, Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom.
| | - Saima Hilal
- Department of Pharmacology, National University of Singapore, Singapore; Memory Ageing and Cognition Center, National University Health System, Singapore
| | - Anil M Tuladhar
- Department of Neurology, Donders Center for Medical Neuroscience, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Lukas Pirpamer
- Department of Neurology, Medical University of Graz, Graz, Austria
| | - Steven Bell
- Stroke Research Group, Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
| | - Edith Hofer
- Department of Neurology, Medical University of Graz, Graz, Austria; Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Graz, Austria
| | - Marco Duering
- Institute for Stroke and Dementia Research, University Hospital, LMU Munich, Munich, Germany; Medical Image Analysis Center (MIAC) and Department of Biomedical Engineering, University of Basel, Basel, Switzerland
| | - James Wason
- Population Health Sciences Institute, Newcastle University, Baddiley-Clark Building, Newcastle Upon Tyne, United Kingdom
| | - Robin G Morris
- Department of Psychology (R.G.M.), King's College, Institute of Psychiatry, Psychology and Neuroscience, London, United Kingdom
| | - Martin Dichgans
- Institute for Stroke and Dementia Research, University Hospital, LMU Munich, Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Reinhold Schmidt
- Department of Neurology, Medical University of Graz, Graz, Austria
| | - Daniel J Tozer
- Stroke Research Group, Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
| | - Thomas R Barrick
- Neurosciences Research Centre, Institute for Molecular and Clinical Sciences, St George's, University of London, United Kingdom
| | - Christopher Chen
- Department of Pharmacology, National University of Singapore, Singapore; Memory Ageing and Cognition Center, National University Health System, Singapore
| | - Frank-Erik de Leeuw
- Department of Neurology, Donders Center for Medical Neuroscience, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Hugh S Markus
- Stroke Research Group, Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
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