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Increased power by harmonizing structural MRI site differences with the ComBat batch adjustment method in ENIGMA

Joaquim Radua, Eduard Vieta, Russell Shinohara, Peter Kochunov, Yann Quidé, Melissa Green, Cynthia Weickert, Thomas Weickert, Jason Bruggemann, Tilo Kircher, Igor Nenadic, Murray Cairns (+99 others)
2020 NeuroImage  
Here we tested whether the batch adjustment method, ComBat, can further reduce site-related heterogeneity and thus increase statistical power.  ...  ComBat also showed increased statistical power when we repeated the analyses with fewer sites.  ...  Here we tested whether the batch adjustment method, ComBat, can further reduce site-related heterogeneity and thus increase statistical power.  ... 
doi:10.1016/j.neuroimage.2020.116956 pmid:32470572 pmcid:PMC7524039 fatcat:kxrcgoyznve3fdgk5h7sl5wyki

Multi-site benchmark classification of major depressive disorder using machine learning on cortical and subcortical measures [article]

Vladimir Belov, Tracy Erwin-Grabner, Ali Saffet Gonul, Alyssa R. Amod, Amar Ojha, Andre Aleman, Annemiek Dols, Anouk Scharntee, Aslihan Uyar-Demir, Ben J Harrison, Benson M. Irungu, Bianca Besteher (+54 others)
2022 arXiv   pre-print
Using brain measures from standardized ENIGMA analysis pipelines in FreeSurfer, we were able to classify MDD vs HC with around 62% balanced accuracy, but when harmonizing the data using ComBat balanced  ...  However, the diagnostic predictive power of the existing algorithms has been limited by small sample sizes, lack of representativeness, data leakage, and/or overfitting.  ...  In our case, the test set was adjusted to a unified batch made by integrating all cohorts from the training set and adjusting to common mean and variance by the ComBat, which allowed to harmonize unseen  ... 
arXiv:2206.08122v2 fatcat:wdlaav43wvduhpgpl7jsgcyoie

A Comparison of Methods to Harmonize Cortical Thickness Measurements Across Scanners and Sites [article]

Delin Sun, Gopalkumar Rakesh, Emily K. Clarke-Rubright, Courtney C. Haswell, Mark Logue, Brian M. O'Leary, Andrew S. Cotton, Hong Xie, Emily L. Dennis, Neda Jahanshad, Lauren E. Salminen, Sophia I. Thomopolous (+83 others)
2021 bioRxiv   pre-print
We found that, compared to the other data harmonization methods, data processed with ComBat-GAM were more sensitive to the detection of significant case-control differences in regional cortical thickness  ...  Our results support the use of ComBat-GAM for harmonizing cortical thickness data aggregated from multiple sites and scanners to minimize confounds and increase statistical power.  ...  The p-values were adjusted using the Tukey method for the 6 pairwise comparisons made with the outputs of the 4 harmonization methods.  ... 
doi:10.1101/2021.09.22.461242 fatcat:mmimaxf6vjecze2b4ju3eydx5e

The thalamus and its subnuclei: a gateway to obsessive-compulsive disorder findings from the ENIGMA-OCD Working Group [article]

Cees J Weeland, Selina Kasprzak, Niels T de Joode, Yosinari Abe, Pino Alonso, Stephanie H Ameis, Alan Anticevic, Paul D Arnold, Srinivas Balachander, Nerisa Banaj, Nuria Bargallo, Marcelo C Batistuzzo (+89 others)
2021 biorxiv/medrxiv   pre-print
Method: Structural T1-weighted brain magnetic resonance imaging (MRI) scans from 2,649 OCD patients and 2,774 healthy controls across 29 sites (50 datasets) were processed using the FreeSurfer built-in  ...  Volume measures were harmonized for site effects using ComBat before running separate multiple linear regression models for children, adolescents, and adults to estimate volumetric group differences.  ...  Supported by the Japan Society for the Promotion of Science  ... 
doi:10.1101/2021.09.06.21262530 fatcat:qofdksd6vfdrhgblllmfw7x2me

White matter abnormalities across different epilepsy syndromes in adults: an ENIGMA-Epilepsy study

Sean N Hatton, Khoa H Huynh, Leonardo Bonilha, Eugenio Abela, Saud Alhusaini, Andre Altmann, Marina K M Alvim, Akshara R Balachandra, Emanuele Bartolini, Benjamin Bender, Neda Bernasconi, Andrea Bernasconi (+64 others)
2020 Brain  
Data were harmonized to correct for scanner-specific variations in diffusion measures using a batch-effect correction tool (ComBat).  ...  The epilepsies are commonly accompanied by widespread abnormalities in cerebral white matter.  ...  Figure 2 2 Diffusion MRI harmonization using ComBat.  ... 
doi:10.1093/brain/awaa200 pmid:32814957 pmcid:PMC7567169 fatcat:jqdwqqgjbrfzdnhhm5l4qnjwam

White matter abnormalities across different epilepsy syndromes in adults: an ENIGMA Epilepsy study [article]

Sean N Hatton, Khoa H Huynh, Leonardo Bonilha, Eugenio Abela, Saud Alhusaini, Andre N Altmann, Marina KM Alvim, Akshara R Balachandra, Núria Bargallo, Emanuele Bartolini, Benjamin Bender, Andrea Bernasconi (+61 others)
2019 bioRxiv   pre-print
Data were harmonized to correct for scanner-specific variations in diffusion measures using a batch-effect correction tool (ComBat).  ...  The epilepsies are commonly accompanied by widespread abnormalities in cerebral white matter.  ...  Figure 5 . 5 Syndromic difference in average FA and MD in five ROIs. Table 1 ( 1 by site) and Table 2 (across site).  ... 
doi:10.1101/2019.12.19.883405 fatcat:3m64fo5ngnbobjveffbbp65lt4

Mega‐analysis methods in ENIGMA : The experience of the generalized anxiety disorder working group

André Zugman, Anita Harrewijn, Elise M. Cardinale, Hannah Zwiebel, Gabrielle F. Freitag, Katy E. Werwath, Janna M. Bas‐Hoogendam, Nynke A. Groenewold, Moji Aghajani, Kevin Hilbert, Narcis Cardoner, Daniel Porta‐Casteràs (+76 others)
2020 Human Brain Mapping  
The ENIGMA group on Generalized Anxiety Disorder (ENIGMA-Anxiety/GAD) is part of a broader effort to investigate anxiety disorders using imaging and genetic data across multiple sites worldwide.  ...  In this process, the group was confronted with many methodological challenges related to study planning and implementation, between-country transfer of subject-level data, quality control of a considerable  ...  ACKNOWLEDGMENTS The authors thank all the many research sites worldwide who considered contributing data to the ENIGMA-Anxiety/GAD project. André  ... 
doi:10.1002/hbm.25096 pmid:32596977 pmcid:PMC8675407 fatcat:63p4hznrljfvncaq3iqxjdgz6a

Subcortical volumes across the lifespan: Data from 18,605 healthy individuals aged 3-90 years

Danai Dima, Amirhossein Modabbernia, Efstathios Papachristou, Gaelle E Doucet, Ingrid Agartz, Moji Aghajani, Theophilus N Akudjedu, Anton Albajes-Eizagirre, Dag Alnaes, Kathryn I Alpert, Micael Andersson, Nancy C Andreasen (+190 others)
2021 Human Brain Mapping  
All subcortical structure volumes were at their maximum value early in life.  ...  (with some degree of decline in thalamus) until the sixth decade of life after which they also showed a steep negative association with age.  ...  Originally developed to adjust for batch effect in genetic studies, ComBat uses an empirical Bayes to adjust for inter-site variability in the data, while preserving variability related to the variables  ... 
doi:10.1002/hbm.25320 pmid:33570244 pmcid:PMC8675429 fatcat:zbdl52td7vg2tlhiwfojeshouu

The ENIGMA‐Epilepsy working group: Mapping disease from large data sets

Sanjay M. Sisodiya, Christopher D. Whelan, Sean N. Hatton, Khoa Huynh, Andre Altmann, Mina Ryten, Annamaria Vezzani, Maria Eugenia Caligiuri, Angelo Labate, Antonio Gambardella, Victoria Ives‐Deliperi, Stefano Meletti (+60 others)
2020 Human Brain Mapping  
Through the infrastructure and concepts now well-established by the ENIGMA Consortium, ENIGMA-Epilepsy was established to strengthen epilepsy neuroscience by greatly increasing sample sizes, leveraging  ...  MRI has been fundamental in advancing our understanding of brain processes in the epilepsies.  ...  Following the approach utilized in two prior megaanalyses, we applied a novel batch-effect correction tool, ComBat, to adjust for scanner/site specific variations in diffusivity measures (Fortin et al  ... 
doi:10.1002/hbm.25037 pmid:32468614 pmcid:PMC8675408 fatcat:dx43hssccbfalcrtbbph5cqvhy

In vivo white matter microstructure in adolescents with early-onset psychosis: a multi-site mega-analysis via the ENIGMA Consortium [article]

Claudia Barth, Sinead Kelly, Stener Nerland, Neda Jahanshad, Clara Alloza, Sonia Ambrogi, Ole Andreassen, Dimitrios Andreou, Celso Arango, Inmaculada Baeza, Nerisa Banaj, Carrie E Bearden (+32 others)
2022 medRxiv   pre-print
ComBat harmonization was performed for all DTI measures to adjust for scanner differences.  ...  Results: We found widespread lower FA in EOP compared to CTR, with the largest effect sizes in the superior longitudinal fasciculus (Cohens d = 0.37), posterior corona radiata (d = 0.32), and superior  ...  ACKNOWLEDGMENTS ENIGMA Core: U.S. National Institutes of Health grants, R01 EB015611, U54 EB020403,  ... 
doi:10.1101/2022.02.11.22270818 fatcat:2fvxa4sskrgslgc7n6wiuw5tse

Harmonization of Brain Diffusion MRI: Concepts and Methods

Maíra Siqueira Pinto, Roberto Paolella, Thibo Billiet, Pieter Van Dyck, Pieter-Jan Guns, Ben Jeurissen, Annemie Ribbens, Arnold J. den Dekker, Jan Sijbers
2020 Frontiers in Neuroscience  
Overall, the methods for the harmonization of multi-site diffusion images can be categorized in two main groups: diffusion parametric map harmonization (DPMH) and diffusion weighted image harmonization  ...  Nevertheless, in this paper we provide two classification tools, namely a feature table and a flowchart, which aim to guide the readers in selecting an appropriate harmonization method for their study.  ...  The need for harmonization has increased with the availability of large diffusion MRI multi-center datasets.  ... 
doi:10.3389/fnins.2020.00396 pmid:32435181 pmcid:PMC7218137 fatcat:il5p2l7a5fd2vheehvyobgg5lm

Harmonization of multi-site diffusion tensor imaging data

Jean-Philippe Fortin, Drew Parker, Birkan Tunç, Takanori Watanabe, Mark A. Elliott, Kosha Ruparel, David R. Roalf, Theodore D. Satterthwaite, Ruben C. Gur, Raquel E. Gur, Robert T. Schultz, Ragini Verma (+1 others)
2017 NeuroImage  
Finally, we assess the different harmonization methods in the presence of different levels of confounding between site and age, in addition to test robustness to small sample size studies.  ...  Then, we propose and compare several harmonization approaches for DTI data, and show that ComBat, a popular batch-effect correction tool used in genomics, performs best at modeling and removing the unwanted  ...  Analysis of partial volume effects in diffusion-tensor mri. Magnetic Resonance in Medicine, 45  ... 
doi:10.1016/j.neuroimage.2017.08.047 pmid:28826946 pmcid:PMC5736019 fatcat:jq7gozcuxnfyjkpszy5cqaj7ve

Harmonization Of Multi-Site Diffusion Tensor Imaging Data [article]

Jean-Philippe Fortin, Drew Parker, Birkan Tunc, Takanori Watanabe, Mark A Elliott, Kosha Ruparel, David R Roalf, Theodore D Satterthwaite, Ruben C Gur, Raquel E Gur, Robert T Schultz, Ragini Verma (+1 others)
2017 bioRxiv   pre-print
Finally, we assess the different harmonization methods in the presence of different levels of confounding between site and age, in addition to test robustness to small sample size studies.  ...  Then, we propose and compare several harmonization approaches for DTI data, and show that ComBat, a popular batch-effect correction tool used in genomics, performs best at modeling and removing the unwanted  ...  Analysis of partial volume effects in diffusion-tensor mri. Magnetic Resonance in Medicine, 45  ... 
doi:10.1101/116541 fatcat:wmljeai6trhq3gwc7cvgroewz4

Federated Multi-Site Normative Modeling using Hierarchical Bayesian Regression [article]

Seyed Mostafa Kia, Hester Huijsdens, Saige Rutherford, Richard Dinga, Thomas Wolfers, Maarten Mennes, Ole Andreassen, Lars T. Westlye, Christian F Beckmann, Andre F Marquand
2021 bioRxiv   pre-print
Our experimental results confirm the superiority of HBR in deriving more accurate normative ranges on large multi-site neuroimaging datasets compared to the current standard methods.  ...  The proposed method completes the life-cycle of normative modeling by providing the possibilities to learn, update, and adapt the model parameters on decentralized neuroimaging data.  ...  Considering the real-world limitations in developing and deploying a reference normative model (multi-site data and data privacy/access issues), the modeling approach that is employed for estimating the  ... 
doi:10.1101/2021.05.28.446120 fatcat:iqzwoxwyjbcuheixe3zpubvdqa

Subcortical Volume Trajectories across the Lifespan: Data from 18,605 healthy individuals aged 3-90 years [article]

Danai Dima, Efstathios Papachristou, Amirhossein Modabbernia, Gaelle E Doucet, Ingrid Agartz, Moji Aghajani, Theophilus N Akudjedu, Anton Albajes-Eizagirre, Dag Alnæs, Kathryn I Alpert, Micael Andersson, Nancy Andreasen (+185 others)
2020 biorxiv/medrxiv   pre-print
hippocampus remained largely stable (with some degree of decline in thalamus) until the sixth decade of life followed by a steep decline thereafter.  ...  Significant age-related increase in inter-individual variability was found for the hippocampus and amygdala and the lateral ventricles.  ...  The values of the subcortical volumes were then harmonized between sites using the ComBat method in R (Fortin, et al. 2017; 2018; Radua et al., 2019 this issue) .  ... 
doi:10.1101/2020.05.05.079475 fatcat:gyo7t35arjcklml7bmj4qnfjbm
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