Statistical harmonization corrects site effects in functional connectivity measurements from multi-site fMRI data.
Meichen Yu,Kristin A. Linn,Philip A. Cook,Mary L. Phillips,Melvin G. McInnis,Maurizio Fava,Madhukar H. Trivedi,Myrna M. Weissman,Russell T. Shinohara,Yvette I. Sheline +9 more
Reads0
Chats0
TLDR
The proposed ComBat harmonization approach for fMRI‐derived connectivity measures facilitates reliable and efficient analysis of retrospective and prospective multi‐site fMRI neuroimaging studies and increased the power to detect age associations when using optimal combinations of connectivity metrics and brain atlases.Abstract:
Acquiring resting-state functional magnetic resonance imaging (fMRI) datasets at multiple MRI scanners and clinical sites can improve statistical power and generalizability of results. However, multi-site neuroimaging studies have reported considerable nonbiological variability in fMRI measurements due to different scanner manufacturers and acquisition protocols. These undesirable sources of variability may limit power to detect effects of interest and may even result in erroneous findings. Until now, there has not been an approach that removes unwanted site effects. In this study, using a relatively large multi-site (4 sites) fMRI dataset, we investigated the impact of site effects on functional connectivity and network measures estimated by widely used connectivity metrics and brain parcellations. The protocols and image acquisition of the dataset used in this study had been homogenized using identical MRI phantom acquisitions from each of the neuroimaging sites; however, intersite acquisition effects were not completely eliminated. Indeed, in this study, we found that the magnitude of site effects depended on the choice of connectivity metric and brain atlas. Therefore, to further remove site effects, we applied ComBat, a harmonization technique previously shown to eliminate site effects in multi-site diffusion tensor imaging (DTI) and cortical thickness studies. In the current work, ComBat successfully removed site effects identified in connectivity and network measures and increased the power to detect age associations when using optimal combinations of connectivity metrics and brain atlases. Our proposed ComBat harmonization approach for fMRI-derived connectivity measures facilitates reliable and efficient analysis of retrospective and prospective multi-site fMRI neuroimaging studies.read more
Citations
More filters
Journal ArticleDOI
Harmonization of large MRI datasets for the analysis of brain imaging patterns throughout the lifespan.
Raymond Pomponio,Guray Erus,Mohamad Habes,Jimit Doshi,Dhivya Srinivasan,Elizabeth Mamourian,Vishnu Bashyam,Ilya M. Nasrallah,Theodore D. Satterthwaite,Yong Fan,Lenore J. Launer,Colin L. Masters,Paul Maruff,Chuanjun Zhuo,Henry Völzke,Sterling C. Johnson,Jurgen Fripp,Nikolaos Koutsouleris,Daniel H. Wolf,Raquel E. Gur,Ruben C. Gur,John C. Morris,Marilyn S. Albert,Hans J. Grabe,Susan M. Resnick,R. Nick Bryan,David A. Wolk,Russell T. Shinohara,Haochang Shou,Christos Davatzikos +29 more
TL;DR: A comprehensive effort is described that merges and harmonizes a large-scale dataset of 10,477 structural brain MRI scans from participants without a known neurological or psychiatric disorder from 18 different studies that represent geographic diversity to derive age trends of brain structure through the lifespan.
Journal ArticleDOI
Childhood trauma history is linked to abnormal brain connectivity in major depression.
Meichen Yu,Kristin A. Linn,Russell T. Shinohara,Desmond J. Oathes,Philip A. Cook,Romain Duprat,Tyler M. Moore,Maria A. Oquendo,Mary L. Phillips,Melvin G. McInnis,Maurizio Fava,Madhukar H. Trivedi,Patrick J. McGrath,Ramin V. Parsey,Myrna M. Weissman,Yvette I. Sheline +15 more
TL;DR: This study showed that traumatic childhood experiences and dimensional symptoms are linked to abnormal network architecture in MDD, and suggests that RSN connectivity may explain underlying neurobiological mechanisms of MDD symptoms and has the potential to serve as an effective diagnostic biomarker.
Journal ArticleDOI
Harmonization of resting-state functional MRI data across multiple imaging sites via the separation of site differences into sampling bias and measurement bias
Ayumu Yamashita,Noriaki Yahata,Noriaki Yahata,Takashi Itahashi,Giuseppe Lisi,Takashi Yamada,Naho Ichikawa,Masahiro Takamura,Yujiro Yoshihara,Akira Kunimatsu,Naohiro Okada,Hirotaka Yamagata,Koji Matsuo,Koji Matsuo,Ryuichiro Hashimoto,Ryuichiro Hashimoto,Go Okada,Yuki Sakai,Jun Morimoto,Jin Narumoto,Yasuhiro Shimada,Kiyoto Kasai,Nobumasa Kato,Hidehiko Takahashi,Yasumasa Okamoto,Saori C. Tanaka,Mitsuo Kawato,Okito Yamashita,Hiroshi Imamizu +28 more
TL;DR: This work utilized a traveling-subject dataset in conjunction with a multisite, multidisorder dataset to demonstrate that site differences are composed of biological sampling bias and engineering measurement bias, and indicated that each site can sample only from a subpopulation of participants.
Journal ArticleDOI
Increased power by harmonizing structural MRI site differences with the ComBat batch adjustment method in ENIGMA.
Joaquim Radua,Eduard Vieta,Russell T. Shinohara,Peter Kochunov,Yann Quidé,Yann Quidé,Melissa J. Green,Melissa J. Green,Cynthia Shannon Weickert,Cynthia Shannon Weickert,Cynthia Shannon Weickert,Thomas W. Weickert,Thomas W. Weickert,Jason M. Bruggemann,Jason M. Bruggemann,Tilo Kircher,Igor Nenadic,Murray J. Cairns,Marc L. Seal,Ulrich Schall,Frans Henskens,Janice M. Fullerton,Janice M. Fullerton,Bryan J. Mowry,Christos Pantelis,Rhoshel K. Lenroot,Rhoshel K. Lenroot,Rhoshel K. Lenroot,Vanessa Cropley,Carmel M. Loughland,Rodney J. Scott,Daniel H. Wolf,Theodore D. Satterthwaite,Yunlong Tan,Kang Sim,Kang Sim,Fabrizio Piras,Gianfranco Spalletta,Nerisa Banaj,Edith Pomarol-Clotet,Aleix Solanes,Anton Albajes-Eizagirre,Erick J. Canales-Rodríguez,S. Sarró,Annabella Di Giorgio,Annabella Di Giorgio,Alessandro Bertolino,Michael Stäblein,Viola Oertel,Christian Knöchel,Stefan Borgwardt,Stefan S. du Plessis,Je-Yeon Yun,Je-Yeon Yun,Jun Soo Kwon,Jun Soo Kwon,Udo Dannlowski,Tim Hahn,Dominik Grotegerd,Clara Alloza,Celso Arango,Joost Janssen,Covadonga M. Díaz-Caneja,Wenhao Jiang,Vince D. Calhoun,Stefan Ehrlich,Kun Yang,Nicola G. Cascella,Yoichiro Takayanagi,Yoichiro Takayanagi,Akira Sawa,Alexander Tomyshev,Irina V. Lebedeva,Kaleda Vg,Matthias Kirschner,Matthias Kirschner,Cyril Höschl,Cyril Höschl,David Tomecek,David Tomecek,David Tomecek,Antonin Skoch,Therese van Amelsvoort,Geor Bakker,Anthony A. James,Adrian Preda,Andrea Weideman,Dan J. Stein,Fleur M. Howells,Anne Uhlmann,Anne Uhlmann,Henk Temmingh,Carlos López-Jaramillo,Ana M. Díaz-Zuluaga,Lydia Fortea,Eloy Martinez-Heras,Elisabeth Solana,Sara Llufriu,Neda Jahanshad,Paul M. Thompson,Jessica A. Turner,Theo G.M. van Erp,David C. Glahn,David C. Glahn,David C. Glahn,Godfrey D. Pearlson,Godfrey D. Pearlson,Elliot Hong,Axel Krug,Vaughan J. Carr,Vaughan J. Carr,Paul A. Tooney,Gavin Cooper,Paul E. Rasser,Patricia T. Michie,Stanley V. Catts,Raquel E. Gur,Ruben C. Gur,Fude Yang,Fengmei Fan,Jingxu Chen,Hua Guo,Shuping Tan,Zhiren Wang,Hong Xiang,Federica Piras,Francesca Assogna,Raymond Salvador,Peter J. McKenna,Aurora Bonvino,Margaret D. King,Stefan Kaiser,Dana Nguyen,Julian A Pineda-Zapata +133 more
TL;DR: Whether the batch adjustment method, ComBat, can further reduce site-related heterogeneity and thus increase statistical power and recommend applying the ComBat function to attenuate potential effects of site in ENIGMA projects and other multi-site structural imaging work.
Journal ArticleDOI
Longitudinal ComBat: A method for harmonizing longitudinal multi-scanner imaging data.
Joanne C. Beer,Nicholas J. Tustison,Philip A. Cook,Christos Davatzikos,Yvette I. Sheline,Russell T. Shinohara,Kristin A. Linn +6 more
TL;DR: In simulation studies, it is shown that longitudinal ComBat is more powerful for detecting longitudinal change than cross-sectional ComBat and controls the type I error rate better than unharmonized data with scanner included as a covariate.
References
More filters
Journal ArticleDOI
Controlling the false discovery rate: a practical and powerful approach to multiple testing
Yoav Benjamini,Yosef Hochberg +1 more
TL;DR: In this paper, a different approach to problems of multiple significance testing is presented, which calls for controlling the expected proportion of falsely rejected hypotheses -the false discovery rate, which is equivalent to the FWER when all hypotheses are true but is smaller otherwise.
Journal ArticleDOI
A rating scale for depression
TL;DR: The present scale has been devised for use only on patients already diagnosed as suffering from affective disorder of depressive type, used for quantifying the results of an interview, and its value depends entirely on the skill of the interviewer in eliciting the necessary information.
Journal ArticleDOI
A note on two problems in connexion with graphs
TL;DR: A tree is a graph with one and only one path between every two nodes, where at least one path exists between any two nodes and the length of each branch is given.
Journal ArticleDOI
Automated Anatomical Labeling of Activations in SPM Using a Macroscopic Anatomical Parcellation of the MNI MRI Single-Subject Brain
Nathalie Tzourio-Mazoyer,B. Landeau,D. Papathanassiou,Fabrice Crivello,Octave Etard,Nicolas Delcroix,Bernard Mazoyer,Marc Joliot +7 more
TL;DR: An anatomical parcellation of the spatially normalized single-subject high-resolution T1 volume provided by the Montreal Neurological Institute was performed and it is believed that this tool is an improvement for the macroscopical labeling of activated area compared to labeling assessed using the Talairach atlas brain.
Journal ArticleDOI
An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest.
Rahul S. Desikan,Florent Ségonne,Bruce Fischl,Bruce Fischl,Brian T. Quinn,Bradford C. Dickerson,Deborah Blacker,Randy L. Buckner,Randy L. Buckner,Anders M. Dale,R. Paul Maguire,Bradley T. Hyman,Marilyn S. Albert,Ronald J. Killiany +13 more
TL;DR: An automated labeling system for subdividing the human cerebral cortex into standard gyral-based neuroanatomical regions is both anatomically valid and reliable and may be useful for both morphometric and functional studies of the cerebral cortex.
Related Papers (5)
Adjusting batch effects in microarray expression data using empirical Bayes methods
The organization of the human cerebral cortex estimated by intrinsic functional connectivity
The autism brain imaging data exchange: towards a large-scale evaluation of the intrinsic brain architecture in autism
A Di Martino,C-G Yan,Qingyang Li,E Denio,Francisco X. Castellanos,Francisco X. Castellanos,Kaat Alaerts,Kaat Alaerts,Jeffrey S. Anderson,Michal Assaf,Susan Y. Bookheimer,Mirella Dapretto,Ben Deen,Ben Deen,Sonja Delmonte,Ilan Dinstein,Ilan Dinstein,Birgit Ertl-Wagner,Damien A. Fair,Louise Gallagher,Daniel P. Kennedy,Daniel P. Kennedy,Christopher L. Keown,Christian Keysers,Christian Keysers,Janet E. Lainhart,Catherine Lord,Beatriz Luna,Vinod Menon,Nancy J. Minshew,Christopher S. Monk,Sophia Mueller,R-A Müller,Mary Beth Nebel,Joel T. Nigg,Kirsten O'Hearn,Kevin A. Pelphrey,Scott Peltier,Jeffrey D. Rudie,Stefan Sunaert,Mark Thioux,Mark Thioux,J M Tyszka,Lucina Q. Uddin,Judith Verhoeven,Nicole Wenderoth,Jillian Lee Wiggins,Stewart H. Mostofsky,Stewart H. Mostofsky,Michael P. Milham,Michael P. Milham +50 more