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A Method for Harmonizing Longitudinal Multi-scanner Imaging Data [article]

Joanne C. Beer, Nicholas J. Tustison, Philip A. Cook, Yvette I. Sheline, Russell T. Shinohara, Kristin A. Linn
<span title="2019-12-08">2019</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
We propose a method for the harmonization of longitudinal multi-scanner imaging data based on ComBat, a method originally developed for genomics and later adapted to cross-sectional neuroimaging data.  ...  ComBat, and data harmonized using longitudinal ComBat.  ...  Thus, in the present study, we proposed and validated longitudinal ComBat, a novel method for harmonizing longitudinal data across different scanners.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/868810">doi:10.1101/868810</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/yyugvmos55gnxbsnjxcxkpn3bi">fatcat:yyugvmos55gnxbsnjxcxkpn3bi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210429012220/https://www.biorxiv.org/content/biorxiv/early/2020/06/25/868810.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/60/47/60470a829da8d4910b7d99e70d5caa41cf9af856.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/868810"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

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
<span title="2020-07-05">2020</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/sa477uo7lveh7hchpikpixop5u" style="color: black;">NeuroImage</a> </i> &nbsp;
We propose a method for harmonizing longitudinal multi-scanner imaging data based on ComBat, a method originally developed for genomics and later adapted to cross-sectional neuroimaging data.  ...  , and data harmonized using longitudinal ComBat.  ...  Acknowledgements Data collection and sharing for this project was funded by the Alzheimer's Disease Neuroimaging Initiative (ADNI) (National Institutes of Health Grant U01 AG024904) and DOD ADNI (Department  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.neuroimage.2020.117129">doi:10.1016/j.neuroimage.2020.117129</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32640273">pmid:32640273</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7605103/">pmcid:PMC7605103</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4ngmfvob25bfnpm4tqrridyklu">fatcat:4ngmfvob25bfnpm4tqrridyklu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210527064207/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC7605103&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/a1/fd/a1fd89a27d47e4ff251ca94429671d48c0868dd6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.neuroimage.2020.117129"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7605103" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Longitudinal Neuroimaging following Combat Concussion sub-acute, 1-year, and 5-years post-injury

Christine L Mac Donald, Jason Barber, Jalal Andre, Chris Panks, Kody Zalewski, Nancy Temkin
<span title="2019-11-05">2019</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/xgtxpuxfjzedvjklgehqpq4beq" style="color: black;">Brain Communications</a> </i> &nbsp;
age, education, gender, scanner, and subsequent head injury exposure followed by correction for multiple comparisons.  ...  Longitudinal evaluation of the number of abnormal diffusion tensor imaging and volumetric regions in concussive blast patients revealed distinct trends by imaging modality.  ...  Funding Funding for this longitudinal analysis and 5-year follow-up wave has been provided by a National Institute of Health RO1 grant from the National Institute of Neurological Disorders and Stroke (  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/braincomms/fcz031">doi:10.1093/braincomms/fcz031</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31915753">pmid:31915753</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6935683/">pmcid:PMC6935683</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/walxsp5z5nevldrrj7rirvapni">fatcat:walxsp5z5nevldrrj7rirvapni</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200511064906/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC6935683&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/41/80/4180cb899b335213fee3b02691c2220625366b91.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/braincomms/fcz031"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6935683" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Exploring the limits of ComBat method for multi-site diffusion MRI harmonization [article]

Suheyla Cetin-Karayumak, Katharina Stegmayer, Sebastian Walther, Philip R. Szeszko, Tim Crow, Anthony James, Matcheri Keshavan, Marek Kubicki, Yogesh Rathi
<span title="2020-11-21">2020</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
was adapted for multi-site dMRI harmonization to reduce scanner/site effect.  ...  Thus, our findings suggest paying careful attention to the data being harmonized as well as using the same processing pipeline while using ComBat for data harmonization.  ...  However, scanner induced bias in dMRI signal limits direct pooling of the multi-site dMRI data.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.11.20.390120">doi:10.1101/2020.11.20.390120</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/rzbwo345hjdkneoy4uc4zjirzu">fatcat:rzbwo345hjdkneoy4uc4zjirzu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210429130951/https://www.biorxiv.org/content/biorxiv/early/2020/11/21/2020.11.20.390120.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/56/aa/56aadfda183c46e4dfa91b435b8a8f6ccb2515bb.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.11.20.390120"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Harmonization of Multi-Center Diffusion Tensor Tractography in Neonates with Congenital Heart Disease: Optimizing Post-Processing and Application of ComBat [article]

Benjamin D Meyers, Vincent K Lee, Lauren G Dennis, Julia Wallace, Vince Schmithorst, Jodie K Votava-Smith, Vidya Rajagopalan, Elizabeth Herrup, Tracy Baust, Nhu N Tran, Daniel J Licht, William J Gaynor (+3 others)
<span title="2021-10-04">2021</span> <i title="Cold Spring Harbor Laboratory"> medRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
This proves to be a barrier in the analysis of large multi-center studies and is a particularly salient problem given the relative scarcity of neonatal imaging data.  ...  Our method is an open-source pipeline for delineating white matter tracts in subject space but provides the necessary modular components for performing atlas space analysis.  ...  compartmentalizing the unwanted sources of variance, allowing for a final harmonization of multi-site, high anatomical variance data.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2021.10.01.21264443">doi:10.1101/2021.10.01.21264443</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zaarliuzs5aojhbftu4zwsrygu">fatcat:zaarliuzs5aojhbftu4zwsrygu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20211020081333/https://www.medrxiv.org/content/medrxiv/early/2021/10/04/2021.10.01.21264443.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c5/63/c563f9f89d5128602c74112c0376aa7e27ef514f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2021.10.01.21264443"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> medrxiv.org </button> </a>

Cross-Sectional and Longitudinal Hippocampal Atrophy, Not Cortical Thinning, Occurs in Amyloid-Negative, p-Tau-Positive, Older Adults With Non-Amyloid Pathology and Mild Cognitive Impairment

Swati Rane Levendovszky
<span title="2022-06-02">2022</span> <i title="Frontiers Media SA"> Frontiers in Neuroimaging </i> &nbsp;
We compared baseline and longitudinal, hippocampal, and cortical atrophy between groups.MethodsWe applied ComBat harmonization to minimize site-related variability and used FreeSurfer for all measurements.ResultsHarmonization  ...  as participants with A+T+ MCI, but did not show longitudinal cortical atrophy signature.  ...  If a site had multiple scanners, then each scanner was assigned as a separate site for harmonization purposes.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fnimg.2022.828767">doi:10.3389/fnimg.2022.828767</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5v3zqmoxkbdexhjw2gb2sxdhxe">fatcat:5v3zqmoxkbdexhjw2gb2sxdhxe</a> </span>
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Enhanced detection of cortical atrophy in Alzheimer's disease using structural MRI with anatomically constrained longitudinal registration

Emily Iannopollo, Kara Garcia, Alzheimer' Disease Neuroimaging Initiative
<span title="2021-05-14">2021</span> <i title="Wiley (John Wiley &amp; Sons)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wtsn7qcbmrhjppax2iuhu4xj2m" style="color: black;">Human Brain Mapping</a> </i> &nbsp;
Magnetic resonance imaging scans were segmented and registered to a common atlas using previously described techniques (FreeSurfer and ciftify), then longitudinally registered with aMSM.  ...  To capture the impact of both cortical thinning and surface area loss, we used anatomically constrained Multimodal Surface Matching (aMSM), a recently developed tool for mapping change in surface area.  ...  Future studies using ADNI data or other multi-site datasets may benefit from the implementation of a more comprehensive data harmonization process, such as the ComBat (Johnson, Li, & Rabinovic, 2007)  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/hbm.25455">doi:10.1002/hbm.25455</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33988265">pmid:33988265</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8249882/">pmcid:PMC8249882</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/lbn2d3f4nbc2ld32wcqowgt24i">fatcat:lbn2d3f4nbc2ld32wcqowgt24i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210717194809/https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/hbm.25455" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/a4/83/a483ad26726c4be6563880d005154bae0a0a7069.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/hbm.25455"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> wiley.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8249882" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Harmonization of cortical thickness measurements across scanners and sites

Jean-Philippe Fortin, Nicholas Cullen, Yvette I. Sheline, Warren D. Taylor, Irem Aselcioglu, Philip A. Cook, Phil Adams, Crystal Cooper, Maurizio Fava, Patrick J. McGrath, Melvin McInnis, Mary L. Phillips (+3 others)
<span title="">2018</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/sa477uo7lveh7hchpikpixop5u" style="color: black;">NeuroImage</a> </i> &nbsp;
We then propose to use ComBat, a technique adopted from the genomics literature and recently applied to diffusion tensor imaging data, to combine and harmonize cortical thickness values across scanners  ...  We also show that ComBat is useful for combining imaging data with the goal of studying life-span trajectories in the brain.  ...  On the other hand, ComBat does not make such specific assumptions on the nature of the imaging measurements, making it a potential and versatile tool for the harmonization of multi-site imaging studies  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.neuroimage.2017.11.024">doi:10.1016/j.neuroimage.2017.11.024</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29155184">pmid:29155184</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5845848/">pmcid:PMC5845848</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/eb2l7mhef5fqfjzxme72h5wvmm">fatcat:eb2l7mhef5fqfjzxme72h5wvmm</a> </span>
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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
<span title="2020-05-06">2020</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wrk3kouosrhcxiprcbguskdipu" style="color: black;">Frontiers in Neuroscience</a> </i> &nbsp;
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  ...  To allow a reliable comparison and joint analysis of diffusion data across sites and over time, there is a clear need for robust data harmonization methods.  ...  Timmermans et al. (2019) presented global multi-site harmonization models, using phantom data acquired at multiple centers in a longitudinal study.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fnins.2020.00396">doi:10.3389/fnins.2020.00396</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32435181">pmid:32435181</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7218137/">pmcid:PMC7218137</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/il5p2l7a5fd2vheehvyobgg5lm">fatcat:il5p2l7a5fd2vheehvyobgg5lm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200507025726/https://fjfsdata01prod.blob.core.windows.net/articles/files/485829/pubmed-zip/.versions/1/.package-entries/fnins-14-00396/fnins-14-00396.pdf?sv=2015-12-11&amp;sr=b&amp;sig=EKt3Z5jZ72IFyHYw0BaazwJoy0Is2aPsfT1LdKd%2FP4c%3D&amp;se=2020-05-07T02%3A57%3A56Z&amp;sp=r&amp;rscd=attachment%3B%20filename%2A%3DUTF-8%27%27fnins-14-00396.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/b5/ee/b5ee1a8b5669c85b43618cd462dc24327bc09f26.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fnins.2020.00396"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> frontiersin.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7218137" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Diffusion MRI Metrics and their Relation to Dementia Severity: Effects of Harmonization Approaches [article]

Sophia I. Thomopoulos, Talia M. Nir, Julio E. Villalon-Reina, Artemis Zavaliangos-Petropulu, Piyush Maiti, Hong Zheng, Elnaz Nourollahimoghadam, Neda Jahanshad, Paul M. Thompson, for the Alzheimer's Disease Neuroimaging Initiative
<span title="2021-10-05">2021</span> <i title="Cold Spring Harbor Laboratory"> medRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
All harmonization methods gave comparable results while enabling data integration across multiple scanners and protocols.  ...  To harmonize data from different protocols, we applied ComBat, ComBat-GAM, and CovBat to dMRI metrics from 28 white matter regions of interest.  ...  PMT and NJ received a research grant from Biogen, Inc. for research unrelated to this manuscript.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2021.10.04.21263994">doi:10.1101/2021.10.04.21263994</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hn2y22jjhbawhmzuhkwe2pcypa">fatcat:hn2y22jjhbawhmzuhkwe2pcypa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20211020081347/https://www.medrxiv.org/content/medrxiv/early/2021/10/05/2021.10.04.21263994.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/94/19/9419ef5c010075267dabbd5af4ac13be72b2e392.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2021.10.04.21263994"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> medrxiv.org </button> </a>

Detecting and harmonizing scanner differences in the ABCD study - annual release 1.0 [article]

Dylan M Nielson, Francisco Pereira, Charles Y Zheng, Nino Migineishvili, John A Lee, Adam G Thomas, Peter A Bandettini
<span title="2018-05-02">2018</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
In this manuscript, we have explored scanner-related differences in the dataset recently released by the Adolescent Brain Cognitive Development (ABCD) project, a multi-site, longitudinal study of children  ...  We further demonstrate that these differences can be harmonized using an empirical Bayes approach known as ComBat.  ...  This is a multi-site, longitudinal study designed to recruit more than 10,000 children age 9-10 and follow them over 10 years into early adulthood.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/309260">doi:10.1101/309260</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ebcc5nt275hj5cl2cjl66cfjsi">fatcat:ebcc5nt275hj5cl2cjl66cfjsi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190502044155/https://www.biorxiv.org/content/biorxiv/early/2018/05/02/309260.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/8f/16/8f1616fef9eb816379a4fc71c282529b0c40b995.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/309260"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Removal of Scanner Effects in Covariance Improves Multivariate Pattern Analysis in Neuroimaging Data [article]

Andrew A. Chen, Joanne C. Beer, Nicholas J. Tustison, Philip A. Cook, Russell T. Shinohara, Haochang Shou, for the Alzheimer's Disease Neuroimaging Initiative
<span title="2019-12-02">2019</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
We also propose a novel methodology that harmonizes covariance of multivariate image measurements across sites and demonstrate its improved performance in data harmonization, which further facilitates  ...  To address this, the field has focused on harmonizing data via removing the scanner differences in mean and variance of measurements.  ...  Our results demonstrate the need to consider covariance in harmonization methods, and suggest a novel procedure that can be applied to better harmonize data from multi-site imaging studies.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/858415">doi:10.1101/858415</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/yrdf3rltlrgfpexpis3sza6njm">fatcat:yrdf3rltlrgfpexpis3sza6njm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200324133633/https://www.biorxiv.org/content/biorxiv/early/2019/12/02/858415.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/00/45/0045a520954a2c47934400d32aa1556515130ab5.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/858415"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Harmonization of cortical thickness measurements across scanners and sites [article]

Jean-Philippe Fortin, Nicholas Cullen, Yvette I. Sheline, Warren D. Taylor, Irem Aselcioglu, Phil Adams, Crystal Cooper, Mauricio Fava, Patrick J. McGrath, Melvin McInnis, Ramin V. Parsey, Mary L. Phillips (+3 others)
<span title="2017-06-10">2017</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
We then propose to use ComBat, a technique adopted from the genomics literature and recently applied to diffusion tensor imaging data, to combine and harmonize cortical thickness values across scanners  ...  We also show that ComBat is useful for combining imaging data with the goal of studying life-span trajectories in the brain.  ...  We note that for all three harmonization methods, the data points appear to be distributed equally across scanners. We also performed LDA using scanners as the data classes.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/148502">doi:10.1101/148502</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2s6ynnpgezcd3ax2owiv76bk6e">fatcat:2s6ynnpgezcd3ax2owiv76bk6e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190501220521/https://www.biorxiv.org/content/biorxiv/early/2017/06/10/148502.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/148502"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Motion artifact in studies of functional connectivity: Characteristics and mitigation strategies

Theodore D. Satterthwaite, Rastko Ciric, David R. Roalf, Christos Davatzikos, Danielle S. Bassett, Daniel H. Wolf
<span title="2017-11-01">2017</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wtsn7qcbmrhjppax2iuhu4xj2m" style="color: black;">Human Brain Mapping</a> </i> &nbsp;
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  ...  Our proposed ComBat harmonization approach for fMRI-derived connectivity measures facilitates reliable and efficient analysis of retrospective and prospective multi-site fMRI neuroimaging studies.  ...  We thank Maria Prociuk for her assistance with the preparation and submission of the manuscript. We thank all patients and controls for their participation.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/hbm.23665">doi:10.1002/hbm.23665</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29091315">pmid:29091315</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/xugzefj63zdttm7volb73wzjfy">fatcat:xugzefj63zdttm7volb73wzjfy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201107172533/https://deepblue.lib.umich.edu/bitstream/handle/2027.42/146498/hbm24241_am.pdf;jsessionid=41717D3F617094FF5DAEE7B4E11F9B4D?sequence=3" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/6b/e4/6be40663bb12c6cafa4545cc07a0af37fc725058.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/hbm.23665"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> wiley.com </button> </a>

Harmonization with Flow-based Causal Inference [article]

Rongguang Wang, Pratik Chaudhari, Christos Davatzikos
<span title="2021-07-10">2021</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
This paper leverages a recently proposed normalizing-flow-based method to perform counterfactual inference upon a structural causal model (SCM), in order to achieve harmonization of such data.  ...  Heterogeneity in medical data, e.g., from data collected at different sites and with different protocols in a clinical study, is a fundamental hurdle for accurate prediction using machine learning models  ...  Castro for suggestions. This work was supported by the National Institute on Aging (grant numbers RF1AG054409 and U01AG068057) and the National Institute of Mental Health (grant number R01MH112070).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2106.06845v2">arXiv:2106.06845v2</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hildildhc5go3fojq3rjtcjfuy">fatcat:hildildhc5go3fojq3rjtcjfuy</a> </span>
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