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Harmonizing Functional Connectivity Reduces Scanner Effects in Community Detection [article]

Andrew A. Chen, Dhivya Srinivasan, Raymond Pomponio, Yong Fan, Ilya M. Nasrallah, Susan M. Resnick, Lori L. Beason-Held, Christos Davatzikos, Theodore D. Satterthwaite, Dani S. Bassett, Russell T. Shinohara, Haochang Shou
2021 bioRxiv   pre-print
In this study, we identify scanner effects in data-driven community detection results and related network metrics.  ...  Finally, we demonstrate that our new methods reduce scanner effects in community structure and network metrics.  ...  ComBat has been applied to functional connectivity (FC) and shown to substantially reduce scanner effects in several network metrics including global efficiency, local efficiency, and within-community  ... 
doi:10.1101/2021.12.03.469269 fatcat:o6u474d77zdvjnuevs7vr2hn4m

Resolution limit-free community detection reveals unique patterns of resting-state network connectivity in posttraumatic stress disorder: A PGC-ENIGMA PTSD Consortium investigation [article]

Marisa C. Ross, Josh M. Cisler, Saskia B.J. Koch, Miranda Olff, Dick Veltman J. Veltman, Laura Nawijn, Jessie L. L. Frijling, Mirjam van Zuiden, Xi Zhu, Yuval Neria, Benjamin Suarez-Jimenez, Courtney Haswell (+60 others)
2021 medRxiv   pre-print
With a novel, resolution limit-free community detection approach, 16 communities corresponding to functionally meaningful networks were detected with high quality.  ...  This study presents a novel use of resolution limit-free community detection in a large PTSD sample, revealing robust differences in resting-state network topology.  ...  ComBat harmonization 48, 49 in Matlab was applied to connectivity matrices to correct for systematic scanner effects.  ... 
doi:10.1101/2021.06.24.21259102 fatcat:bsydhew5fraiznjj5zmafcpz3q

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
2018 bioRxiv   pre-print
We demonstrate that scanner manufacturer, model, as well as the individual scanner itself, are detectable in the resting and task-based fMRI results of the ABCD dataset.  ...  In order to obtain the sample sizes needed for robustly reproducible effects, it is often necessary to acquire data at multiple sites using different MRI scanners.  ...  Data used in the preparation of this article were obtained from the Adolescent Brain Cognitive Development (ABCD) Study (https://abcdstudy.org), held in the NIMH Data Archive (NDA).  ... 
doi:10.1101/309260 fatcat:ebcc5nt275hj5cl2cjl66cfjsi

European Ultrahigh-Field Imaging Network for Neurodegenerative Diseases (EUFIND)

Emrah Düzel, Julio Acosta-Cabronero, David Berron, Geert Jan Biessels, Isabella Björkman-Burtscher, Michel Bottlaender, Richard Bowtell, Mark v Buchem, Arturo Cardenas-Blanco, Fawzi Boumezbeur, Dennis Chan, Stuart Clare (+19 others)
2019 Alzheimer's and Dementia: Diagnosis, Assessment and Disease Monitoring  
systems/vascular pathology, iron mapping and neuropathology detection, spectroscopy, and quality assurance.  ...  Across these topics, EUFIND considered standard operating procedures, safety, and multivendor harmonization.  ...  We found, however, large sensitivity differences across scanner platforms in detecting perforating arteries.  ... 
doi:10.1016/j.dadm.2019.04.010 pmid:31388558 pmcid:PMC6675944 fatcat:d2stwb6otnekvfs5t6becyaxhm

New fMRI methods for hearing and speech

Alan R. Palmer, John Chambers, Deb A. Hall
2006 Acoustical Science and Technology  
We then describe a series of techniques that have been employed to minimize the effects of the scanner noise on the subject and upon the subject's evoked responses to sound stimuli.  ...  In this short review, we outline the challenges presented by the hostile environment for auditory fMRI.  ...  METHODS FOR MINIMIZING THE EFFECTS OF SCANNER SOUND A number of ways to reduce the effect of the intense background noise have been implemented.  ... 
doi:10.1250/ast.27.125 fatcat:vsmr3dho6vfuxf24whab47lb74

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  
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.  ...  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  ...  Moreover, a unique correction factor per scanner type only partially reduces the harmonization problem due to its intrinsic non-linearity, i.e., scanner type differences are not uniform but vary in a highly  ... 
doi:10.3389/fnins.2020.00396 pmid:32435181 pmcid:PMC7218137 fatcat:il5p2l7a5fd2vheehvyobgg5lm

Aberrant Dynamic Functional Network Connectivity and Graph Properties in Major Depressive Disorder

Dongmei Zhi, Vince D. Calhoun, Luxian Lv, Xiaohong Ma, Qing Ke, Zening Fu, Yuhui Du, Yongfeng Yang, Xiao Yang, Miao Pan, Shile Qi, Rongtao Jiang (+2 others)
2018 Frontiers in Psychiatry  
MDD patients exhibited significantly reduced harmonic centrality primarily involving parietal lobule, lingual gyrus and thalamus.  ...  Previous studies have identified abnormalities in large scale functional brain networks in MDD, yet most of them were based on static functional connectivity.  ...  Recent studies have found reoccurring connectivity patterns among intrinsic networks in multiple diseases including schizophrenia and bipolar disorder, which cannot be detected in static functional connectivity  ... 
doi:10.3389/fpsyt.2018.00339 pmid:30108526 pmcid:PMC6080590 fatcat:xhjggb35ufdydiyukx7jg7mso4

Heritability estimates on resting state fMRI data using ENIGMA analysis pipeline

Bhim M Adhikari, Neda Jahanshad, Dinesh Shukla, David C Glahn, John Blangero, Richard C Reynolds, Robert W Cox, Els Fieremans, Jelle Veraart, Dmitry S Novikov, Thomas E Nichols, L Elliot Hong (+2 others)
2018 Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing  
This harmonization is particularly challenging for resting state fMRI due to the wide variability of acquisition protocols and scanner platforms; this leads to site-to-site variance in quality, resolution  ...  We developed a multi-site rsfMRI analysis pipeline to allow research groups around the world to process rsfMRI scans in a harmonized way, to extract consistent and quantitative measurements of connectivity  ...  An effective harmonization should provide optimal measures for data of different qualities.  ... 
pmid:29218892 pmcid:PMC5728672 fatcat:k43mab5eyresbiyuuivky73eje

Heritability estimates on resting state fMRI data using ENIGMA analysis pipeline

Bhim M. Adhikari, Neda Jahanshad, Dinesh Shukla, David C. Glahn, John Blangero, Richard C. Reynolds, Robert W. Cox, Els Fieremans, Jelle Veraart, Dmitry S. Novikov, Thomas E. Nichols, L. Elliot Hong (+2 others)
2017 Biocomputing 2018  
This harmonization is particularly challenging for resting state fMRI due to the wide variability of acquisition protocols and scanner platforms; this leads to site-to-site variance in quality, resolution  ...  We developed a multi-site rsfMRI analysis pipeline to allow research groups around the world to process rsfMRI scans in a harmonized way, to extract consistent and quantitative measurements of connectivity  ...  An effective harmonization should provide optimal measures for data of different qualities.  ... 
doi:10.1142/9789813235533_0029 fatcat:6sr7azhcozdyjajax2koykwcv4

Artificial intelligence: Deep learning in oncological radiomics and challenges of interpretability and data harmonization

Panagiotis Papadimitroulas, Lennart Brocki, Neo Christopher Chung, Wistan Marchadour, Franck Vermet, Laurent Gaubert, Vasilis Eleftheriadis, Dimitris Plachouris, Dimitris Visvikis, George C. Kagadis, Mathieu Hatt
2021 Physica medica (Testo stampato)  
imaging data and the increased developments of Machine Learning (ML), particularly Deep Learning (DL), triggered the research on uncovering "hidden" biomarkers and quantitative features from anatomical and functional  ...  In this study we review the basics of radiomics feature extraction, DNNs in image analysis, and major interpretability methods that help enable explainable AI.  ...  [135] ) to reduce the variability of radiomic features across different scanner models and reconstruction settings [137] .  ... 
doi:10.1016/j.ejmp.2021.03.009 pmid:33765601 fatcat:ejg4x3n4pjbwrdqw4vxukrk2cm

Harmonizing brain magnetic resonance imaging methods for vascular contributions to neurodegeneration

Eric E. Smith, Geert Jan Biessels, François De Guio, Frank Erik de Leeuw, Simon Duchesne, Marco Düring, Richard Frayne, M. Arfan Ikram, Eric Jouvent, Bradley J. MacIntosh, Michael J. Thrippleton, Meike W. Vernooij (+37 others)
2019 Alzheimer's and Dementia: Diagnosis, Assessment and Disease Monitoring  
The HARNESS initiative provides resources to reduce variability in measurement in MRI studies of cerebral small vessel disease.  ...  Surveys, teleconferences, and an in-person workshop were used to identify gaps in knowledge and to develop tools for harmonizing imaging and analysis.  ...  Lower brain connectivity in strategic network locations, such as long-distance fibers connecting so-called network "hubs", shows promise for prediction of speed and executive functioning [48, 49] .  ... 
doi:10.1016/j.dadm.2019.01.002 pmid:30859119 pmcid:PMC6396326 fatcat:fekvri5wq5gyvosbk4ozpa2d3a

Learning Robust Hierarchical Patterns of Human Brain across Many fMRI Studies [article]

Dushyant Sahoo, Christos Davatzikos
2021 arXiv   pre-print
We introduce a simple yet effective matrix factorization based formulation to reduce site-related effects while preserving biologically relevant variations.  ...  In addition, fMRI data helps in understanding the brain's functional working during resting state and task-induced activity.  ...  [8] used ComBat harmonization [26] to remove site effects in connectivity matrices.  ... 
arXiv:2105.06535v2 fatcat:6boim5m5djfvlglbjvm2rtoyay

FingerScanner: Embedding a Fingerprint Scanner in a Raspberry Pi

Jordi Sapes, Francesc Solsona
2016 Sensors  
Thus, embedding devices on Raspberry-Linux systems is a goal in order to make competitive commercial products.  ...  Cost reduction has lead to an increase in the number of platforms supporting the operating system Linux, jointly with the Raspberry Pi motherboard.  ...  However, security issues concerning the management of a huge number of connected devices cost effectively has emerged in this research field.  ... 
doi:10.3390/s16020220 pmid:26861340 pmcid:PMC4801596 fatcat:wnxttvu6nvac7c7kjbdiko4pou

Quality Assessment in FDG-PET/CT Imaging of Head-and-Neck Cancer: One Home Run Is Better Than Two Doubles

Tim Van den Wyngaert, Stijn De Schepper, Laurens Carp
2020 Frontiers in Oncology  
capabilities of PET/CT scanners (e.g., digital silicon photomultipliers, point-spread function modeling, and time-of-flight, and Bayesian penalized likelihood reconstruction).  ...  Moreover, a coordinated harmonization effort from professional societies (e.g., EANM) and international bodies (e.g., IAEA) has resulted in the creation of quality assurance frameworks (e.g., QUANUM, EARL  ...  Point-spread function modeling • Point-spread function modeling includes the physical processes that cause image degradation, including positron range, photon non-collinearity, and detector-related effects  ... 
doi:10.3389/fonc.2020.01458 pmid:32923399 pmcid:PMC7457015 fatcat:z4mbsgczlva4fnur72cbi6xscu

Maturity of gray matter structures and white matter connectomes, and their relationship with psychiatric symptoms in youth

Alex Luna, Joel Bernanke, Kakyeong Kim, Natalie Aw, Jordan D. Dworkin, Jiook Cha, Jonathan Posner
2021 Human Brain Mapping  
Associations with psychometric measures remained consistent after ComBat harmonization, though only the association with CGAS reached statistical significance in the reduced sample.  ...  in youth.  ...  | Harmonization of brain data ComBat (short for Combating batch effects when combining Batches) can be used to reduce "scanner effects" in processed structural and diffusion imaging data (Fortin et  ... 
doi:10.1002/hbm.25565 pmid:34240783 pmcid:PMC8410534 fatcat:th7ojdyeengkbpiw6bowqjhacu
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