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Zheng G, Fei B, Ge A, Liu Y, Liu Y, Yang Z, Chen Z, Wang X, Wang H, Ding J. U-fiber analysis: a toolbox for automated quantification of U-fibers and white matter hyperintensities. Quant Imaging Med Surg 2024; 14:662-683. [PMID: 38223048 PMCID: PMC10784071 DOI: 10.21037/qims-23-847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 11/13/2023] [Indexed: 01/16/2024]
Abstract
Background Whether white matter hyperintensities (WMHs) involve U-fibers is of great value in understanding the different etiologies of cerebral white matter (WM) lesions. However, clinical practice currently relies only on the naked eye to determine whether WMHs are in the vicinity of U-fibers, and there is a lack of good neuroimaging tools to quantify WMHs and U-fibers. Methods Here, we developed a multimodal neuroimaging toolbox named U-fiber analysis (UFA) that can automatically extract WMHs and quantitatively characterize the volume and number of WMHs in different brain regions. In addition, we proposed an anatomically constrained U-fiber tracking scheme and quantitatively characterized the microstructure diffusion properties, fiber length, and number of U-fibers in different brain regions to help clinicians to quantitatively determine whether WMHs in the proximal cortex disrupt the microstructure of U-fibers. To validate the utility of the UFA toolbox, we analyzed the neuroimaging data from 246 patients with cerebral small vessel disease (cSVD) enrolled at Zhongshan Hospital between March 2018 and November 2019 in a cross-sectional study. Results According to the manual judgment of the clinician, the patients with cSVD were divided into a WMHs involved U-fiber group (U-fiber-involved group, 51 cases) and WMHs not involved U-fiber group (U-fiber-spared group, 163 cases). There were no significant differences between the U-fiber-spared group and the U-fiber-involved group in terms of age (P=0.143), gender (P=0.462), education (P=0.151), Mini-Mental State Examination (MMSE) scores (P=0.151), and Montreal Cognitive Assessment (MoCA) scores (P=0.411). However, patients in the U-fiber-involved group had higher Fazekas scores (P<0.001) and significantly higher whole brain WMHs (P=0.046) and deep WMH volumes (P<0.001) compared to patients in the U-fiber-spared group. Moreover, the U-fiber-involved group had higher WMH volumes in the bilateral frontal [P(left) <0.001, P(right) <0.001] and parietal lobes [P(left) <0.001, P(right) <0.001]. On the other hand, patients in the U-fiber-involved group had higher mean diffusivity (MD) and axial diffusivity (AD) in the bilateral parietal [P(left, MD) =0.048, P(right, MD) =0.045, P(left, AD) =0.015, P(right, AD) =0.015] and right frontal-parietal regions [P(MD) =0.048, P(AD) =0.027], and had significantly reduced mean fiber length and number in the right parietal [P(length) =0.013, P(number) =0.028] and right frontal-parietal regions [P(length) =0.048] compared to patients in the U-fiber-spared group. Conclusions Our results suggest that WMHs in the proximal cortex may disrupt the microstructure of U-fibers. Our tool may provide new insights into the understanding of WM lesions of different etiologies in the brain.
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Affiliation(s)
- Gaoxing Zheng
- Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Beini Fei
- Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Anyan Ge
- Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yuchen Liu
- Institute of Science and Technology for Brain-inspired Intelligence, Fudan University, Shanghai, China
| | - Ying Liu
- Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Zidong Yang
- Institute of Science and Technology for Brain-inspired Intelligence, Fudan University, Shanghai, China
| | - Zhensen Chen
- Institute of Science and Technology for Brain-inspired Intelligence, Fudan University, Shanghai, China
| | - Xin Wang
- Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - He Wang
- Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai, China
- Institute of Science and Technology for Brain-inspired Intelligence, Fudan University, Shanghai, China
| | - Jing Ding
- Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai, China
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Chowell G, Bleichrodt A, Dahal S, Tariq A, Roosa K, Hyman JM, Luo R. A MATLAB toolbox to fit and forecast growth trajectories using phenomenological growth models: Application to epidemic outbreaks. Res Sq 2023:rs.3.rs-2724940. [PMID: 37034746 PMCID: PMC10081381 DOI: 10.21203/rs.3.rs-2724940/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
Background Simple dynamic modeling tools can be useful for generating real-time short-term forecasts with quantified uncertainty of the trajectory of diverse growth processes unfolding in nature and society, including disease outbreaks. An easy-to-use and flexible toolbox for this purpose is lacking. Results In this tutorial-based primer, we introduce and illustrate a user-friendly MATLAB toolbox for fitting and forecasting time-series trajectories using phenomenological dynamic growth models based on ordinary differential equations. This toolbox is accessible to various audiences, including students training in time-series forecasting, dynamic growth modeling, parameter estimation, parameter uncertainty and identifiability, model comparison, performance metrics, and forecast evaluation, as well as researchers and policymakers who need to conduct short-term forecasts in real-time. The models included in the toolbox capture exponential and sub-exponential growth patterns that typically follow a rising pattern followed by a decline phase, a common feature of contagion processes. Models include the 2-parameter generalized-growth model, which has proved useful to characterize and forecast the ascending phase of epidemic outbreaks, and the Gompertz model as well as the 3-parameter generalized logistic-growth model and the Richards model, which have demonstrated competitive performance in forecasting single peak outbreaks.The toolbox provides a tutorial for forecasting time-series trajectories that include the full uncertainty distribution, derived through parametric bootstrapping, which is needed to construct prediction intervals and evaluate their accuracy. Functions are available to assess forecasting performance across different models, estimation methods, error structures in the data, and forecasting horizons. The toolbox also includes functions to quantify forecasting performance using metrics that evaluate point and distributional forecasts, including the weighted interval score. Conclusions We have developed the first comprehensive toolbox to characterize and forecast time-series data using simple phenomenological growth models. As a contagion process takes off, the tools presented in this tutorial can facilitate policymaking to guide the implementation of control strategies and assess the impact of interventions. The toolbox functionality is demonstrated through various examples, including a tutorial video, and is illustrated using weekly data on the monkeypox epidemic in the USA.
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Affiliation(s)
- Gerardo Chowell
- Department of Population Health Sciences, School of Public Health, Georgia State University, Atlanta, GA, USA
| | - Amanda Bleichrodt
- Department of Population Health Sciences, School of Public Health, Georgia State University, Atlanta, GA, USA
| | - Sushma Dahal
- Department of Population Health Sciences, School of Public Health, Georgia State University, Atlanta, GA, USA
| | - Amna Tariq
- Stanford University, School of Medicine, CA, USA
| | - Kimberlyn Roosa
- National Institute for Mathematical and Biological Synthesis (NIMBioS), University of Tennessee, Knoxville, TN, USA
| | - James M Hyman
- Department of Mathematics, Center for Computational Science, Tulane University, New Orleans, LA, USA
| | - Ruiyan Luo
- Department of Population Health Sciences, School of Public Health, Georgia State University, Atlanta, GA, USA
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3
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Chowell G, Bleichrodt A, Dahal S, Tariq A, Roosa K, Hyman JM, Luo R. A MATLAB toolbox to fit and forecast growth trajectories using phenomenological growth models: Application to epidemic outbreaks. Res Sq 2023:rs.3.rs-2724940. [PMID: 37034746 PMCID: PMC10081381 DOI: 10.21203/rs.3.rs-2724940/v2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
BACKGROUND Simple dynamic modeling tools can be useful for generating real-time short-term forecasts with quantified uncertainty of the trajectory of diverse growth processes unfolding in nature and society, including disease outbreaks. An easy-to-use and flexible toolbox for this purpose is lacking. RESULTS In this tutorial-based primer, we introduce and illustrate a user-friendly MATLAB toolbox for fitting and forecasting time-series trajectories using phenomenological dynamic growth models based on ordinary differential equations. This toolbox is accessible to various audiences, including students training in time-series forecasting, dynamic growth modeling, parameter estimation, parameter uncertainty and identifiability, model comparison, performance metrics, and forecast evaluation, as well as researchers and policymakers who need to conduct short-term forecasts in real-time. The models included in the toolbox capture exponential and sub-exponential growth patterns that typically follow a rising pattern followed by a decline phase, a common feature of contagion processes. Models include the 2-parameter generalized-growth model, which has proved useful to characterize and forecast the ascending phase of epidemic outbreaks, and the Gompertz model as well as the 3-parameter generalized logistic-growth model and the Richards model, which have demonstrated competitive performance in forecasting single peak outbreaks.The toolbox provides a tutorial for forecasting time-series trajectories that include the full uncertainty distribution, derived through parametric bootstrapping, which is needed to construct prediction intervals and evaluate their accuracy. Functions are available to assess forecasting performance across different models, estimation methods, error structures in the data, and forecasting horizons. The toolbox also includes functions to quantify forecasting performance using metrics that evaluate point and distributional forecasts, including the weighted interval score. CONCLUSIONS We have developed the first comprehensive toolbox to characterize and forecast time-series data using simple phenomenological growth models. As a contagion process takes off, the tools presented in this tutorial can facilitate policymaking to guide the implementation of control strategies and assess the impact of interventions. The toolbox functionality is demonstrated through various examples, including a tutorial video, and is illustrated using weekly data on the monkeypox epidemic in the USA.
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Affiliation(s)
- Gerardo Chowell
- Department of Population Health Sciences, School of Public Health, Georgia State University, Atlanta, GA, USA
| | - Amanda Bleichrodt
- Department of Population Health Sciences, School of Public Health, Georgia State University, Atlanta, GA, USA
| | - Sushma Dahal
- Department of Population Health Sciences, School of Public Health, Georgia State University, Atlanta, GA, USA
| | - Amna Tariq
- Stanford University, School of Medicine, CA, USA
| | - Kimberlyn Roosa
- National Institute for Mathematical and Biological Synthesis (NIMBioS), University of Tennessee, Knoxville, TN, USA
| | - James M Hyman
- Department of Mathematics, Center for Computational Science, Tulane University, New Orleans, LA, USA
| | - Ruiyan Luo
- Department of Population Health Sciences, School of Public Health, Georgia State University, Atlanta, GA, USA
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Lapresa M, Zollo L, Cordella F. A user-friendly automatic toolbox for hand kinematic analysis, clinical assessment and postural synergies extraction. Front Bioeng Biotechnol 2022; 10:1010073. [PMID: 36440447 PMCID: PMC9686293 DOI: 10.3389/fbioe.2022.1010073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 10/27/2022] [Indexed: 12/07/2023] Open
Abstract
The clinical assessment of the human hand is typically conducted through questionnaires or tests that include objective (e.g., time) and subjective (e.g., grasp quality) outcome measures. However, there are other important indicators that should be considered to quantify grasp and movement quality in addition to the time needed by a subject to execute a task, and this is essential for human and artificial hands that attempt to replicate the human hand properties. The correct estimation of hand kinematics is fundamental for computing these indicators with high fidelity, and a technical background is typically required to perform this analysis. In addition, to understand human motor control strategies as well as to replicate them on artificial devices, postural synergies were widely explored in recent years. Synergies should be analyzed not only to investigate possible modifications due to musculoskeletal and/or neuromuscular disorders, but also to test biomimetic hands. The aim of this work is to present an open source toolbox to perform all-in-one kinematic analysis and clinical assessment of the hand, as well as to perform postural synergies extraction. In the example provided in this work, the tool takes as input the position of 28 retroreflective markers with a diameter of 6 mm, positioned on specific anatomical landmarks of the hand and recorded with an optoelectronic motion capture system, and automatically performs 1) hand kinematic analysis (i.e., computation of 23 joint angles); 2) clinical assessment, by computing indicators that allow quantifying movement efficiency (Peak Grip Aperture), smoothness (Normalized Dimensionless Jerk Grasp Aperture) and speed (Peak Velocity of Grasp Aperture), planning capabilities (Time to Peak Grip Aperture), spatial posture (Wrist and Finger Joint Angles) and grasp stability (Posture of Hand Finger Joints), and 3) postural synergies extraction and analysis through the Pareto, Scree and Loadings plots. Two examples are described to demonstrate the applicability of the toolbox: the first one aiming at performing a clinical assessment of a volunteer and the second one aiming at extracting and analyzing the volunteer's postural synergies. The tool allows calculating joint angles with high accuracy (reconstruction errors below 4 mm and 3.2 mm for the fingers and wrist respectively) and automatically performing clinical assessment and postural synergies extraction. Results can be visually inspected, and data can be saved for any desired post processing analysis. Custom-made protocols to extract joint angles, based on different markersets, could be also integrated in the toolbox. The tool can be easily exploitable in clinical contexts, as it does not require any particular technical knowledge to be used, as confirmed by the usability evaluation conducted (perceived usability = 94.2 ± 5.4). In addition, it can be integrated with the SynGrasp toolbox to perform grasp analysis of underactuated virtual hands based on postural synergies.
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Affiliation(s)
- Martina Lapresa
- Department of Engineering, Research Unit of Advanced Robotics and Human-Centred Technologies, Università Campus Bio-Medico di Roma, Roma, Italy
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5
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Flotho P, Nomura S, Kuhn B, Strauss DJ. Software for non-parametric image registration of 2-photon imaging data. J Biophotonics 2022; 15:e202100330. [PMID: 35289100 DOI: 10.1002/jbio.202100330] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
Functional 2-photon microscopy is a key technology for imaging neuronal activity. The recorded image sequences, however, can contain non-rigid movement artifacts which requires high-accuracy movement correction. Variational optical flow (OF) estimation is a group of methods for motion analysis with established performance in many computer vision areas. However, it has yet to be adapted to the statistics of 2-photon neuroimaging data. In this work, we present the motion compensation method Flow-Registration that outperforms previous alignment tools and allows to align and reconstruct even low signal-to-noise ratio 2-photon imaging data and is able to compensate high-divergence displacements during local drug injections. The method is based on statistics of such data and integrates previous advances in variational OF estimation. Our method is available as an easy-to-use ImageJ/FIJI plugin as well as a MATLAB toolbox with modular, object oriented file IO, native multi-channel support and compatibility with existing 2-photon imaging suites.
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Affiliation(s)
- Philipp Flotho
- Systems Neuroscience and Neurotechnology Unit, Neurocenter, Faculty of Medicine, Saarland University & School of Engineering, htw saar, Germany
- Summer Program, Japan Society for the Promotion of Science (JSPS), Tokyo
- Center for Digital Neurotechnologies Saar (CDNS), Homburg, Germany
| | - Shinobu Nomura
- Optical Neuroimaging Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa
| | - Bernd Kuhn
- Optical Neuroimaging Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa
| | - Daniel J Strauss
- Systems Neuroscience and Neurotechnology Unit, Neurocenter, Faculty of Medicine, Saarland University & School of Engineering, htw saar, Germany
- Center for Digital Neurotechnologies Saar (CDNS), Homburg, Germany
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6
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Zhao Y, Sun PP, Tan FL, Hou X, Zhu CZ. NIRS-ICA: A MATLAB Toolbox for Independent Component Analysis Applied in fNIRS Studies. Front Neuroinform 2021; 15:683735. [PMID: 34335218 PMCID: PMC8317505 DOI: 10.3389/fninf.2021.683735] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 06/08/2021] [Indexed: 11/22/2022] Open
Abstract
Independent component analysis (ICA) is a multivariate approach that has been widely used in analyzing brain imaging data. In the field of functional near-infrared spectroscopy (fNIRS), its promising effectiveness has been shown in both removing noise and extracting neuronal activity-related sources. The application of ICA remains challenging due to its complexity in usage, and an easy-to-use toolbox dedicated to ICA processing is still lacking in the fNIRS community. In this study, we propose NIRS-ICA, an open-source MATLAB toolbox to ease the difficulty of ICA application for fNIRS studies. NIRS-ICA incorporates commonly used ICA algorithms for source separation, user-friendly GUI, and quantitative evaluation metrics assisting source selection, which facilitate both removing noise and extracting neuronal activity-related sources. The options used in the processing can also be reported easily, which promotes using ICA in a more reproducible way. The proposed toolbox is validated and demonstrated based on both simulative and real fNIRS datasets. We expect the release of the toolbox will extent the application for ICA in the fNIRS community.
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Affiliation(s)
- Yang Zhao
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China
| | - Pei-Pei Sun
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China
| | - Fu-Lun Tan
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China
| | - Xin Hou
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China
| | - Chao-Zhe Zhu
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China
- IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, China
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7
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Raggam P, Bauernfeind G, Wriessnegger SC. NICA: A Novel Toolbox for Near-Infrared Spectroscopy Calculations and Analyses. Front Neuroinform 2020; 14:26. [PMID: 32523524 PMCID: PMC7261925 DOI: 10.3389/fninf.2020.00026] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 04/29/2020] [Indexed: 11/13/2022] Open
Abstract
Functional near-infrared spectroscopy (fNIRS) measures the functional activity of the cerebral cortex. The concentration changes of oxygenated (oxy-Hb) and deoxygenated hemoglobin (deoxy-Hb) can be detected and associated with activation of the cortex in the investigated area (neurovascular coupling). Recorded signals of hemodynamic responses may contain influences from physiological signals (systemic influences, physiological artifacts) which do not originate from the cerebral cortex activity. The physiological artifacts contain the blood pressure (BP), respiratory patterns, and the pulsation of the heart. In order to perform a comprehensive analysis of recorded fNIRS data, a proper correction of these physiological artifacts is necessary. This article introduces NICA – a novel toolbox for near-infrared spectroscopy calculations and analyses based on MATLAB. With NICA it is possible to process and visualize fNIRS data, including different signal processing methods for physiological artifact correction. The artifact correction methods used in this toolbox are common average reference (CAR), independent component analysis (ICA), and transfer function (TF) models. A practical example provides results from a study, where NICA was used for analyzing the measurement data, in order to demonstrate the signal processing steps and the physiological artifact correction. The toolbox was developed for fNIRS data recorded with the NIRScout 1624 measurement device and the corresponding recording software NIRStar.
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Affiliation(s)
- Philipp Raggam
- Institute of Neural Engineering, Graz University of Technology, Graz, Austria
| | | | - Selina C Wriessnegger
- Institute of Neural Engineering, Graz University of Technology, Graz, Austria.,BioTechMed-Graz, Graz, Austria
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8
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Leitold D, Vathy-Fogarassy Á, Abonyi J. Network-based Observability and Controllability Analysis of Dynamical Systems: the NOCAD toolbox. F1000Res 2019; 8:646. [PMID: 31608146 PMCID: PMC6777013 DOI: 10.12688/f1000research.19029.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/11/2019] [Indexed: 11/20/2022] Open
Abstract
The network science-based determination of driver nodes and sensor placement has become increasingly popular in the field of dynamical systems over the last decade. In this paper, the applicability of the methodology in the field of life sciences is introduced through the analysis of the neural network of Caenorhabditis elegans. Simultaneously, an Octave and MATLAB-compatible NOCAD toolbox is proposed that provides a set of methods to automatically generate the relevant structural controllability and observability associated measures for linear or linearised systems and compare the different sensor placement methods.
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Affiliation(s)
- Dániel Leitold
- Department of Computer Science and Systems Technology, University of Pannonia, Egyetem u. 10, Veszprém, 8200, Hungary.,MTA-PE Lendulet Complex Systems Monitoring Research Group, University of Pannonia, Egyetem u. 10, POB. 158, Veszprém, 8200, Hungary
| | - Ágnes Vathy-Fogarassy
- Department of Computer Science and Systems Technology, University of Pannonia, Egyetem u. 10, Veszprém, 8200, Hungary.,MTA-PE Lendulet Complex Systems Monitoring Research Group, University of Pannonia, Egyetem u. 10, POB. 158, Veszprém, 8200, Hungary
| | - János Abonyi
- MTA-PE Lendulet Complex Systems Monitoring Research Group, University of Pannonia, Egyetem u. 10, POB. 158, Veszprém, 8200, Hungary
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Bahrami M, Laurienti PJ, Simpson SL. A MATLAB toolbox for multivariate analysis of brain networks. Hum Brain Mapp 2018; 40:175-186. [PMID: 30256496 DOI: 10.1002/hbm.24363] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 07/23/2018] [Accepted: 08/07/2018] [Indexed: 11/10/2022] Open
Abstract
Complex brain networks formed via structural and functional interactions among brain regions are believed to underlie information processing and cognitive function. A growing number of studies indicate that altered brain network topology is associated with physiological, behavioral, and cognitive abnormalities. Graph theory is showing promise as a method for evaluating and explaining brain networks. However, multivariate frameworks that provide statistical inferences about how such networks relate to covariates of interest, such as disease phenotypes, in different study populations are yet to be developed. We have developed a freely available MATLAB toolbox with a graphical user interface that bridges this important gap between brain network analyses and statistical inference. The modeling framework implemented in this toolbox utilizes a mixed-effects multivariate regression framework that allows assessing brain network differences between study populations as well as assessing the effects of covariates of interest such as age, disease phenotype, and risk factors on the density and strength of brain connections in global (i.e., whole-brain) and local (i.e., subnetworks) brain networks. Confounding variables, such as sex, are controlled for through the implemented framework. A variety of neuroimaging data such as fMRI, EEG, and DTI can be analyzed with this toolbox, which makes it useful for a wide range of studies examining the structure and function of brain networks. The toolbox uses SAS, R, or Python (depending on software availability) to perform the statistical modeling. We also provide a clustering-based data reduction method that helps with model convergence and substantially reduces modeling time for large data sets.
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Affiliation(s)
- Mohsen Bahrami
- Laboratory for Complex Brain Networks, Wake Forest School of Medicine, Winston-Salem, North Carolina.,Department of Biomedical Engineering, Virginia Tech - Wake Forest School of Biomedical Engineering and Sciences, Winston-Salem, North Carolina
| | - Paul J Laurienti
- Laboratory for Complex Brain Networks, Wake Forest School of Medicine, Winston-Salem, North Carolina.,Department of Radiology, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Sean L Simpson
- Laboratory for Complex Brain Networks, Wake Forest School of Medicine, Winston-Salem, North Carolina.,Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina
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10
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Dong L, Luo C, Liu X, Jiang S, Li F, Feng H, Li J, Gong D, Yao D. Neuroscience Information Toolbox: An Open Source Toolbox for EEG-fMRI Multimodal Fusion Analysis. Front Neuroinform 2018; 12:56. [PMID: 30197593 PMCID: PMC6117508 DOI: 10.3389/fninf.2018.00056] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 08/10/2018] [Indexed: 11/30/2022] Open
Abstract
Recently, scalp electroencephalography (EEG) and functional magnetic resonance imaging (fMRI) multimodal fusion has been pursued in an effort to study human brain function and dysfunction to obtain more comprehensive information on brain activity in which the spatial and temporal resolutions are both satisfactory. However, a more flexible and easy-to-use toolbox for EEG–fMRI multimodal fusion is still lacking. In this study, we therefore developed a freely available and open-source MATLAB graphical user interface toolbox, known as the Neuroscience Information Toolbox (NIT), for EEG–fMRI multimodal fusion analysis. The NIT consists of three modules: (1) the fMRI module, which has batch fMRI preprocessing, nuisance signal removal, bandpass filtering, and calculation of resting-state measures; (2) the EEG module, which includes artifact removal, extracting EEG features (event onset, power, and amplitude), and marking interesting events; and (3) the fusion module, in which fMRI-informed EEG analysis and EEG-informed fMRI analysis are included. The NIT was designed to provide a convenient and easy-to-use toolbox for researchers, especially for novice users. The NIT can be downloaded for free at http://www.neuro.uestc.edu.cn/NIT.html, and detailed information, including the introduction of NIT, user’s manual and example data sets, can also be observed on this website. We hope that the NIT is a promising toolbox for exploring brain information in various EEG and fMRI studies.
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Affiliation(s)
- Li Dong
- The Clinical Hospital of Chengdu Brain Science Institute, MOE Key Lab for Neuroinformation, University of Electronic Science and Technology of China, Chengdu, China.,School of Life Science and Technology, Center for Information in Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Cheng Luo
- The Clinical Hospital of Chengdu Brain Science Institute, MOE Key Lab for Neuroinformation, University of Electronic Science and Technology of China, Chengdu, China.,School of Life Science and Technology, Center for Information in Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Xiaobo Liu
- The Clinical Hospital of Chengdu Brain Science Institute, MOE Key Lab for Neuroinformation, University of Electronic Science and Technology of China, Chengdu, China.,School of Life Science and Technology, Center for Information in Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Sisi Jiang
- The Clinical Hospital of Chengdu Brain Science Institute, MOE Key Lab for Neuroinformation, University of Electronic Science and Technology of China, Chengdu, China.,School of Life Science and Technology, Center for Information in Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Fali Li
- The Clinical Hospital of Chengdu Brain Science Institute, MOE Key Lab for Neuroinformation, University of Electronic Science and Technology of China, Chengdu, China.,School of Life Science and Technology, Center for Information in Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Hongshuo Feng
- School of Life Science and Technology, Center for Information in Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Jianfu Li
- The Clinical Hospital of Chengdu Brain Science Institute, MOE Key Lab for Neuroinformation, University of Electronic Science and Technology of China, Chengdu, China.,School of Life Science and Technology, Center for Information in Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Diankun Gong
- The Clinical Hospital of Chengdu Brain Science Institute, MOE Key Lab for Neuroinformation, University of Electronic Science and Technology of China, Chengdu, China.,School of Life Science and Technology, Center for Information in Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Dezhong Yao
- The Clinical Hospital of Chengdu Brain Science Institute, MOE Key Lab for Neuroinformation, University of Electronic Science and Technology of China, Chengdu, China.,School of Life Science and Technology, Center for Information in Medicine, University of Electronic Science and Technology of China, Chengdu, China
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Dong L, Li F, Liu Q, Wen X, Lai Y, Xu P, Yao D. MATLAB Toolboxes for Reference Electrode Standardization Technique (REST) of Scalp EEG. Front Neurosci 2017; 11:601. [PMID: 29163006 PMCID: PMC5670162 DOI: 10.3389/fnins.2017.00601] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 10/13/2017] [Indexed: 02/02/2023] Open
Abstract
Reference electrode standardization technique (REST) has been increasingly acknowledged and applied as a re-reference technique to transform an actual multi-channels recordings to approximately zero reference ones in electroencephalography/event-related potentials (EEG/ERPs) community around the world in recent years. However, a more easy-to-use toolbox for re-referencing scalp EEG data to zero reference is still lacking. Here, we have therefore developed two open-source MATLAB toolboxes for REST of scalp EEG. One version of REST is closely integrated into EEGLAB, which is a popular MATLAB toolbox for processing the EEG data; and another is a batch version to make it more convenient and efficient for experienced users. Both of them are designed to provide an easy-to-use for novice researchers and flexibility for experienced researchers. All versions of the REST toolboxes can be freely downloaded at http://www.neuro.uestc.edu.cn/rest/Down.html, and the detailed information including publications, comments and documents on REST can also be found from this website. An example of usage is given with comparative results of REST and average reference. We hope these user-friendly REST toolboxes could make the relatively novel technique of REST easier to study, especially for applications in various EEG studies.
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Affiliation(s)
- Li Dong
- Key Laboratory for NeuroInformation of Ministry of Education, Center for Information in Medicine, High-Field Magnetic Resonance Brain Imaging Key Laboratory of Sichuan Province, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Fali Li
- Key Laboratory for NeuroInformation of Ministry of Education, Center for Information in Medicine, High-Field Magnetic Resonance Brain Imaging Key Laboratory of Sichuan Province, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Qiang Liu
- Research Center of Brain and Cognitive Neuroscience, Liaoning Normal University, Dalian, China
| | - Xin Wen
- Key Laboratory for NeuroInformation of Ministry of Education, Center for Information in Medicine, High-Field Magnetic Resonance Brain Imaging Key Laboratory of Sichuan Province, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Yongxiu Lai
- Key Laboratory for NeuroInformation of Ministry of Education, Center for Information in Medicine, High-Field Magnetic Resonance Brain Imaging Key Laboratory of Sichuan Province, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Peng Xu
- Key Laboratory for NeuroInformation of Ministry of Education, Center for Information in Medicine, High-Field Magnetic Resonance Brain Imaging Key Laboratory of Sichuan Province, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Dezhong Yao
- Key Laboratory for NeuroInformation of Ministry of Education, Center for Information in Medicine, High-Field Magnetic Resonance Brain Imaging Key Laboratory of Sichuan Province, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
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Lee C, Jung YJ, Lee SJ, Im CH. COMETS2: An advanced MATLAB toolbox for the numerical analysis of electric fields generated by transcranial direct current stimulation. J Neurosci Methods 2016; 277:56-62. [PMID: 27989592 DOI: 10.1016/j.jneumeth.2016.12.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Revised: 12/12/2016] [Accepted: 12/13/2016] [Indexed: 12/22/2022]
Abstract
BACKGROUND Since there is no way to measure electric current generated by transcranial direct current stimulation (tDCS) inside the human head through in vivo experiments, numerical analysis based on the finite element method has been widely used to estimate the electric field inside the head. In 2013, we released a MATLAB toolbox named COMETS, which has been used by a number of groups and has helped researchers to gain insight into the electric field distribution during stimulation. The aim of this study was to develop an advanced MATLAB toolbox, named COMETS2, for the numerical analysis of the electric field generated by tDCS. NEW METHOD COMETS2 can generate any sizes of rectangular pad electrodes on any positions on the scalp surface. To reduce the large computational burden when repeatedly testing multiple electrode locations and sizes, a new technique to decompose the global stiffness matrix was proposed. RESULTS As examples of potential applications, we observed the effects of sizes and displacements of electrodes on the results of electric field analysis. The proposed mesh decomposition method significantly enhanced the overall computational efficiency. COMPARISON WITH EXISTING METHODS We implemented an automatic electrode modeler for the first time, and proposed a new technique to enhance the computational efficiency. CONCLUSIONS In this paper, an efficient toolbox for tDCS analysis is introduced (freely available at http://www.cometstool.com). It is expected that COMETS2 will be a useful toolbox for researchers who want to benefit from the numerical analysis of electric fields generated by tDCS.
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Affiliation(s)
- Chany Lee
- Department of Biomedical Engineering, Hanyang University, Seoul, Republic of Korea
| | - Young-Jin Jung
- Department of Radiological Science, Dongseo University, Busan, Republic of Korea
| | - Sang Jun Lee
- Department of Biomedical Engineering, Hanyang University, Seoul, Republic of Korea
| | - Chang-Hwan Im
- Department of Biomedical Engineering, Hanyang University, Seoul, Republic of Korea.
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Atluri S, Frehlich M, Mei Y, Garcia Dominguez L, Rogasch NC, Wong W, Daskalakis ZJ, Farzan F. TMSEEG: A MATLAB-Based Graphical User Interface for Processing Electrophysiological Signals during Transcranial Magnetic Stimulation. Front Neural Circuits 2016; 10:78. [PMID: 27774054 PMCID: PMC5054290 DOI: 10.3389/fncir.2016.00078] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 09/20/2016] [Indexed: 11/13/2022] Open
Abstract
Concurrent recording of electroencephalography (EEG) during transcranial magnetic stimulation (TMS) is an emerging and powerful tool for studying brain health and function. Despite a growing interest in adaptation of TMS-EEG across neuroscience disciplines, its widespread utility is limited by signal processing challenges. These challenges arise due to the nature of TMS and the sensitivity of EEG to artifacts that often mask TMS-evoked potentials (TEP)s. With an increase in the complexity of data processing methods and a growing interest in multi-site data integration, analysis of TMS-EEG data requires the development of a standardized method to recover TEPs from various sources of artifacts. This article introduces TMSEEG, an open-source MATLAB application comprised of multiple algorithms organized to facilitate a step-by-step procedure for TMS-EEG signal processing. Using a modular design and interactive graphical user interface (GUI), this toolbox aims to streamline TMS-EEG signal processing for both novice and experienced users. Specifically, TMSEEG provides: (i) targeted removal of TMS-induced and general EEG artifacts; (ii) a step-by-step modular workflow with flexibility to modify existing algorithms and add customized algorithms; (iii) a comprehensive display and quantification of artifacts; (iv) quality control check points with visual feedback of TEPs throughout the data processing workflow; and (v) capability to label and store a database of artifacts. In addition to these features, the software architecture of TMSEEG ensures minimal user effort in initial setup and configuration of parameters for each processing step. This is partly accomplished through a close integration with EEGLAB, a widely used open-source toolbox for EEG signal processing. In this article, we introduce TMSEEG, validate its features and demonstrate its application in extracting TEPs across several single- and multi-pulse TMS protocols. As the first open-source GUI-based pipeline for TMS-EEG signal processing, this toolbox intends to promote the widespread utility and standardization of an emerging technology in brain research.
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Affiliation(s)
- Sravya Atluri
- Temerty Centre for Therapeutic Brain Intervention, Centre for Addiction and Mental HealthToronto, ON, Canada; Institute of Biomaterials and Biomedical Engineering, University of TorontoToronto, ON, Canada
| | - Matthew Frehlich
- Temerty Centre for Therapeutic Brain Intervention, Centre for Addiction and Mental HealthToronto, ON, Canada; Department of Electrical and Computer Engineering, University of TorontoToronto, ON, Canada
| | - Ye Mei
- Temerty Centre for Therapeutic Brain Intervention, Centre for Addiction and Mental Health Toronto, ON, Canada
| | - Luis Garcia Dominguez
- Temerty Centre for Therapeutic Brain Intervention, Centre for Addiction and Mental Health Toronto, ON, Canada
| | - Nigel C Rogasch
- Brain and Mental Health Laboratory, School of Psychological Sciences and Monash Biomedical Imaging, Monash Institute of Cognitive and Clinical Neuroscience, Monash University Melbourne, VIC, Australia
| | - Willy Wong
- Institute of Biomaterials and Biomedical Engineering, University of TorontoToronto, ON, Canada; Department of Electrical and Computer Engineering, University of TorontoToronto, ON, Canada
| | - Zafiris J Daskalakis
- Temerty Centre for Therapeutic Brain Intervention, Centre for Addiction and Mental HealthToronto, ON, Canada; Department of Psychiatry, University of TorontoToronto, ON, Canada
| | - Faranak Farzan
- Temerty Centre for Therapeutic Brain Intervention, Centre for Addiction and Mental HealthToronto, ON, Canada; Department of Psychiatry, University of TorontoToronto, ON, Canada
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Wong SM, Ibrahim GM, Ochi A, Otsubo H, Rutka JT, Snead OC, Doesburg SM. moviEEG: An animation toolbox for visualization of intracranial electroencephalography synchronization dynamics. Clin Neurophysiol 2016; 127:2370-8. [PMID: 27178855 DOI: 10.1016/j.clinph.2016.03.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 03/01/2016] [Accepted: 03/03/2016] [Indexed: 11/29/2022]
Abstract
OBJECTIVE We introduce and describe the functions of moviEEG (Multiple Overlay Visualizations for Intracranial ElectroEncephaloGraphy), a novel MATLAB-based toolbox for spatiotemporal mapping of network synchronization dynamics in intracranial electroencephalography (iEEG) data. METHODS The toolbox integrates visualizations of inter-electrode phase-locking relationships in peri-ictal epileptogenic networks with signal spectral properties and graph-theoretical network measures overlaid upon operating room images of the electrode grid. Functional connectivity between every electrode pair is evaluated over a sliding window indexed by phase synchrony. RESULTS Two case studies are presented to provide preliminary evidence for the application of the toolbox to guide network-based mapping of epileptogenic cortex and to distinguish these regions from eloquent brain networks. In both cases, epileptogenic cortex was visually distinct. CONCLUSION We introduce moviEEG, a novel toolbox for animation of oscillatory network dynamics in iEEG data, and provide two case studies showing preliminary evidence for utility of the toolbox in delineating the epileptogenic zone. SIGNIFICANCE Despite evidence that atypical network synchronization has shown to be altered in epileptogenic brain regions, network based techniques have yet to be incorporated into clinical pre-surgical mapping. moviEEG provides a set of functions to enable easy visualization with network based techniques.
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Affiliation(s)
- Simeon M Wong
- Faculty of Applied Science and Engineering, University of Toronto, Canada; Neuroscience & Mental Health Program, Hospital for Sick Children Research Institute, Canada; Department of Diagnostic Imaging, Hospital for Sick Children, Canada.
| | - George M Ibrahim
- Division of Neurosurgery, Hospital for Sick Children, Canada; Institute of Medical Science, University of Toronto, Canada
| | - Ayako Ochi
- Division of Neurology, Hospital for Sick Children, Canada
| | - Hiroshi Otsubo
- Division of Neurology, Hospital for Sick Children, Canada
| | - James T Rutka
- Division of Neurosurgery, Hospital for Sick Children, Canada
| | - O Carter Snead
- Neuroscience & Mental Health Program, Hospital for Sick Children Research Institute, Canada; Institute of Medical Science, University of Toronto, Canada; Division of Neurology, Hospital for Sick Children, Canada
| | - Sam M Doesburg
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Canada
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