iEEGview: an open-source multifunction GUI-based Matlab toolbox for localization and visualization of human intracranial electrodes
Objective. The precise localization of intracranial electrodes is a fundamental step relevant to the analysis of intracranial electroencephalography (iEEG) recordings in various fields. With the increasing development of iEEG studies in human neuroscience, higher requirements have been posed on the...
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| Published in | Journal of neural engineering Vol. 17; no. 1; p. 16016 |
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| Main Authors | , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
England
IOP Publishing
23.12.2019
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| Subjects | |
| Online Access | Get full text |
| ISSN | 1741-2560 1741-2552 1741-2552 |
| DOI | 10.1088/1741-2552/ab51a5 |
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| Abstract | Objective. The precise localization of intracranial electrodes is a fundamental step relevant to the analysis of intracranial electroencephalography (iEEG) recordings in various fields. With the increasing development of iEEG studies in human neuroscience, higher requirements have been posed on the localization process, resulting in urgent demand for more integrated, easy-operation and versatile tools for electrode localization and visualization. With the aim of addressing this need, we develop an easy-to-use and multifunction toolbox called iEEGview, which can be used for the localization and visualization of human intracranial electrodes. Approach. iEEGview is written in Matlab scripts and implemented with a GUI. From the GUI, by taking only pre-implant MRI and post-implant CT images as input, users can directly run the full localization pipeline including brain segmentation, image co-registration, electrode reconstruction, anatomical information identification, activation map generation and electrode projection from native brain space into common brain space for group analysis. Additionally, iEEGview implements methods for brain shift correction, visual location inspection on MRI slices and computation of certainty index in anatomical label assignment. Main results. All the introduced functions of iEEGview work reliably and successfully, and are tested by images from 28 human subjects implanted with depth and/or subdural electrodes. Significance. iEEGview is the first public Matlab GUI-based software for intracranial electrode localization and visualization that holds integrated capabilities together within one pipeline. iEEGview promotes convenience and efficiency for the localization process, provides rich localization information for further analysis and offers solutions for addressing raised technical challenges. Therefore, it can serve as a useful tool in facilitating iEEG studies. |
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| AbstractList | The precise localization of intracranial electrodes is a fundamental step relevant to the analysis of intracranial electroencephalography (iEEG) recordings in various fields. With the increasing development of iEEG studies in human neuroscience, higher requirements have been posed on the localization process, resulting in urgent demand for more integrated, easy-operation and versatile tools for electrode localization and visualization. With the aim of addressing this need, we develop an easy-to-use and multifunction toolbox called iEEGview, which can be used for the localization and visualization of human intracranial electrodes.
iEEGview is written in Matlab scripts and implemented with a GUI. From the GUI, by taking only pre-implant MRI and post-implant CT images as input, users can directly run the full localization pipeline including brain segmentation, image co-registration, electrode reconstruction, anatomical information identification, activation map generation and electrode projection from native brain space into common brain space for group analysis. Additionally, iEEGview implements methods for brain shift correction, visual location inspection on MRI slices and computation of certainty index in anatomical label assignment.
All the introduced functions of iEEGview work reliably and successfully, and are tested by images from 28 human subjects implanted with depth and/or subdural electrodes.
iEEGview is the first public Matlab GUI-based software for intracranial electrode localization and visualization that holds integrated capabilities together within one pipeline. iEEGview promotes convenience and efficiency for the localization process, provides rich localization information for further analysis and offers solutions for addressing raised technical challenges. Therefore, it can serve as a useful tool in facilitating iEEG studies. The precise localization of intracranial electrodes is a fundamental step relevant to the analysis of intracranial electroencephalography (iEEG) recordings in various fields. With the increasing development of iEEG studies in human neuroscience, higher requirements have been posed on the localization process, resulting in urgent demand for more integrated, easy-operation and versatile tools for electrode localization and visualization. With the aim of addressing this need, we develop an easy-to-use and multifunction toolbox called iEEGview, which can be used for the localization and visualization of human intracranial electrodes.OBJECTIVEThe precise localization of intracranial electrodes is a fundamental step relevant to the analysis of intracranial electroencephalography (iEEG) recordings in various fields. With the increasing development of iEEG studies in human neuroscience, higher requirements have been posed on the localization process, resulting in urgent demand for more integrated, easy-operation and versatile tools for electrode localization and visualization. With the aim of addressing this need, we develop an easy-to-use and multifunction toolbox called iEEGview, which can be used for the localization and visualization of human intracranial electrodes.iEEGview is written in Matlab scripts and implemented with a GUI. From the GUI, by taking only pre-implant MRI and post-implant CT images as input, users can directly run the full localization pipeline including brain segmentation, image co-registration, electrode reconstruction, anatomical information identification, activation map generation and electrode projection from native brain space into common brain space for group analysis. Additionally, iEEGview implements methods for brain shift correction, visual location inspection on MRI slices and computation of certainty index in anatomical label assignment.APPROACHiEEGview is written in Matlab scripts and implemented with a GUI. From the GUI, by taking only pre-implant MRI and post-implant CT images as input, users can directly run the full localization pipeline including brain segmentation, image co-registration, electrode reconstruction, anatomical information identification, activation map generation and electrode projection from native brain space into common brain space for group analysis. Additionally, iEEGview implements methods for brain shift correction, visual location inspection on MRI slices and computation of certainty index in anatomical label assignment.All the introduced functions of iEEGview work reliably and successfully, and are tested by images from 28 human subjects implanted with depth and/or subdural electrodes.MAIN RESULTSAll the introduced functions of iEEGview work reliably and successfully, and are tested by images from 28 human subjects implanted with depth and/or subdural electrodes.iEEGview is the first public Matlab GUI-based software for intracranial electrode localization and visualization that holds integrated capabilities together within one pipeline. iEEGview promotes convenience and efficiency for the localization process, provides rich localization information for further analysis and offers solutions for addressing raised technical challenges. Therefore, it can serve as a useful tool in facilitating iEEG studies.SIGNIFICANCEiEEGview is the first public Matlab GUI-based software for intracranial electrode localization and visualization that holds integrated capabilities together within one pipeline. iEEGview promotes convenience and efficiency for the localization process, provides rich localization information for further analysis and offers solutions for addressing raised technical challenges. Therefore, it can serve as a useful tool in facilitating iEEG studies. Objective. The precise localization of intracranial electrodes is a fundamental step relevant to the analysis of intracranial electroencephalography (iEEG) recordings in various fields. With the increasing development of iEEG studies in human neuroscience, higher requirements have been posed on the localization process, resulting in urgent demand for more integrated, easy-operation and versatile tools for electrode localization and visualization. With the aim of addressing this need, we develop an easy-to-use and multifunction toolbox called iEEGview, which can be used for the localization and visualization of human intracranial electrodes. Approach. iEEGview is written in Matlab scripts and implemented with a GUI. From the GUI, by taking only pre-implant MRI and post-implant CT images as input, users can directly run the full localization pipeline including brain segmentation, image co-registration, electrode reconstruction, anatomical information identification, activation map generation and electrode projection from native brain space into common brain space for group analysis. Additionally, iEEGview implements methods for brain shift correction, visual location inspection on MRI slices and computation of certainty index in anatomical label assignment. Main results. All the introduced functions of iEEGview work reliably and successfully, and are tested by images from 28 human subjects implanted with depth and/or subdural electrodes. Significance. iEEGview is the first public Matlab GUI-based software for intracranial electrode localization and visualization that holds integrated capabilities together within one pipeline. iEEGview promotes convenience and efficiency for the localization process, provides rich localization information for further analysis and offers solutions for addressing raised technical challenges. Therefore, it can serve as a useful tool in facilitating iEEG studies. |
| Author | Schalk, Gerwin Chen, Chen Brunner, Peter Zhang, Dingguo Wu, Zehan Chen, Liang Jiang, Shize Li, Guangye |
| AuthorAffiliation | b Department of Neurosurgery of Huashan Hospital, Fudan University, Shanghai, China a State Key Laboratory of Mechanical Systems and Vibrations, Institute of Robotics, Shanghai Jiao Tong University, Shanghai, China c Department of Neurology, Albany Medical College, Albany, NY, USA e Department of Electronic and Electrical Engineering, University of Bath, Bath, UK d National Center for Adaptive Neurotechnologies, Wadsworth Center, New York State Department of Health, Albany, NY, USA |
| AuthorAffiliation_xml | – name: d National Center for Adaptive Neurotechnologies, Wadsworth Center, New York State Department of Health, Albany, NY, USA – name: a State Key Laboratory of Mechanical Systems and Vibrations, Institute of Robotics, Shanghai Jiao Tong University, Shanghai, China – name: c Department of Neurology, Albany Medical College, Albany, NY, USA – name: e Department of Electronic and Electrical Engineering, University of Bath, Bath, UK – name: b Department of Neurosurgery of Huashan Hospital, Fudan University, Shanghai, China |
| Author_xml | – sequence: 1 givenname: Guangye orcidid: 0000-0003-2530-3916 surname: Li fullname: Li, Guangye organization: National Center for Adaptive Neurotechnologies , Wadsworth Center, New York State Department of Health, Albany, NY, United States of America – sequence: 2 givenname: Shize surname: Jiang fullname: Jiang, Shize organization: Fudan University Department of Neurosurgery of Huashan Hospital, Shanghai, People's Republic of China – sequence: 3 givenname: Chen orcidid: 0000-0002-3007-4364 surname: Chen fullname: Chen, Chen organization: Shanghai Jiao Tong University State Key Laboratory of Mechanical Systems and Vibrations, Institute of Robotics, Shanghai, People's Republic of China – sequence: 4 givenname: Peter surname: Brunner fullname: Brunner, Peter organization: National Center for Adaptive Neurotechnologies , Wadsworth Center, New York State Department of Health, Albany, NY, United States of America – sequence: 5 givenname: Zehan surname: Wu fullname: Wu, Zehan organization: Fudan University Department of Neurosurgery of Huashan Hospital, Shanghai, People's Republic of China – sequence: 6 givenname: Gerwin surname: Schalk fullname: Schalk, Gerwin organization: National Center for Adaptive Neurotechnologies , Wadsworth Center, New York State Department of Health, Albany, NY, United States of America – sequence: 7 givenname: Liang surname: Chen fullname: Chen, Liang organization: Fudan University Department of Neurosurgery of Huashan Hospital, Shanghai, People's Republic of China – sequence: 8 givenname: Dingguo surname: Zhang fullname: Zhang, Dingguo email: d.zhang@bath.ac.uk organization: Author to whom any correspondence should be addressed |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/31658449$$D View this record in MEDLINE/PubMed |
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| Snippet | Objective. The precise localization of intracranial electrodes is a fundamental step relevant to the analysis of intracranial electroencephalography (iEEG)... The precise localization of intracranial electrodes is a fundamental step relevant to the analysis of intracranial electroencephalography (iEEG) recordings in... |
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| SubjectTerms | Brain - diagnostic imaging Brain - physiology Brain Mapping - instrumentation Brain Mapping - methods ECoG Electrocorticography - instrumentation Electrocorticography - methods electrodes Electrodes, Implanted Electroencephalography - instrumentation Electroencephalography - methods Humans iEEG localization Magnetic Resonance Imaging - methods Matlab toolbox SEEG visualization |
| Title | iEEGview: an open-source multifunction GUI-based Matlab toolbox for localization and visualization of human intracranial electrodes |
| URI | https://iopscience.iop.org/article/10.1088/1741-2552/ab51a5 https://www.ncbi.nlm.nih.gov/pubmed/31658449 https://www.proquest.com/docview/2310301264 https://pubmed.ncbi.nlm.nih.gov/PMC7745846 |
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