iELVis: An open source MATLAB toolbox for localizing and visualizing human intracranial electrode data

David M. Groppe, Stephan Bickel, Andrew R. Dykstra, Xiuyuan Wang, Pierre Mégevand, Manuel R. Mercier, Fred A. Lado, Ashesh D. Mehta, Christopher J. Honey

Research output: Contribution to journalArticle

33 Citations (Scopus)

Abstract

Background Intracranial electrical recordings (iEEG) and brain stimulation (iEBS) are invaluable human neuroscience methodologies. However, the value of such data is often unrealized as many laboratories lack tools for localizing electrodes relative to anatomy. To remedy this, we have developed a MATLAB toolbox for intracranial electrode localization and visualization, iELVis. New method iELVis uses existing tools (BioImage Suite, FSL, and FreeSurfer) for preimplant magnetic resonance imaging (MRI) segmentation, neuroimaging coregistration, and manual identification of electrodes in postimplant neuroimaging. Subsequently, iELVis implements methods for correcting electrode locations for postimplant brain shift with millimeter-scale accuracy and provides interactive visualization on 3D surfaces or in 2D slices with optional functional neuroimaging overlays. iELVis also localizes electrodes relative to FreeSurfer-based atlases and can combine data across subjects via the FreeSurfer average brain. Results It takes 30–60 min of user time and 12–24 h of computer time to localize and visualize electrodes from one brain. We demonstrate iELVis's functionality by showing that three methods for mapping primary hand somatosensory cortex (iEEG, iEBS, and functional MRI) provide highly concordant results. Comparison with existing methods iELVis is the first public software for electrode localization that corrects for brain shift, maps electrodes to an average brain, and supports neuroimaging overlays. Moreover, its interactive visualizations are powerful and its tutorial material is extensive. Conclusions iELVis promises to speed the progress and enhance the robustness of intracranial electrode research. The software and extensive tutorial materials are freely available as part of the EpiSurg software project: https://github.com/episurg/episurg.

Original languageEnglish (US)
Pages (from-to)40-48
Number of pages9
JournalJournal of Neuroscience Methods
Volume281
DOIs
StatePublished - Apr 1 2017

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Electrodes
Brain
Neuroimaging
Software
Magnetic Resonance Imaging
Functional Neuroimaging
Somatosensory Cortex
Deep Brain Stimulation
Atlases
Neurosciences
Anatomy
Hand
Research

Keywords

  • ECoG
  • iEEG
  • Intracranial
  • Neuroimaging
  • Software
  • Stimulation

ASJC Scopus subject areas

  • Neuroscience(all)

Cite this

Groppe, D. M., Bickel, S., Dykstra, A. R., Wang, X., Mégevand, P., Mercier, M. R., ... Honey, C. J. (2017). iELVis: An open source MATLAB toolbox for localizing and visualizing human intracranial electrode data. Journal of Neuroscience Methods, 281, 40-48. https://doi.org/10.1016/j.jneumeth.2017.01.022

iELVis : An open source MATLAB toolbox for localizing and visualizing human intracranial electrode data. / Groppe, David M.; Bickel, Stephan; Dykstra, Andrew R.; Wang, Xiuyuan; Mégevand, Pierre; Mercier, Manuel R.; Lado, Fred A.; Mehta, Ashesh D.; Honey, Christopher J.

In: Journal of Neuroscience Methods, Vol. 281, 01.04.2017, p. 40-48.

Research output: Contribution to journalArticle

Groppe, DM, Bickel, S, Dykstra, AR, Wang, X, Mégevand, P, Mercier, MR, Lado, FA, Mehta, AD & Honey, CJ 2017, 'iELVis: An open source MATLAB toolbox for localizing and visualizing human intracranial electrode data', Journal of Neuroscience Methods, vol. 281, pp. 40-48. https://doi.org/10.1016/j.jneumeth.2017.01.022
Groppe, David M. ; Bickel, Stephan ; Dykstra, Andrew R. ; Wang, Xiuyuan ; Mégevand, Pierre ; Mercier, Manuel R. ; Lado, Fred A. ; Mehta, Ashesh D. ; Honey, Christopher J. / iELVis : An open source MATLAB toolbox for localizing and visualizing human intracranial electrode data. In: Journal of Neuroscience Methods. 2017 ; Vol. 281. pp. 40-48.
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abstract = "Background Intracranial electrical recordings (iEEG) and brain stimulation (iEBS) are invaluable human neuroscience methodologies. However, the value of such data is often unrealized as many laboratories lack tools for localizing electrodes relative to anatomy. To remedy this, we have developed a MATLAB toolbox for intracranial electrode localization and visualization, iELVis. New method iELVis uses existing tools (BioImage Suite, FSL, and FreeSurfer) for preimplant magnetic resonance imaging (MRI) segmentation, neuroimaging coregistration, and manual identification of electrodes in postimplant neuroimaging. Subsequently, iELVis implements methods for correcting electrode locations for postimplant brain shift with millimeter-scale accuracy and provides interactive visualization on 3D surfaces or in 2D slices with optional functional neuroimaging overlays. iELVis also localizes electrodes relative to FreeSurfer-based atlases and can combine data across subjects via the FreeSurfer average brain. Results It takes 30–60 min of user time and 12–24 h of computer time to localize and visualize electrodes from one brain. We demonstrate iELVis's functionality by showing that three methods for mapping primary hand somatosensory cortex (iEEG, iEBS, and functional MRI) provide highly concordant results. Comparison with existing methods iELVis is the first public software for electrode localization that corrects for brain shift, maps electrodes to an average brain, and supports neuroimaging overlays. Moreover, its interactive visualizations are powerful and its tutorial material is extensive. Conclusions iELVis promises to speed the progress and enhance the robustness of intracranial electrode research. The software and extensive tutorial materials are freely available as part of the EpiSurg software project: https://github.com/episurg/episurg.",
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