title: iELVis: An open source MATLAB toolbox for localizing and visualizing human intracranial electrode data.
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 30-60min of user time and 12-24h 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.
authors.affiliation: Department of Psychology, University of Toronto, Toronto, ON M5SSG3, Canada; Department of Neurosurgery, Hofstra Northwell School of Medicine, and Feinstein Institute for Medical Research, Manhasset, NY 11030, USA. Electronic address: david.m.groppe@gmail.com.
authors.forename: David M
authors.initials: DM
authors.lastname: Groppe
authors.affiliation: Department of Neurology, Montefiore Medical Center, Bronx, NY 10467, USA; Department of Neurology, Stanford University, Stanford, CA 94305, USA.
authors.forename: Stephan
authors.initials: S
authors.lastname: Bickel
authors.affiliation: Department of Neurology, Ruprecht-Karls-Universität Heidelberg, 69120 Heidelberg, Germany.
authors.forename: Andrew R
authors.initials: AR
authors.lastname: Dykstra
authors.affiliation: Department of Neurology, New York University School of Medicine, New York, NY 10016, USA; Department of Radiology, New York University School of Medicine, New York, NY 10016, USA.
authors.forename: Xiuyuan
authors.initials: X
authors.lastname: Wang
authors.affiliation: Department of Neurosurgery, Hofstra Northwell School of Medicine, and Feinstein Institute for Medical Research, Manhasset, NY 11030, USA; Division of Neurology, Department of Clinical Neuroscience, Hôpitaux Universitaires de Genève, Geneva 1211, Switzerland.
authors.forename: Pierre
authors.initials: P
authors.lastname: Mégevand
authors.affiliation: Department of Neurology, Montefiore Medical Center, Bronx, NY 10467, USA; Centre de Recherche Cerveau et Cognition (CerCo), CNRS, Université Paul Sabatier, UMR5549, CHU Purpan, Toulouse, France; Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
authors.forename: Manuel R
authors.initials: MR
authors.lastname: Mercier
authors.affiliation: Department of Neurology, Montefiore Medical Center, Bronx, NY 10467, USA; Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
authors.forename: Fred A
authors.initials: FA
authors.lastname: Lado
authors.affiliation: Department of Neurosurgery, Hofstra Northwell School of Medicine, and Feinstein Institute for Medical Research, Manhasset, NY 11030, USA.
authors.forename: Ashesh D
authors.initials: AD
authors.lastname: Mehta
authors.affiliation: Department of Psychology, University of Toronto, Toronto, ON M5SSG3, Canada; Department of Psychological & Brain Sciences, Johns Hopkins University, Baltimore, MD 21218, USA.
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Honey
mesh_terms: D000465:Algorithms; D001271:Atlases as Topic; D001921:Brain / Q000000981:diagnostic imaging* / Q000502:physiology* / Q000601:surgery; D000069280:Electrocorticography / Q000295:instrumentation* / Q000379:methods; D004567:Electrodes, Implanted; D006801:Humans; D021621:Imaging, Three-Dimensional; D008279:Magnetic Resonance Imaging / Q000379:methods*; D009038:Motion; D059906:Neuroimaging / Q000379:methods; D010363:Pattern Recognition, Automated / Q000379:methods; D011184:Postoperative Period; D057234:Preoperative Period; D012984:Software
keywords: ECoG; Intracranial; Neuroimaging; Software; Stimulation; iEEG