The interactive electrode localization utility: software for automatic sorting and labeling of intracranial subdural electrodes

  • Roan A. LaPlanteEmail author
  • Wei Tang
  • Noam Peled
  • Deborah I. Vallejo
  • Mia Borzello
  • Darin D. Dougherty
  • Emad N. Eskandar
  • Alik S. Widge
  • Sydney S. Cash
  • Steven M. Stufflebeam
Original Article



Existing methods for sorting, labeling, registering, and across-subject localization of electrodes in intracranial encephalography (iEEG) may involve laborious work requiring manual inspection of radiological images.


We describe a new open-source software package, the interactive electrode localization utility which presents a full pipeline for the registration, localization, and labeling of iEEG electrodes from CT and MR images. In addition, we describe a method to automatically sort and label electrodes from subdural grids of known geometry.


We validated our software against manual inspection methods in twelve subjects undergoing iEEG for medically intractable epilepsy. Our algorithm for sorting and labeling performed correct identification on 96% of the electrodes.


The sorting and labeling methods we describe offer nearly perfect performance and the software package we have distributed may simplify the process of registering, sorting, labeling, and localizing subdural iEEG grid electrodes by manual inspection.


Electrocorticography Image registration CT MRI Software 



We thank Giovanni Piantoni for his assistance with hardware and technical support. We thank Kristen K. Ellard, Samuel Zorowitz, Tatiana Sitnikova, Afsana Afzal, Anna L. Gilmour, Amanda R. Arulpragasam, and Thilo Deckersbach for their assistance with data collection. This work was made possible by grants NCRR S10RR014978, NIH S10RR031599, R01-NS069696, 5RO1-NS060918, U01MH093765, 1S10RR023043, 1S10RR023401, P41-EB015896. This work was sponsored by the U.S. Army Research Office and Defense Advanced Research Projects Agency under Cooperative Agreement Number W911NF-14-2-0045. The aforementioned sponsor played no role in collection, analysis, or interpretation of data, and played no role in preparation of the manuscript.

Compliance with ethical standards

Conflict of interest

The authors have no conflicts of interest to declare.

Statement of human rights

All procedures performed in studies involving human participants were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki Declaration and its later amendments or comparable ethical standards.

Statement on the welfare of animals

This article does not contain any studies with animals performed by any of the authors.


  1. 1.
    Penfield W, Jasper HH (1954) Epilepsy and the functional anatomy of the human brain. Oxford University Press, OxfordGoogle Scholar
  2. 2.
    Engel AK, Moll CK, Fried I, Ojemann G (2005) Invasive recordings from the human brain: clinical insights and beyond. Nat Rev Neurosci 6:35–47CrossRefPubMedGoogle Scholar
  3. 3.
    Tao JX, Ray A, Hawes-Ebersole S, Ebersole JS (2005) Intracranial EEG substrates of scalp EEG interictal spikes. Epilepsia 46:669–676CrossRefPubMedGoogle Scholar
  4. 4.
    Crone NE, Boatman D, Gordon B, Hao L (2001) Induced electrocorticographic gamma activity during auditory perception. Clin Neurophysiol 112:565–582CrossRefPubMedGoogle Scholar
  5. 5.
    Meltzer JA, Zaveri HP, Goncharova II, Distasio MM, Papademetris X, Spencer SS, Constable RT (2008) Effects of working memory load on oscillatory power in human intracranial EEG. Cereb Cortex 18:1843–1855CrossRefPubMedGoogle Scholar
  6. 6.
    Lachaux JP, Fonlupt P, Kahane P, Minotti L, Hoffman D, Bertrand O, Baclu M (2007) Relationship between task-related gamma oscillations and BOLD signal: new insights from combined fMRI and intracranial EEG. Hum Brain Mapp 28:1368–1375CrossRefPubMedGoogle Scholar
  7. 7.
    Jerbi K, Ossandon T, Hamame CM, Senova S, Dalal SS, Jung J, Minotti L, Bertrand O, Berthaz A, Kahane P, Lachaux JP (2009) Task-related gamma-band dynamics from an intracerebral perspective: review and implications for surface EEG and MEG. Hum Brain Mapp 30:1758–1771CrossRefPubMedGoogle Scholar
  8. 8.
    Cash SS, Halgren E, Dehghani N, Rossetti AO, Thesen T, Wang C, Devinsky O, Kuzniecky R, Doyle W, Madsen JR, Bromfield E (2009) The human K-complex represents an isolated cortical down-state. Science 324:1084–1087CrossRefPubMedCentralPubMedGoogle Scholar
  9. 9.
    Hermes D, Miller KJ, Noordmans HJ, Vansteensel MJ, Ramsey NF (2010) Automated electrocorticographic electrode localization on individually rendered brain surfaces. J Neurosci Methods 185:293–298CrossRefPubMedGoogle Scholar
  10. 10.
    Dalal SS, Edwards E, Kirsch HE, Barbaro NM, Knight RT, Nagarajan SS (2008) Localization of neurosurgically implanted electrodes via photograph-MRI-radiograph coregistration. J Neurosci Methods 174:106–115CrossRefPubMedCentralPubMedGoogle Scholar
  11. 11.
    Yang AI, Wang X, Doyle WK, Halgren E, Carlson C, Belcher TL, Cash SS, Devinsky O, Thesen T (2012) Localization of dense intracranial electrode arrays using magnetic resonance imaging. NeuroImage 63:157–165CrossRefPubMedCentralPubMedGoogle Scholar
  12. 12.
    Schulze-Bonhage AH, Huppertz HJ, Comeau RM, Honegger JB, Spreer JM, Zentner JK (2002) Visualization of subdural strip and grid electrodes using curvilinear reformatting of 3D MR imaging data sets. Am J Neuroradiol 23:400–403PubMedGoogle Scholar
  13. 13.
    Kovalev D, Spreer JM, Honegger JB, Zentner JK, Schulze-Bonhage AH, Huppertz H-J (2005) Rapid and fully automated visualization of subdural electrodes in the presurgical evaluation of epilepsy patients. Am J Neuroradiol 26:1078–1083PubMedGoogle Scholar
  14. 14.
    Kamida T, Anan M, Shimotaka K, Abe T, Fujiki M, Kobayashi H (2010) Visualization of subdural electrodes with fusion CT scan/MRI during neuronavigation-guided epilepsy surgery. J Clin Neurosci 17:511–513CrossRefPubMedGoogle Scholar
  15. 15.
    Reuter M, Rosas HD, Fischl B (2010) Highly accurate inverse consistent registration: a robust approach. NeuroImage 53:1181–1196CrossRefPubMedCentralPubMedGoogle Scholar
  16. 16.
    Dykstra AR, Chan AM, Quinn BT, Zepeda R, Keller CJ, Cormier J, Madsen JR, Eskandar EN, Cash SS (2012) Individualized localization and cortical surface-based registration of intracranial electrodes. NeuroImage 59:3563–3570CrossRefPubMedGoogle Scholar
  17. 17.
    Taimouri V, Akhonda-Asi A, Tomas-Fernandez T, Peters JM, Prabhu SP, Poduri A, Takeoka M, Loddenkemper T, Bergin AMR, Harini C, Madsen JR, Warfield SK (2014) Electrode localization for planning surgical resection of the epileptogenic zone in pediatric epilepsy. Int J Comput Assist Radiol Surg 9:91–105CrossRefPubMedGoogle Scholar
  18. 18.
    Princich JP, Wassermann D, Latini F, Oddo S, Blenkmann AO, Seifer G, Kochen S (2013) Rapid and efficient localization of depth electrodes and cortical labeling using free and open source medical software in epilepsy surgery candidates. Front Neurosci 7:260CrossRefPubMedCentralPubMedGoogle Scholar
  19. 19.
    Hill DL, Maurer CR, Maciunas RJ, Barwise JA, Fitzpatrick MJ, Wang MY (1998) Measurement of intraoperative brain surface deformation under a craniotomy. Neurosurgery 43:514–526CrossRefPubMedGoogle Scholar
  20. 20.
    Van Laarhoven PJ, Aarts EH (1987) Simulated annealing: theory and applications. Springer, BerlinCrossRefGoogle Scholar
  21. 21.
    Ramachandran P, Varoquaux G (2011) Mayavi: 3D visualization of scientific data. Comput Sci Eng 13:40–51CrossRefGoogle Scholar
  22. 22.
    Hunter JD (2007) Matplotlib: A 2D graphics environment. IEEE Comput Sci Eng 9:90–95CrossRefGoogle Scholar
  23. 23.
    Gramfort A, Luessi M, Larson E, Engemann DA, Strohmeier D, Brodbeck C, Goj R, Jas M, Brooks T, Parkkonen L, Hämäläinen M (2013) MEG and EEG data analysis with MNE-python. Front Neurosci 7:267CrossRefPubMedCentralPubMedGoogle Scholar
  24. 24.
    Fischl B (2012) FreeSurfer. NeuroImage 62:774–781CrossRefPubMedCentralPubMedGoogle Scholar

Copyright information

© CARS 2016

Authors and Affiliations

  • Roan A. LaPlante
    • 1
    • 9
    Email author
  • Wei Tang
    • 2
  • Noam Peled
    • 1
    • 3
  • Deborah I. Vallejo
    • 4
  • Mia Borzello
    • 4
  • Darin D. Dougherty
    • 5
  • Emad N. Eskandar
    • 6
  • Alik S. Widge
    • 5
    • 7
  • Sydney S. Cash
    • 4
  • Steven M. Stufflebeam
    • 1
    • 3
    • 8
  1. 1.Athinoula A. Martinos Center for Biomedical ImagingMassachusetts General Hospital and Harvard Medical SchoolBostonUSA
  2. 2.Department of Neurobiology and AnatomyUniversity of Rochester School of Medicine and DentistryRochesterUSA
  3. 3.Department of RadiologyHarvard Medical SchoolBostonUSA
  4. 4.Cortical Physiology Laboratory, Department of NeurologyMassachusetts General Hospital and Harvard Medical SchoolBostonUSA
  5. 5.Department of PsychiatryMassachusetts General Hospital and Harvard Medical SchoolBostonUSA
  6. 6.Department of Neurological SurgeryMassachusetts General Hospital and Harvard Medical SchoolBostonUSA
  7. 7.Picower Institute for Learning and MemoryMassachusetts Institute of TechnologyCambridgeUSA
  8. 8.Harvard-MIT Health Sciences and TechnologyCambridgeUSA
  9. 9.Athinoula A. Martinos Center for Biomedical Imaging, Department of RadiologyMassachusetts General HospitalCharlestownUSA

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