publication . Other literature type . Preprint . Article . 2016

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.;
  • Published: 11 Aug 2016
  • Publisher: Elsevier BV
Abstract
<jats:title>Abstract</jats:title><jats:sec><jats:title>Background</jats:title><jats:p>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.</jats:p></jats:sec><jats:sec><jats:title>New Method</jats:title><jats:p>iELVis uses existing tools (BioImage Suite, FSL, and FreeSurfer) for preimplant magnetic resonance imaging (MRI) segmentation, neuroimaging cor...
Subjects
free text keywords: Interactive visualization, Visualization, Computer vision, Matlab toolbox, Artificial intelligence, business.industry, business, Computer science, Functional neuroimaging, Software, Brain stimulation, Robustness (computer science), Bioinformatics, Neuroimaging, Anatomy, Segmentation, Biology
Funded by
SNSF| Neocortical oscillations subtend the multisensory integration of auditory and visual speech
Project
  • Funder: Swiss National Science Foundation (SNSF)
  • Project Code: P300P3_148388
  • Funding stream: Careers;Fellowships | Advanced Postdoc.Mobility
,
SNSF| 'See me, hear me' - cortical oscillations in the integration of auditory and visual speech
Project
  • Funder: Swiss National Science Foundation (SNSF)
  • Project Code: PBGEP3_139829
  • Funding stream: Careers;Fellowships | Fellowships for prospective researchers
Communities
Neuroinformatics
37 references, page 1 of 3

Akalin Acar, Z., Palmer, J., Worrell, G., & Makeig, S. (2011). Electrocortical source imaging of intracranial EEG data in epilepsy. Engineering in Medicine and Biology Society, EMBC, 2011 Annual International Conference of the IEEE, 1411-1414. [OpenAIRE]

Crone, N. E., Korzeniewska, A., & Franaszczuk, P. J. (2011). Cortical gamma responses: Searching high and low. International Journal of Psychophysiology, 79(1), 9-15. http://doi.org/10.1016/j.ijpsycho.2010.10.013 [OpenAIRE]

Dalal, S. S., Edwards, E., Kirsch, H. E., Barbaro, N. M., Knight, R. T., & Nagarajan, S. S. (2008). Localization of neurosurgically implanted electrodes via photograph-MRI-radiograph coregistration. Journal of Neuroscience Methods, 174(1), 106-115. http://doi.org/10.1016/j.jneumeth.2008.06.028

Delorme, A., & Makeig, S. (2004). EEGLAB: an open source toolbox for analysis of single-trial EEG dynamics including independent component analysis. Journal of Neuroscience Methods, 134(1), 9-21. http://doi.org/10.1016/j.jneumeth.2003.10.009 [OpenAIRE]

Delorme, A., Mullen, T., Kothe, C., Akalin Acar, Z., Bigdely-Shamlo, N., Vankov, A., & Makeig, S. (2011). EEGLAB, SIFT, NFT, BCILAB, and ERICA: New Tools for Advanced EEG Processing. Computational Intelligence and Neuroscience, 2011(1), 1-12. http://doi.org/10.1162/pres.19.1.35

Desikan, R. S., Ségonne, F., Fischl, B., Quinn, B. T., Dickerson, B. C., Blacker, D., et al. (2006). An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest. NeuroImage, 31(3), 968-980. http://doi.org/10.1016/j.neuroimage.2006.01.021 [OpenAIRE]

Destrieux, C., Fischl, B., Dale, A., & Halgren, E. (2010). Automatic parcellation of human cortical gyri and sulci using standard anatomical nomenclature. NeuroImage, 53(1), 1-15. http://doi.org/10.1016/j.neuroimage.2010.06.010 [OpenAIRE]

Dykstra, A. R., Chan, A. M., Quinn, B. T., Zepeda, R., Keller, C. J., Cormier, J., et al. (2011). Individualized localization and cortical surface-based registration of intracranial electrodes. NeuroImage, 1-42. http://doi.org/10.1016/j.neuroimage.2011.11.046

Fischl, B., Sereno, M. I., Tootell, R. B. H., & Dale, A. M. (1999). High-resolution intersubject averaging and a coordinate system for the cortical surface. Human Brain Mapping, 8(4), 272-284.

Fox, M. D., Qian, T., Madsen, J. R., Wang, D., Li, M., Ge, M., et al. (2016). Combining task-evoked and spontaneous activity to improve pre-operative brain mapping with fMRI. NeuroImage, 124(Part A), 714-723. http://doi.org/10.1016/j.neuroimage.2015.09.030

Golumbic, E. Z., Ding, N., Bickel, S., Lakatos, P., Schevon, C. A., McKhann, G. M., Goodman, R. R., Emerson, R., Mehta, A. D., Simon, J. Z., Poeppel, D., & Schroeder, C. (2013). Mechanisms underlying selective neuronal tracking of attended speech at a “cocktail party.” Neuron, 77(5), 980-991. [OpenAIRE]

Gonzalez-Martinez, J., Mullin, J., Vadera, S., Bulacio, J., Hughes, G., Jones, S., et al. (2014). Stereotactic placement of depth electrodes in medically intractable epilepsy. Journal of Neurosurgery, 120(3), 639-644. http://doi.org/10.3171/2013.11.JNS13635

Greve, D. N., & Fischl, B. (2009). Accurate and robust brain image alignment using boundary-based registration. NeuroImage, 48(1), 63-72. http://doi.org/10.1016/j.neuroimage.2009.06.060

Groppe, D. M., Bickel, S., Keller, C. J., Jain, S. K., Hwang, S. T., Harden, C., & Mehta, A. D. (2013). Dominant frequencies of resting human brain activity as measured by the electrocorticogram. NeuroImage, 79(C), 1-11. http://doi.org/10.1016/j.neuroimage.2013.04.044

Hastreiter, P., Rezk-Salama, C., Soza, G., Bauer, M., Greiner, G., Fahlbusch, R., et al. (2004). Strategies for brain shift evaluation. Medical Image Analysis, 8(4), 447-464. http://doi.org/10.1016/j.media.2004.02.001 [OpenAIRE]

37 references, page 1 of 3
Abstract
<jats:title>Abstract</jats:title><jats:sec><jats:title>Background</jats:title><jats:p>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.</jats:p></jats:sec><jats:sec><jats:title>New Method</jats:title><jats:p>iELVis uses existing tools (BioImage Suite, FSL, and FreeSurfer) for preimplant magnetic resonance imaging (MRI) segmentation, neuroimaging cor...
Subjects
free text keywords: Interactive visualization, Visualization, Computer vision, Matlab toolbox, Artificial intelligence, business.industry, business, Computer science, Functional neuroimaging, Software, Brain stimulation, Robustness (computer science), Bioinformatics, Neuroimaging, Anatomy, Segmentation, Biology
Funded by
SNSF| Neocortical oscillations subtend the multisensory integration of auditory and visual speech
Project
  • Funder: Swiss National Science Foundation (SNSF)
  • Project Code: P300P3_148388
  • Funding stream: Careers;Fellowships | Advanced Postdoc.Mobility
,
SNSF| 'See me, hear me' - cortical oscillations in the integration of auditory and visual speech
Project
  • Funder: Swiss National Science Foundation (SNSF)
  • Project Code: PBGEP3_139829
  • Funding stream: Careers;Fellowships | Fellowships for prospective researchers
Communities
Neuroinformatics
37 references, page 1 of 3

Akalin Acar, Z., Palmer, J., Worrell, G., & Makeig, S. (2011). Electrocortical source imaging of intracranial EEG data in epilepsy. Engineering in Medicine and Biology Society, EMBC, 2011 Annual International Conference of the IEEE, 1411-1414. [OpenAIRE]

Crone, N. E., Korzeniewska, A., & Franaszczuk, P. J. (2011). Cortical gamma responses: Searching high and low. International Journal of Psychophysiology, 79(1), 9-15. http://doi.org/10.1016/j.ijpsycho.2010.10.013 [OpenAIRE]

Dalal, S. S., Edwards, E., Kirsch, H. E., Barbaro, N. M., Knight, R. T., & Nagarajan, S. S. (2008). Localization of neurosurgically implanted electrodes via photograph-MRI-radiograph coregistration. Journal of Neuroscience Methods, 174(1), 106-115. http://doi.org/10.1016/j.jneumeth.2008.06.028

Delorme, A., & Makeig, S. (2004). EEGLAB: an open source toolbox for analysis of single-trial EEG dynamics including independent component analysis. Journal of Neuroscience Methods, 134(1), 9-21. http://doi.org/10.1016/j.jneumeth.2003.10.009 [OpenAIRE]

Delorme, A., Mullen, T., Kothe, C., Akalin Acar, Z., Bigdely-Shamlo, N., Vankov, A., & Makeig, S. (2011). EEGLAB, SIFT, NFT, BCILAB, and ERICA: New Tools for Advanced EEG Processing. Computational Intelligence and Neuroscience, 2011(1), 1-12. http://doi.org/10.1162/pres.19.1.35

Desikan, R. S., Ségonne, F., Fischl, B., Quinn, B. T., Dickerson, B. C., Blacker, D., et al. (2006). An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest. NeuroImage, 31(3), 968-980. http://doi.org/10.1016/j.neuroimage.2006.01.021 [OpenAIRE]

Destrieux, C., Fischl, B., Dale, A., & Halgren, E. (2010). Automatic parcellation of human cortical gyri and sulci using standard anatomical nomenclature. NeuroImage, 53(1), 1-15. http://doi.org/10.1016/j.neuroimage.2010.06.010 [OpenAIRE]

Dykstra, A. R., Chan, A. M., Quinn, B. T., Zepeda, R., Keller, C. J., Cormier, J., et al. (2011). Individualized localization and cortical surface-based registration of intracranial electrodes. NeuroImage, 1-42. http://doi.org/10.1016/j.neuroimage.2011.11.046

Fischl, B., Sereno, M. I., Tootell, R. B. H., & Dale, A. M. (1999). High-resolution intersubject averaging and a coordinate system for the cortical surface. Human Brain Mapping, 8(4), 272-284.

Fox, M. D., Qian, T., Madsen, J. R., Wang, D., Li, M., Ge, M., et al. (2016). Combining task-evoked and spontaneous activity to improve pre-operative brain mapping with fMRI. NeuroImage, 124(Part A), 714-723. http://doi.org/10.1016/j.neuroimage.2015.09.030

Golumbic, E. Z., Ding, N., Bickel, S., Lakatos, P., Schevon, C. A., McKhann, G. M., Goodman, R. R., Emerson, R., Mehta, A. D., Simon, J. Z., Poeppel, D., & Schroeder, C. (2013). Mechanisms underlying selective neuronal tracking of attended speech at a “cocktail party.” Neuron, 77(5), 980-991. [OpenAIRE]

Gonzalez-Martinez, J., Mullin, J., Vadera, S., Bulacio, J., Hughes, G., Jones, S., et al. (2014). Stereotactic placement of depth electrodes in medically intractable epilepsy. Journal of Neurosurgery, 120(3), 639-644. http://doi.org/10.3171/2013.11.JNS13635

Greve, D. N., & Fischl, B. (2009). Accurate and robust brain image alignment using boundary-based registration. NeuroImage, 48(1), 63-72. http://doi.org/10.1016/j.neuroimage.2009.06.060

Groppe, D. M., Bickel, S., Keller, C. J., Jain, S. K., Hwang, S. T., Harden, C., & Mehta, A. D. (2013). Dominant frequencies of resting human brain activity as measured by the electrocorticogram. NeuroImage, 79(C), 1-11. http://doi.org/10.1016/j.neuroimage.2013.04.044

Hastreiter, P., Rezk-Salama, C., Soza, G., Bauer, M., Greiner, G., Fahlbusch, R., et al. (2004). Strategies for brain shift evaluation. Medical Image Analysis, 8(4), 447-464. http://doi.org/10.1016/j.media.2004.02.001 [OpenAIRE]

37 references, page 1 of 3
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publication . Other literature type . Preprint . Article . 2016

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.;