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Long S, Bruzzone M, Mitropanopoulos S, Kalamangalam G, Gunduz A. Identification and classification of pathology and artifacts for human intracranial cognitive research. Neuroimage 2023; 270:119961. [PMID: 36848970 PMCID: PMC10461234 DOI: 10.1016/j.neuroimage.2023.119961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 02/27/2023] Open
Abstract
Intracranial electroencephalography (iEEG) presents a unique opportunity to extend human neuroscientific understanding. However, typically iEEG is collected from patients diagnosed with focal drug-resistant epilepsy (DRE) and contains transient bursts of pathological activity. This activity disrupts performances on cognitive tasks and can distort findings from human neurophysiology studies. In addition to manual marking by a trained expert, numerous IED detectors have been developed to identify these pathological events. Even so, the versatility and usefulness of these detectors is limited by training on small datasets, incomplete performance metrics, and lack of generalizability to iEEG. Here, we employed a large annotated public iEEG dataset from two institutions to train a random forest classifier (RFC) to distinguish data segments as either 'non-cerebral artifact' (n = 73,902), 'pathological activity' (n = 67,797), or 'physiological activity' (n = 151,290). We found our model performed with an accuracy of 0.941, specificity of 0.950, sensitivity of 0.908, precision of 0.911, and F1 score of 0.910, averaged across all three event types. We extended the generalizability of our model to continuous bipolar data collected in a task-state at a different institution with a lower sampling rate and found our model performed with an accuracy of 0.789, specificity of 0.806, and sensitivity of 0.742, averaged across all three event types. Additionally, we created a custom graphical user interface to implement our classifier and enhance usability.
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Affiliation(s)
- Sarah Long
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, United States
| | - Maria Bruzzone
- Wilder Center for Epilepsy, Department of Neurology, University of Florida, United States
| | | | - Giridhar Kalamangalam
- Wilder Center for Epilepsy, Department of Neurology, University of Florida, United States
| | - Aysegul Gunduz
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, United States; Wilder Center for Epilepsy, Department of Neurology, University of Florida, United States.
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2
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Liu AA, Henin S, Abbaspoor S, Bragin A, Buffalo EA, Farrell JS, Foster DJ, Frank LM, Gedankien T, Gotman J, Guidera JA, Hoffman KL, Jacobs J, Kahana MJ, Li L, Liao Z, Lin JJ, Losonczy A, Malach R, van der Meer MA, McClain K, McNaughton BL, Norman Y, Navas-Olive A, de la Prida LM, Rueckemann JW, Sakon JJ, Skelin I, Soltesz I, Staresina BP, Weiss SA, Wilson MA, Zaghloul KA, Zugaro M, Buzsáki G. A consensus statement on detection of hippocampal sharp wave ripples and differentiation from other fast oscillations. Nat Commun 2022; 13:6000. [PMID: 36224194 PMCID: PMC9556539 DOI: 10.1038/s41467-022-33536-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 09/21/2022] [Indexed: 02/05/2023] Open
Abstract
Decades of rodent research have established the role of hippocampal sharp wave ripples (SPW-Rs) in consolidating and guiding experience. More recently, intracranial recordings in humans have suggested their role in episodic and semantic memory. Yet, common standards for recording, detection, and reporting do not exist. Here, we outline the methodological challenges involved in detecting ripple events and offer practical recommendations to improve separation from other high-frequency oscillations. We argue that shared experimental, detection, and reporting standards will provide a solid foundation for future translational discovery.
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Affiliation(s)
- Anli A Liu
- Department of Neurology, NYU Grossman School of Medicine, New York, NY, USA
- Neuroscience Institute, NYU Langone Medical Center, New York, NY, USA
| | - Simon Henin
- Department of Neurology, NYU Grossman School of Medicine, New York, NY, USA
| | - Saman Abbaspoor
- Department of Psychology, Vanderbilt University, Nashville, TN, USA
| | - Anatol Bragin
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Elizabeth A Buffalo
- Department of Physiology and Biophysics, Washington National Primate Center, University of Washington, Seattle, WA, USA
| | - Jordan S Farrell
- Department of Neurosurgery, Stanford University, Stanford, CA, USA
| | - David J Foster
- Department of Psychology and Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Loren M Frank
- Kavli Institute for Fundamental Neuroscience, Center for Integrative Neuroscience and Department of Physiology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Tamara Gedankien
- Department of Biomedical Engineering, Department of Neurological Surgery, Columbia University, New York, NY, USA
| | - Jean Gotman
- Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Jennifer A Guidera
- Kavli Institute for Fundamental Neuroscience, Center for Integrative Neuroscience and Department of Physiology, University of California San Francisco, San Francisco, CA, USA
- Medical Scientist Training Program, Department of Bioengineering, University of California, San Francisco, San Francisco, CA, USA
| | - Kari L Hoffman
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA
| | - Joshua Jacobs
- Department of Biomedical Engineering, Department of Neurological Surgery, Columbia University, New York, NY, USA
| | - Michael J Kahana
- Department of Psychology, University of Pennsylvania, Philadelphia, PA, USA
| | - Lin Li
- Department of Biomedical Engineering, University of North Texas, Denton, TX, USA
| | - Zhenrui Liao
- Department of Neuroscience, Columbia University, New York, NY, USA
| | - Jack J Lin
- Department of Neurology, Center for Mind and Brain, University of California Davis, Oakland, CA, USA
| | - Attila Losonczy
- Department of Neuroscience, Columbia University, New York, NY, USA
| | - Rafael Malach
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
| | | | - Kathryn McClain
- Neuroscience Institute, NYU Langone Medical Center, New York, NY, USA
| | - Bruce L McNaughton
- The Canadian Centre for Behavioural Neuroscience, University of Lethbridge, Lethbridge, AB, Canada
| | - Yitzhak Norman
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
| | | | | | - Jon W Rueckemann
- Department of Physiology and Biophysics, Washington National Primate Center, University of Washington, Seattle, WA, USA
| | - John J Sakon
- Department of Psychology, University of Pennsylvania, Philadelphia, PA, USA
| | - Ivan Skelin
- Department of Neurology, Center for Mind and Brain, University of California Davis, Oakland, CA, USA
| | - Ivan Soltesz
- Department of Neurosurgery, Stanford University, Stanford, CA, USA
| | - Bernhard P Staresina
- Department of Experimental Psychology, Oxford Centre for Human Brain Activity, Wellcome Centre for Integrative Neuroimaging, Department of Psychiatry, University of Oxford, Oxford, UK
| | - Shennan A Weiss
- Brookdale Hospital Medical Center, SUNY Downstate Medical Center, Brooklyn, NY, USA
| | - Matthew A Wilson
- Department of Brain and Cognitive Sciences and Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kareem A Zaghloul
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke (NINDS), National Institutes of Health, Bethesda, MD, USA
| | - Michaël Zugaro
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - György Buzsáki
- Department of Neurology, NYU Grossman School of Medicine, New York, NY, USA.
- Neuroscience Institute, NYU Langone Medical Center, New York, NY, USA.
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3
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Food intake precipitates seizures in temporal lobe epilepsy. Sci Rep 2021; 11:16515. [PMID: 34389785 PMCID: PMC8363749 DOI: 10.1038/s41598-021-96106-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/03/2021] [Indexed: 11/09/2022] Open
Abstract
Various factors have been considered as potential seizure precipitants. We here assessed the temporal association of food intake and seizure occurrence, and characteristics of seizures and epilepsy syndromes involved. 596 seizures from 100 consecutive patients undergoing long-term video-EEG monitoring were analyzed. Preictal periods of 60 min were assessed as to the occurrence of food intake, and latencies between food intake and seizure onset were analyzed. Seizures of temporal origin were highly significantly more frequently preceded by food intake compared to those of extratemporal origin; and were associated with shorter food intake-seizure latency. Seizure precipitation by food intake showed male predominance. Shorter food intake-seizure latency was associated with less severe seizures and less frequent contralateral spread of epileptic discharges. We here show for the first time that not only in specific rare reflex epilepsies but in the most frequent form of focal epilepsy, temporal lobe epilepsy, seizures are significantly precipitated by food intake. Seizure occurrence was increased over a period of up to one hour following food intake, and remained more localized in terms of both ictal EEG spread and as reflected by seizure severity. This finding supports the emerging concepts of ictogenesis, implying a continuum between reflex and spontaneous seizures-instead a dichotomy between them.
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Norman Y, Raccah O, Liu S, Parvizi J, Malach R. Hippocampal ripples and their coordinated dialogue with the default mode network during recent and remote recollection. Neuron 2021; 109:2767-2780.e5. [PMID: 34297916 DOI: 10.1016/j.neuron.2021.06.020] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 05/13/2021] [Accepted: 06/16/2021] [Indexed: 12/19/2022]
Abstract
Hippocampal ripples are prominent synchronization events generated by hippocampal neuronal assemblies. To date, ripples have been primarily associated with navigational memory in rodents and short-term episodic recollections in humans. Here, we uncover different profiles of ripple activity in the human hippocampus during the retrieval of recent and remote autobiographical events and semantic facts. We found that the ripple rate increased significantly before reported recall compared to control conditions. Patterns of ripple activity across multiple hippocampal sites demonstrated remarkable specificity for memory type. Intriguingly, these ripple patterns revealed a semantization dimension, in which patterns associated with autobiographical contents become similar to those of semantic memory as a function of memory age. Finally, widely distributed sites across the neocortex exhibited ripple-coupled activations during recollection, with the strongest activation found within the default mode network. Our results thus reveal a key role for hippocampal ripples in orchestrating hippocampal-cortical communication across large-scale networks involved in conscious recollection.
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Affiliation(s)
- Yitzhak Norman
- Department of Neurobiology, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Omri Raccah
- Laboratory of Behavioral and Cognitive Neuroscience, Stanford Human Intracranial Cognitive Electrophysiology Program, Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305, USA
| | - Su Liu
- Laboratory of Behavioral and Cognitive Neuroscience, Stanford Human Intracranial Cognitive Electrophysiology Program, Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305, USA
| | - Josef Parvizi
- Laboratory of Behavioral and Cognitive Neuroscience, Stanford Human Intracranial Cognitive Electrophysiology Program, Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305, USA
| | - Rafael Malach
- Department of Neurobiology, Weizmann Institute of Science, Rehovot 76100, Israel.
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Norman Y, Yeagle EM, Khuvis S, Harel M, Mehta AD, Malach R. Hippocampal sharp-wave ripples linked to visual episodic recollection in humans. Science 2019; 365:365/6454/eaax1030. [DOI: 10.1126/science.aax1030] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 07/04/2019] [Indexed: 12/12/2022]
Abstract
Hippocampal sharp-wave ripples (SWRs) constitute one of the most synchronized activation events in the brain and play a critical role in offline memory consolidation. Yet their cognitive content and function during awake, conscious behavior remains unclear. We directly examined this question using intracranial recordings in human patients engaged in episodic free recall of previously viewed photographs. Our results reveal a content-selective increase in hippocampal ripple rate emerging 1 to 2 seconds prior to recall events. During recollection, high-order visual areas showed pronounced SWR-coupled reemergence of activation patterns associated with recalled content. Finally, the SWR rate during encoding predicted subsequent free-recall performance. These results point to a role for hippocampal SWRs in triggering spontaneous recollections and orchestrating the reinstatement of cortical representations during free episodic memory retrieval.
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Guler S, Dannhauer M, Roig-Solvas B, Gkogkidis A, Macleod R, Ball T, Ojemann JG, Brooks DH. Computationally optimized ECoG stimulation with local safety constraints. Neuroimage 2018; 173:35-48. [PMID: 29427847 PMCID: PMC5911187 DOI: 10.1016/j.neuroimage.2018.01.088] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 01/03/2018] [Accepted: 01/31/2018] [Indexed: 12/22/2022] Open
Abstract
Direct stimulation of the cortical surface is used clinically for cortical mapping and modulation of local activity. Future applications of cortical modulation and brain-computer interfaces may also use cortical stimulation methods. One common method to deliver current is through electrocorticography (ECoG) stimulation in which a dense array of electrodes are placed subdurally or epidurally to stimulate the cortex. However, proximity to cortical tissue limits the amount of current that can be delivered safely. It may be desirable to deliver higher current to a specific local region of interest (ROI) while limiting current to other local areas more stringently than is guaranteed by global safety limits. Two commonly used global safety constraints bound the total injected current and individual electrode currents. However, these two sets of constraints may not be sufficient to prevent high current density locally (hot-spots). In this work, we propose an efficient approach that prevents current density hot-spots in the entire brain while optimizing ECoG stimulus patterns for targeted stimulation. Specifically, we maximize the current along a particular desired directional field in the ROI while respecting three safety constraints: one on the total injected current, one on individual electrode currents, and the third on the local current density magnitude in the brain. This third set of constraints creates a computational barrier due to the huge number of constraints needed to bound the current density at every point in the entire brain. We overcome this barrier by adopting an efficient two-step approach. In the first step, the proposed method identifies the safe brain region, which cannot contain any hot-spots solely based on the global bounds on total injected current and individual electrode currents. In the second step, the proposed algorithm iteratively adjusts the stimulus pattern to arrive at a solution that exhibits no hot-spots in the remaining brain. We report on simulations on a realistic finite element (FE) head model with five anatomical ROIs and two desired directional fields. We also report on the effect of ROI depth and desired directional field on the focality of the stimulation. Finally, we provide an analysis of optimization runtime as a function of different safety and modeling parameters. Our results suggest that optimized stimulus patterns tend to differ from those used in clinical practice.
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Affiliation(s)
- Seyhmus Guler
- Computational Radiology Laboratory (CRL), Boston Children's Hospital and Harvard Medical School, Boston, MA, USA.
| | - Moritz Dannhauer
- Center for Integrative Biomedical Computing (CIBC), University of Utah, Salt Lake City, UT, USA; Scientific Computing Institute (SCI), University of Utah, Salt Lake City, UT, USA
| | - Biel Roig-Solvas
- SPIRAL Group, Department of Electrical and Computer Engineering, Northeastern University, Boston, MA, USA
| | - Alexis Gkogkidis
- Intracranial EEG and Brain Imaging Lab, Epilepsy Center, University Hospital Freiburg, Freiburg, Germany; BrainLinks-BrainTools Cluster of Excellence and Bernstein Center Freiburg, University of Freiburg, Freiburg, Germany
| | - Rob Macleod
- Center for Integrative Biomedical Computing (CIBC), University of Utah, Salt Lake City, UT, USA; Scientific Computing Institute (SCI), University of Utah, Salt Lake City, UT, USA
| | - Tonio Ball
- Intracranial EEG and Brain Imaging Lab, Epilepsy Center, University Hospital Freiburg, Freiburg, Germany; BrainLinks-BrainTools Cluster of Excellence and Bernstein Center Freiburg, University of Freiburg, Freiburg, Germany
| | - Jeffrey G Ojemann
- Department of Neurological Surgery and the Center for Sensorimotor Neural Engineering, University of Washington, Seattle, WA, USA
| | - Dana H Brooks
- Center for Integrative Biomedical Computing (CIBC), University of Utah, Salt Lake City, UT, USA; SPIRAL Group, Department of Electrical and Computer Engineering, Northeastern University, Boston, MA, USA
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Iljina O, Derix J, Schirrmeister RT, Schulze-Bonhage A, Auer P, Aertsen A, Ball T. Neurolinguistic and machine-learning perspectives on direct speech BCIs for restoration of naturalistic communication. BRAIN-COMPUTER INTERFACES 2017. [DOI: 10.1080/2326263x.2017.1330611] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Olga Iljina
- GRK 1624 ‘Frequency effects in language’, University of Freiburg, Freiburg, Germany
- Department of German Linguistics, University of Freiburg, Freiburg, Germany
- Hermann Paul School of Linguistics, University of Freiburg, Germany
- BrainLinks-BrainTools, University of Freiburg, Freiburg, Germany
- Neurobiology and Biophysics, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Johanna Derix
- BrainLinks-BrainTools, University of Freiburg, Freiburg, Germany
- Translational Neurotechnology Lab, Department of Neurosurgery, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Robin Tibor Schirrmeister
- BrainLinks-BrainTools, University of Freiburg, Freiburg, Germany
- Translational Neurotechnology Lab, Department of Neurosurgery, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Andreas Schulze-Bonhage
- Epilepsy Center, Department of Neurosurgery, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- BrainLinks-BrainTools, University of Freiburg, Freiburg, Germany
| | - Peter Auer
- GRK 1624 ‘Frequency effects in language’, University of Freiburg, Freiburg, Germany
- Department of German Linguistics, University of Freiburg, Freiburg, Germany
- Hermann Paul School of Linguistics, University of Freiburg, Germany
- Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Freiburg, Germany
| | - Ad Aertsen
- Neurobiology and Biophysics, Faculty of Biology, University of Freiburg, Freiburg, Germany
- Bernstein Center Freiburg, University of Freiburg, Germany
| | - Tonio Ball
- BrainLinks-BrainTools, University of Freiburg, Freiburg, Germany
- Translational Neurotechnology Lab, Department of Neurosurgery, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
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Huiskamp G, Oostendorp TF, De Munck JC. Multimodal Source Imaging: Basic Methods, Signal Processing Techniques, and Applications. IEEE Trans Biomed Eng 2016; 63:2550-2551. [PMID: 27875124 DOI: 10.1109/tbme.2016.2620154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Multimodal source imaging is an emerging field in biomedical engineering. Its central goal is to combine different imaging modalities in a single model or data representation, such that the combination provides an enhanced insight into the underlying physiological organ, compared to each modality separately. It requires advanced signal acquisition and processing techniques and has applications in cognitive neuroscience, clinical neuroscience and electrocardiology. Therefore, it belongs to the heart of biomedical engineering.
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