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Thalamic interictal epileptic and non-epileptic events during NREM sleep in patients with focal epilepsy: a Stereo-EEG study.

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Paper

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The authors' code

MATLAB · 98 lines · 2.5 KB · MIT

  1. % Visually check detected spikes;
  3. %%
  4. spikes_noss = []; spike_gamma_noss = [];
  5. % load data
  6. set(0,'defaultfigurecolor','w');
  7. id = 2; % Set
  8. spike_marker = spikes{id}./ double(sr); % for MNI detectors
  9. plotsoz = false;
  10. if exist('soz_signal', 'var')
  11. plotsoz = true;
  12. end
  13. raw_data = data;
  14. signal = raw_data(id,:);
  15. signal = double(signal)';
  16. fs = sr;
  17. seg_len = 2 * fs;
  18. disp(channels{id});
  19. fl = 30;
  20. fh = 100;
  21. % [b,a] = butter(4,[fl*2/fs, fh*2/fs],'bandpass');
  22. % FIR
  23. filterOrder = 200;
  24. normalizedCutoff = [fl, fh] * 2 / fs;
  25. b = fir1(filterOrder, normalizedCutoff, 'bandpass');
  26. freqz(b, 1, 1024, fs);
  28. %% view
  29. for i = 1:1:length(spike_marker)
  30. cur_sample = int32(spike_marker(i)*fs);
  31. spike_signal = signal(cur_sample-int32(seg_len/2)+1 : cur_sample+int32(seg_len/2));
  32. xaxis = 0:1/fs:length(spike_signal)/fs-1/fs;
  33. fspike_signal = filtfilt(b, 1, spike_signal);
  35. figure(100);
  36. set(gcf, 'Position', [400 50 800 800]);
  37. subplot(4,1,1)
  38. plot(xaxis, spike_signal, 'color', [0 0 0]);
  39. ylabel('Raw iEEG (μV)');
  40. title(['Time: ',num2str(spike_marker(i))]);
  41. box off;
  43. subplot(4,1,2)
  44. plot(xaxis, fspike_signal);
  45. ylabel('30-100 Hz filtered');
  46. xlabel('Time (s)');
  47. title(['Chn: ', channels{id}]);
  48. box off;
  50. % TFR
  51. [ps,tfr] = getTFRfromFT(spike_signal, fs);
  52. xaxis_tfr = tfr.time;
  53. yaxis_tfr= tfr.freq;
  54. subplot(4,1,3)
  55. imagesc(xaxis_tfr,yaxis_tfr,ps);axis xy; xlabel('Time (s)');ylabel('Frequency (Hz)');
  56. colormap jet
  57. title(['Time: ',num2str(spike_marker(i)), ', Chn: ', channels{id}]);
  58. if plotsoz
  59. cur_soz_signal = soz_signal(cur_sample-int32(seg_len/2)+1 : cur_sample+int32(seg_len/2));
  60. subplot(4,1,4)
  61. plot(xaxis, cur_soz_signal, 'color', [0 0 0]);
  62. ylabel('SOZ iEEG (μV)');
  63. box off;
  64. end
  66. disp('Press Y to mark, or any other key to skip.');
  67. key = getkey;
  68. switch key
  69. case 'y'
  70. spikes_noss(end+1) = cur_sample;
  71. case 'Y'
  72. spikes_noss(end+1) = cur_sample;
  73. otherwise
  74. end
  75. % pause %ctr+c exit
  76. end
  77. disp('End')
  79. %%
  80. function [ps,tfr] = getTFRfromFT(signal, fs)
  81. ftdata=[];
  82. ftdata.trial{1} = signal';
  83. ftdata.label = {'Th'};
  84. ftdata.time{1} = 0:1/fs:2.0-1/fs;
  85. ftdata.fsample = fs;
  87. cfg = [];
  88. cfg.method = 'mtmconvol';
  89. cfg.toi = 0:0.02:2.0;
  90. cfg.foi = 10:1:100;
  91. cfg.taper = 'hanning';
  92. cfg.t_ftimwin = 5./cfg.foi;
  94. freq = ft_freqanalysis(cfg, ftdata);
  95. ps = squeeze(freq.powspctrm(1,:,:));
  96. tfr = freq;
  98. end

View_spikecheck.m at commit 35475ba, under MIT · at the source

Overview

Authors: Hongyi Ye1,2, Kassem Jaber2,3, Alyssa Ho2, Lingqi Ye4, John Thomas3,5, Xiaowei Xu1, Cong Chen1, Yihe Chen1, Guoping Ren2,6, Matthew Moye2, Tamir Avigdor2, Irena Doležalová2, Petr Klimes2, Prachi Parikh2, Derek Southwell7, Zhe Zheng8, Junming Zhu8, Shuang Wang1, Birgit Frauscher2,3,9
ORCID iDs: Hongyi Ye, John Thomas, Xiaowei Xu
  1. Department of Neurology and Epilepsy Center, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
  2. Department of Neurology, Duke University, Durham, NC, USA
  3. Department of Biomedical Engineering, Duke University, Durham, NC, USA
  4. Department of Neurology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
  5. Department of Electrical and Computer Engineering Technology, Rochester Institute of Technology, Rochester, NY, USA
  6. Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
  7. Department of Neurosurgery, Duke University, Durham, NC, USA
  8. Department of Neurosurgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
  9. Montreal Neurological Institute and Hospital, McGill University, Montreal, QC, Canada
Institutions: Duke University (United States); Second Affiliated Hospital of Zhejiang University (China); Zhejiang University (China); Sir Run Run Shaw Hospital (China); Rochester Institute of Technology (United States); Capital Medical University (China); Beijing Tian Tan Hospital (China); Montreal Neurological Institute and Hospital (Canada); McGill University (Canada)
Journal: EBioMedicine, volume 128, article 106287
Dates: received 22 August 2025; accepted 23 April 2026; published online 12 May 2026; in print June 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1016/j.ebiom.2026.106287 · PMID 42119303 · PMCID PMC13193782 · OpenAlex W4417331485
Open access: gold, a free copy (OpenAlex)
Preprint: doi:10.64898/2025.12.11.693651
Status: code verified
Categories: EEG (modality), intracranial EEG (iEEG / ECoG / SEEG) (modality), human (organism), epilepsy (population), clinical / translational (subfield)
Methods: Spectral & time-frequency, Preprocessing, Connectivity, Statistics, Physiology & signal measures
Keywords: Drug-resistant epilepsy, Electroencephalogram, Thalamus, Epilepsy biomarker, Non-rapid eye movement sleep
MeSH: Electroencephalography*, Epilepsies, Partial*, Thalamus*, Adolescent, Adult, Child, Female, Humans, Male, Middle Aged, Young Adult (* major topic)
Topic: Epilepsy research and treatment (Psychiatry and Mental health, Medicine), according to OpenAlex
Funding: Canadian Institutes of Health Research (PJT-175056); American Academy of Sleep Medicine Foundation; Duke University; Natural Science Foundation of Zhejiang Province (LD24H090003); National Natural Science Foundation of China (82301636, 82471469)
Citations: not cited yet (Europe PMC); 70 references in the paper

Abstract

Background: Thalamic recordings are increasingly incorporated into stereo-electroencephalography (SEEG) evaluations of drug-resistant focal epilepsy to guide neuromodulation targeting. Human thalamic electrophysiology, however, is poorly defined, limiting the distinction between pathological and physiological activity. Here, we characterised interictal epileptic and non-epileptic events during non-rapid eye movement (NREM) sleep across multiple thalamic nuclei and examined their associations to seizure outcomes.

Methods: We analysed NREM sleep SEEG recordings from 64 patients with drug-resistant focal epilepsy. Electrodes sampled four thalamic nuclei: centromedian (CM), pulvinar (Pu), ventral lateral (VL), and ventral posterolateral (VPL). Patients were classified into three outcome groups: favourable, unfavourable, and surgically non-remediable. Rates of thalamic spikes, high-frequency oscillations (HFOs), spike-fast activity, and sleep spindles were analysed and compared across nuclei and outcomes.

Findings: Recordings of the thalamus revealed both pathological and physiological interictal events. Interictal epileptic events were infrequent. Only ∼0.2% of seizure-onset zone spikes propagated to the thalamus. Thalamic spike-fast activity was indicative of unfavourable surgical outcomes (CM: p = 0.047, d = 0.46) or surgically non-remediable epilepsy (VL: p = 0.002, d = 0.84). In contrast, thalamic sleep spindles were ubiquitous but reduced in surgically non-remediable patients (CM: p = 0.031, d = −0.58; VL: p = 0.005, d = −0.79). Finally, unique thalamic SEEG patterns were identified, including spikes concomitant with spindles, isolated spikes, and physiological fast ripples.

Interpretation: This study provides a comprehensive characterisation of thalamic interictal events during NREM sleep, enriching our understanding of thalamic pathophysiology and highlighting the value of thalamic recordings in presurgical evaluation.

Funding: Start-up funding of Duke University; National Natural Science Foundation of China (82471469, 82301636); Zhejiang Provincial Natural Science Foundation (LD24H090003); Canadian Institutes of Health Research funding (PJT-175056).

Reproduced under the paper's license (CC BY), from the paper cited above.

Repository

Its files are read in the Code ↔ Paper reader above.

Lab-Frauscher/Thalamus_Interictal

License: MIT
State: the link answers, verified on 28 September 2026
Evidence: files inventoried
Commit: 35475ba1dc4b8f827cb154974bd57935fa748472, 13 March 2026
Languages: MATLAB (5)
Size: 7 files, 5 scripts
Software Heritage: not archived
Found in: “Data sharing statement”
Holds: README, license file
Not found: CITATION.cff, environment file, tests, continuous integration, documentation
Tools: FieldTrip (1 file), Signal Processing Toolbox (1 file)
Availability: 1 check, the latest on 28 September 2026: the link answers
  • 28 September 2026: the link answers
7 files
At the source: github.com/Lab-Frauscher/Thalamus_Interictal

The paper's code and data availability statement is in the Data section.

Tracing map

Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.

What the map holds:

  • 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 5 scripts, each with its path and the digest of its content;
  • no match between paragraphs and code yet;
  • neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

No dataset and no data link were found in the paper.

Data sharing statement

The MATLAB code for interictal event detection can be found in the Supplementary Materials, and the code for signal analysis is available on GitHub (https://github.com/Lab-Frauscher/Thalamus_Interictal). Clinical data will be shared with qualified academic investigators upon reasonable request to the senior authors following publication, provided that the requesting team obtains institutional review board approval and executes a formal data sharing agreement.

Reproduced under the paper's license (CC BY), from the paper cited above.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 2, 28 September 2026

  • Authors: added Hongyi Ye (0009-0004-6499-9455); Xiaowei Xu (0000-0001-8790-2450); removed Hongyi Ye; Xiaowei Xu

Version 1, 28 September 2026: the first record

Recorded: type, language, journal, volume, pages, dates, 19 authors, 5 keywords, 11 MeSH terms, 5 funders, 69 references.

Cite

This paper

Ye, H., Jaber, K., Ho, A., Ye, L., Thomas, J., Xu, X., Chen, C., Chen, Y., Ren, G., Moye, M., Avigdor, T., Doležalová, I., Klimes, P., Parikh, P., Southwell, D., Zheng, Z., Zhu, J., Wang, S., & Frauscher, B. (2026). Thalamic interictal epileptic and non-epileptic events during NREM sleep in patients with focal epilepsy: a Stereo-EEG study. EBioMedicine, 128, 106287. https://doi.org/10.1016/j.ebiom.2026.106287

BibTeX

@article{ye2026thalamic,
author = {Ye, Hongyi and Jaber, Kassem and Ho, Alyssa and Ye, Lingqi and Thomas, John and Xu, Xiaowei and Chen, Cong and Chen, Yihe and Ren, Guoping and Moye, Matthew and Avigdor, Tamir and Doležalová, Irena and Klimes, Petr and Parikh, Prachi and Southwell, Derek and Zheng, Zhe and Zhu, Junming and Wang, Shuang and Frauscher, Birgit},
title = {{Thalamic interictal epileptic and non-epileptic events during NREM sleep in patients with focal epilepsy: a Stereo-EEG study}},
journal = {EBioMedicine},
year = {2026},
month = may,
volume = {128},
pages = {106287},
publisher = {Elsevier},
issn = {2352-3964},
doi = {10.1016/j.ebiom.2026.106287},
url = {https://doi.org/10.1016/j.ebiom.2026.106287},
pmid = {42119303},
pmcid = {PMC13193782}
}

RIS

TY - JOUR
AU - Ye, Hongyi
AU - Jaber, Kassem
AU - Ho, Alyssa
AU - Ye, Lingqi
AU - Thomas, John
AU - Xu, Xiaowei
AU - Chen, Cong
AU - Chen, Yihe
AU - Ren, Guoping
AU - Moye, Matthew
AU - Avigdor, Tamir
AU - Doležalová, Irena
AU - Klimes, Petr
AU - Parikh, Prachi
AU - Southwell, Derek
AU - Zheng, Zhe
AU - Zhu, Junming
AU - Wang, Shuang
AU - Frauscher, Birgit
TI - Thalamic interictal epileptic and non-epileptic events during NREM sleep in patients with focal epilepsy: a Stereo-EEG study
T2 - EBioMedicine
J2 - EBioMedicine
PY - 2026
DA - 2026/05/12
VL - 128
SP - 106287
SN - 2352-3964
PB - Elsevier
DO - 10.1016/j.ebiom.2026.106287
UR - https://doi.org/10.1016/j.ebiom.2026.106287
LA - en
ER -

CSL-JSON

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