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Thalamocortical seizure onset patterns in drug-resistant focal epilepsy.

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  1. [1] § Results › Patient and seizure characteristics ↔ get_amps5.m, lines 121–142 · score 0.73 · Grand av, sEEG1, voltage amplitude, S2L, S2R, RMS

Paper

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The authors' code

MATLAB · 165 lines · 4 KB · no license · 1 match

  1. %Script for plotting RMS amplitudes of cortical SOZ vs thalamus
  2. % Hugh Simpson
  3. % V1: Dec 2021
  4. % V2: Sep-Oct 2023
  5. % V3: Aug 2025
  7. figdir = 'my_dir';
  9. %load RCS_main_vars_2025-02-15.mat %Reproduces MS fig
  10. %load IRB_main_vars_2025-02-14_new.mat
  11. load RCS_main_vars_2025-08-04_new.mat
  12. load IRB_main_vars_2025-08-04_new.mat
  14. %Inputs: amp_IRB cell
  15. n_IRB = 10;
  16. n_RCS = 4;
  18. amp_IRB_all = []; %All sz in one matrix
  19. amp_RCS_all = []; %All sz in one matrix
  21. hFigSpec = figure;
  22. %set(hFigSpec, 'Position', [200 100 1200 800])
  23. mark_sz = 8;
  25. hold on
  27. %% IRB sEEG first:
  28. mc = zeros(1,n_IRB); %mean_cortex
  29. sc = zeros(1,n_IRB); %std_cortex
  30. mt = zeros(1,n_IRB); %mean_thal
  31. st = zeros(1,n_IRB); %std_cx
  32. %amp_IRB_cum = [];
  34. for i=1:n_IRB
  36. c0 = log10(amp_IRB{i}(:,1));
  37. mc0 = mean(c0,'omitnan');
  38. sc0 = std(c0,'omitnan')./sqrt(size(c0,1));
  39. mc(i) = mc0; sc(i) = sc0;
  41. t0 = log10(amp_IRB{i}(:,2));
  42. mt0 = mean(t0,'omitnan');
  43. st0 = std(t0,'omitnan')./sqrt(size(t0,1));
  44. mt(i) = mt0; st(i) = st0;
  46. amp_IRB_all = [amp_IRB_all ; amp_IRB{i}];
  48. end
  50. %All IRB/sEEG subj
  51. c0 = log10(amp_IRB_all(:,1));
  52. mc0 = mean(c0,'omitnan');
  53. sc0 = std(c0,'omitnan')./sqrt(size(c0,1));
  55. t0 = log10(amp_IRB_all(:,2));
  56. mt0 = mean(t0,'omitnan');
  57. st0 = std(t0,'omitnan')./sqrt(size(t0,1));
  59. x = [1 2]; y = [mc0 mt0]; err = [sc0 st0];
  61. %Plot
  62. errorbar(1:n_IRB+1,[mc mc0],[sc sc0],'r*','MarkerSize',mark_sz)
  63. errorbar(1:n_IRB+1,[mt mt0],[st st0],'b*','MarkerSize',mark_sz)
  65. %% RC+S now:
  66. mc = zeros(1,n_RCS); %mean_cortex
  67. sc = zeros(1,n_RCS); %std_cortex
  68. mt = zeros(1,n_RCS); %mean_thal
  69. st = zeros(1,n_RCS); %std_cx
  70. %amp_IRB_cum = [];
  72. for i=1:n_RCS
  74. c0 = log10(amp_RCS{i}(:,1));
  75. mc0 = mean(c0,'omitnan');
  76. sc0 = std(c0,'omitnan')./sqrt(size(c0,1));
  77. mc(i) = mc0; sc(i) = sc0;
  79. t0 = log10(amp_RCS{i}(:,2));
  80. mt0 = mean(t0,'omitnan');
  81. st0 = std(t0,'omitnan')./sqrt(size(t0,1));
  82. mt(i) = mt0; st(i) = st0;
  84. amp_RCS_all = [amp_RCS_all ; amp_RCS{i}];
  86. end
  88. %All RC+S subj
  89. c0 = log10(amp_RCS_all(:,1));
  90. mc0 = mean(c0,'omitnan');
  91. sc0 = std(c0,'omitnan')./sqrt(size(c0,1));
  93. t0 = log10(amp_RCS_all(:,2));
  94. mt0 = mean(t0,'omitnan');
  95. st0 = std(t0,'omitnan')./sqrt(size(t0,1));
  97. x = [1 2]; y = [mc0 mt0]; err = [sc0 st0];
  99. %Plot
  100. errorbar(n_IRB+2:n_IRB+n_RCS+2,[mc mc0],[sc sc0],'r*','MarkerSize',mark_sz)
  101. errorbar(n_IRB+2:n_IRB+n_RCS+2,[mt mt0],[st st0],'b*','MarkerSize',mark_sz)
  103. %% Grand average
  104. amp_all = [amp_IRB_all ; amp_RCS_all ];
  106. %All subj
  107. c0 = log10(amp_all(:,1));
  108. mc0 = mean(c0,'omitnan');
  109. sc0 = std(c0,'omitnan')./sqrt(size(c0,1));
  111. t0 = log10(amp_all(:,2));
  112. mt0 = mean(t0,'omitnan');
  113. st0 = std(t0,'omitnan')./sqrt(size(t0,1));
  115. %x = [1 2]; y = [mc0 mt0]; err = [sc0 st0];
  117. %Plot
  118. errorbar(n_IRB+n_RCS+3,mc0,sc0,'r*','MarkerSize',mark_sz)
  119. errorbar(n_IRB+n_RCS+3,mt0,st0,'b*','MarkerSize',mark_sz)
  121. %% Adjust axes and labels
  122. xlim([0.5 17.5]),
  123. xticks(0:19),xticklabels({' ','sEEG1','sEEG2','sEEG3','sEEG4','sEEG5','sEEG6','sEEG7','sEEG8',...
  124. 'sEEG9','sEEG10','sEEG - av','RC+S1','RC+S2L','RC+S2R','RC+S3','RC+S - av','Grand av',' '});
  125. xline(10.5,'--k')
  126. xline(11.5,'-k')
  127. xline(15.5,'--k')
  128. xline([16.5 17.5],'-k')
  129. hold off
  131. set(gca,'FontSize',16)
  133. %xlabel('Subject ID','FontSize',12)
  134. ylabel('log10 RMS amplitude (uV)','FontSize',17);
  135. legend('Cortical SOZ','Thalamus','Location','northeast')
  136. %title('Ictal RMS voltage amplitudes','FontSize',14)
  137. ylim([1 3.5])
  140. saveas(gcf,'filename')
  142. %return
  144. %%Stats time
  147. amp_cx = amp_all(:,1);
  148. amp_th = amp_all(:,2);
  149. %remove NaNs frmo thalamus:
  150. amp_th = amp_th(~isnan(amp_th));
  152. % Median
  153. median1 = median(amp_cx), mean1 = mean(amp_cx)
  154. median2 = median(amp_th), mean2 = mean(amp_th)
  156. % IQR
  157. iqr1 = iqr(log(amp_cx)), q1 = quantile(amp_cx, [0.25 0.75])
  158. iqr2 = iqr(amp_th), q2 = quantile(amp_th, [0.25 0.75])
  160. % Range
  161. range1 = [min(amp_cx), max(amp_cx)]
  162. range2 = [min(amp_th), max(amp_th)]
  164. %Mann-Whitney U:
  165. [p,h,stats] = ranksum(amp_cx,amp_th)

get_amps5.m at commit 0cf18ff, no license · at the source

Overview

Authors: Hugh D Simpson1,2,3, Vaclav Kremen1,4,5, Vladimir Sladky1,4,5, Benjamin H Brinkmann1, Nicholas M Gregg1, Brian N Lundstrom1, Kai J Miller6, Jamie J Van Gompel6, Gregory A Worrell1
ORCID iDs: Hugh D Simpson, Vaclav Kremen, Vladimir Sladky, Benjamin H Brinkmann, Nicholas M Gregg, Brian N Lundstrom, Kai J Miller
  1. Department of Neurology, Mayo Clinic, Rochester, MN 55905, USA
  2. Department of Neurology, The Alfred Hospital, Melbourne, VIC 3004, Australia
  3. Department of Neuroscience, Monash University, Melbourne, VIC 3004, Australia
  4. Czech Institute of Informatics, Robotics, and Cybernetics, Czech Technical University in Prague, Prague 16000, Czech Republic
  5. Department of Natural Sciences, Faculty of Biomedical Engineering, Czech Technical University in Prague, Kladno 27201, Czech Republic
  6. Department of Neurosurgery, Mayo Clinic, Rochester, MN 55905, USA
Institutions: Mayo Clinic (United States); The Alfred Hospital (Australia); Monash University (Australia); Czech Technical University in Prague (Czechia)
Journal: Brain communications, volume 8, issue 4, article fcag227
Dates: received 7 October 2025; accepted 2 April 2026; published online 19 June 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1093/braincomms/fcag227 · PMID 42396599 · PMCID PMC13326942 · OpenAlex W4409569684
Open access: gold, a free copy (OpenAlex)
Preprint: doi:10.1101/2025.04.11.25325282
Status: code verified
Categories: EEG (modality), epilepsy (population)
Methods: Statistics, Physiology & signal measures
Keywords: epilepsy, neurostimulation, thalamus, EEG, seizure
Topic: EEG and Brain-Computer Interfaces (Cognitive Neuroscience, Neuroscience), according to OpenAlex
Funding: NIH (UH3-NS095495); Neurophysiologically Based Brain State Tracking & Modulation in Focal Epilepsy; European Union’s HORIZON EUROPE (101136607)
Citations: cited by 1 paper (Europe PMC); 30 references in the paper

Abstract

Drug-resistant epilepsy affects tens of millions of people worldwide and is associated with considerable morbidity and mortality. Thalamic deep brain stimulation and cortical responsive neurostimulation are proven treatments for focal epilepsy. Both have been used to target a range of thalamic nuclei; yet, the roles of these thalamic nuclei in focal seizure generation remain incompletely understood. Thirteen patients with drug-resistant focal epilepsy undergoing intracranial EEG were consented to undergo investigation of thalamocortical networks. Sampled regions included cortical, mesial temporal, and thalamic brain regions. Visual and spectral analyses were performed to identify seizure onset patterns and correlate thalamic and cortical seizure activity. Thalamic ictal discharges were observed in 89% of seizures. Of these, 56% demonstrated synchronous thalamocortical activity with distinct patterns. These onset patterns included hypersynchronous spiking, low-voltage fast activity, ictal baseline shifts, and broadband suppression. Multiple thalamic nuclei were involved in ictal organization and propagation, with the specific nuclei depending on the cortical seizure network. The thalamus plays a crucial role in focal onset seizure generation and propagation, with distinct seizure onset patterns and nuclei involved. These findings support exploring a broader range of thalamic nuclei in epilepsy neurostimulation and have implications for seizure detection settings in intracranial sensing devices.

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

Repository

Its files are read in the Code ↔ Paper reader above, with 1 match between paragraphs and lines of code.

hdsimpson/tsr-analysis-2026

License: none: the authors keep all their rights
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: 0cf18ff7914c69a1365d96d5cd76096ba9f4902c, 9 March 2026
Languages: MATLAB (7)
Size: 7 files, 7 scripts
Software Heritage: not archived
Found in: “Data availability”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: Signal Processing Toolbox (5 files), Statistics and Machine Learning Toolbox (3 files)
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
7 files
At the source: github.com/hdsimpson/tsr-analysis-2026

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

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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;
  • 7 scripts, each with its path and the digest of its content;
  • 1 match between paragraphs of the paper and lines of the code (method lexical-v1);
  • 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 availability

The source data for the results presented in this manuscript are available from the authors on reasonable request. Code used to analyse and visualize the data is available at: https://github.com/hdsimpson/tsr-analysis-2026.

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 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 9 authors, 5 keywords, 3 funders, 30 references.

Cite

This paper

Simpson, H. D., Kremen, V., Sladky, V., Brinkmann, B. H., Gregg, N. M., Lundstrom, B. N., Miller, K. J., Van Gompel, J. J., & Worrell, G. A. (2026). Thalamocortical seizure onset patterns in drug-resistant focal epilepsy. Brain communications, 8(4), fcag227. https://doi.org/10.1093/braincomms/fcag227

BibTeX

@article{simpson2026thalamocortical,
author = {Simpson, Hugh D and Kremen, Vaclav and Sladky, Vladimir and Brinkmann, Benjamin H and Gregg, Nicholas M and Lundstrom, Brian N and Miller, Kai J and Van Gompel, Jamie J and Worrell, Gregory A},
title = {{Thalamocortical seizure onset patterns in drug-resistant focal epilepsy}},
journal = {Brain communications},
year = {2026},
month = jun,
volume = {8},
number = {4},
pages = {fcag227},
publisher = {Oxford University Press},
issn = {2632-1297},
doi = {10.1093/braincomms/fcag227},
url = {https://doi.org/10.1093/braincomms/fcag227},
pmid = {42396599},
pmcid = {PMC13326942}
}

RIS

TY - JOUR
AU - Simpson, Hugh D
AU - Kremen, Vaclav
AU - Sladky, Vladimir
AU - Brinkmann, Benjamin H
AU - Gregg, Nicholas M
AU - Lundstrom, Brian N
AU - Miller, Kai J
AU - Van Gompel, Jamie J
AU - Worrell, Gregory A
TI - Thalamocortical seizure onset patterns in drug-resistant focal epilepsy
T2 - Brain communications
J2 - Brain Commun
PY - 2026
DA - 2026/06/19
VL - 8
IS - 4
SP - fcag227
SN - 2632-1297
PB - Oxford University Press
DO - 10.1093/braincomms/fcag227
UR - https://doi.org/10.1093/braincomms/fcag227
LA - en
ER -

CSL-JSON

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"title": "Thalamocortical seizure onset patterns in drug-resistant focal epilepsy",
"container-title": "Brain communications",
"author": [
{
"family": "Simpson",
"given": "Hugh D"
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{
"family": "Kremen",
"given": "Vaclav"
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{
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"PMID": "42396599",
"PMCID": "PMC13326942",
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"date-parts": [
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19
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}

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