Frequency-dependent effects of motor thalamus deep brain stimulation on speech and swallowing.
The 9 matches · 1 of them tie a paragraph to a whole file, not to given lines: a weak match, whose lines are not tinted
- [1] § Methods › Kinematic recordings and analysis ↔ Fig2_F_G_Amplitude.m, lines 4–58 · score 0.82 · DeepLabCut, upper lip, lower lip, facial tasks, nose, velocity
- [2] § Methods › Analysis of videofluoroscopic swallow study ↔ InterraterReliabilityMBS.m, lines 1–20 · score 0.79 · interrater reliability, quadratic weighted Cohen, scores, agreement, kappa, Swallowing
- [3] § Methods › Speech assessment › Formant frequencies ↔ fig4C_formantChangePlots.m, lines 1–38 · score 0.71 · vowel phoneme, median filter, formant, spline, warping, pre
- [4] § Methods › Motor-evoked potential experiments ↔ Fig2_B_C_TMS_MEP.m, lines 1–52 · score 0.66 · motor evoked potentials, pulse, TMS, MASS, oris, MEPs
- [5] § Methods › Motor-evoked potential experiments ↔ Fig1_intraOp_comparison_contra_vs_ipsi_muscle.m, lines 1–56 · score 0.64 · stimulation frequencies, MENT, MYLO, CRICO, EMG, MASS
- [6] § Methods › Kinematic recordings and analysis ↔ Fig2_H_plotDLC_area_20230630.m, lines 61–117 · score 0.63 · upper lip, lower lip, nose, cheek, chin, jaw
- [7] § Methods › Motor-evoked potential experiments ↔ Fig2_B_C_TMS_MEP.m, lines 1–52 · score 0.62 · low pass filtered, pulses, TMS, evoke, MEPs, stimulus
- [8] § Methods › Statistical procedures ↔ utilities/bootstrapCompMeans.m, the whole file · a weak match · score 0.60 · confidence interval, replacement, resampling, rejected, alphas, bootstrap
- [9] § Methods › Statistical procedures ↔ Fig2_H_plotDLC_area_20230630.m, lines 327–362 · score 0.59 · confidence interval, replacement, resampling, rejected, alphas, bootstrap
Paper
Loaded from Europe PMC by your browser, not stored by OSCR: doi.org · Europe PMC
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The authors' code
MATLAB · 311 lines · 9.7 KB · MIT · 2 matches
- %% Fig2_B_C_TMS_MEP
- % TMS motor evoked potential (MEP) analysis comparing no-stimulation and
- % DBS conditions across facial and hand muscles.
- %
- % Creates figures 2B and 2C for the manuscript.
- %
- % Generates the following figures:
- % F Per-muscle QC traces: raw vs. low-pass filtered, one figure per condition (not saved)
- % T All traces overlaid per condition, raw and filtered (not saved)
- % G Peak-to-peak and AUC boxplots across conditions
- % V Percentage increase in AUC from no-stim baseline (saved)
- %
- % Required Data:
- % Fig2_B_Nostim.mat TMS recording during no-stimulation condition
- % Fig2_B_55Hz.mat TMS recording during 55 Hz DBS condition
- % Each file contains per-muscle snip arrays and a snipTime vector.
- % MEP data is stored as: Data.(muscleName) — cell array of {avg, snips}
- %
- % User Configuration:
- % pathName Path to the folder containing the .mat data files
- % savePATH Path to the folder where figures will be saved
- % Trial2Load Which body part to analyze: 'Face' or 'Hand'
- % savePlots Set to 1 to save figures as PDF, 0 to skip saving
- %
- % Created by Lilly Tang, Erinn Grigsby, and Arianna Damiani
- % Copyright (C) 2026
- clear, close all
- % Data path information
- curPath = pwd; addpath(genpath(curPath));
- pathName = '/Users/zira/Data/mThal_NatComm_2026';
- savePATH = '/Users/zira/analysisFigures/mThal_NatComm_2026_figs';
- savePlots = 0; % Set to 1 to save figures as PDF
- % General variables for the function
- muscles = {'L_APB' 'L_MASS' 'L_ORIS' 'R_APB' 'R_MASS' 'R_ORIS'};
- stim = {'noStim' '55Hz Tremor'};
- Fs = 2500; % Sampling rate (Hz)
- % Trial2Load selects the body part and sets the MEP time window (in ms)
- % and the .mat filenames to load.
- Trial2Load = 'Face';
- switch Trial2Load
- case 'Face'
- Trial = {'Fig2_B_Nostim','Fig2_B_55Hz'};
- TimeWindow = [75 100]; % MEP window in ms post-TMS pulse
- case 'Hand' % Not used in the current manuscript but code is set up to easily switch to hand data if desired
- Trial = {'5' '13'};
- TimeWindow = [100 140];
- end
- %% Load data
- D = dir(fullfile(pathName,'*.mat'));
- for s = 1:length(Trial)
- for d = 1:size(D,1)
- if contains(D(d).name, Trial{s})
- Data(s) = load(fullfile(D(d).folder, D(d).name));
- end
- end
- end
- % Extract MEP snip traces from the loaded data structs.
- % Each muscle field contains {avg, snips} — index 2 gives the individual trial snips.
- fieldN = fieldnames(Data);
- for m = 1:length(muscles)
- idxM = find(contains(fieldN, muscles{m}));
- if ~isempty(idxM)
- for s = 1:length(Data)
- for i = 1:length(idxM)
- MEPsnips{i} = Data(s).(fieldN{idxM(i)});
- end
- MEPtraces{s,m} = MEPsnips{2}; % Individual trial snips (not the average)
- snipTime{s} = Data(s).snipTime;
- end
- end
- end
- %% Low-pass filter and QC traces
- % Creates one figure per (stim × muscle) for visual inspection. Not saved.
- close all
- count = 1;
- % Compute filter coefficients once
- [Bbp, Abp] = butter(4, 100/(Fs/2), 'low');
- % Iterate through all the muscles and simtimulation parameters
- for s = 1:size(MEPtraces,1)
- for m = 1:size(MEPtraces,2)
- F(count) = figure;
- F(count).Name = sprintf('%s %s Lowpass 100Hz', stim{s}, muscles{m});
- for ii = 1:size(MEPtraces{s,m},1)
- filtMEP{s,m}(ii,:) = filtfilt(Bbp, Abp, MEPtraces{s,m}(ii,:));
- ax(1) = subplot(2,1,1); hold on
- plot(snipTime{s}, MEPtraces{s,m}(ii,:))
- title('Raw')
- ax(2) = subplot(2,1,2); hold on
- plot(snipTime{s}, filtMEP{s,m}(ii,:))
- title('Low-pass (100 Hz)')
- xlabel('Time (ms)')
- % Overlay the trial mean in black on the last rep
- if ii == size(MEPtraces{s,m},1)
- subplot(2,1,1), hold on
- plot(snipTime{s}, mean(MEPtraces{s,m},1), 'LineWidth',2, 'Color','k')
- subplot(2,1,2), hold on
- plot(snipTime{s}, mean(filtMEP{s,m},1), 'LineWidth',2, 'Color','k')
- end
- sgtitle(sprintf('%s %s', muscles{m}, stim{s}), 'Interpreter','none')
- end
- linkaxes(ax, 'xy')
- xlim([60 200])
- count = count + 1;
- end
- end
- %% All traces overlaid per condition
- % Layout: rows = muscles, columns = raw | filtered. Not saved.
- close all
- tracefilt = {'Raw' 'Filtered'};
- for s = 1:size(MEPtraces,1)
- T(s) = figure; hold on
- T(s).Name = sprintf('MEP traces %s', stim{s});
- for f = 1:2
- if f == 1
- traces2Plot = MEPtraces;
- else
- traces2Plot = filtMEP;
- end
- for m = 1:size(traces2Plot,2)
- % figIdx maps (muscle, filter type) to subplot index in a
- % nMuscle × 2 grid (columns = raw/filtered)
- figIdx = (m-1)*2 + f;
- subplot(size(traces2Plot,2), size(traces2Plot,1), figIdx); hold on
- for ii = 1:size(traces2Plot{s,m},1)
- plot(snipTime{s}, traces2Plot{s,m}(ii,:))
- end
- plot(snipTime{s}, mean(traces2Plot{s,m}), 'LineWidth',2, 'Color','k')
- xlabel('Time (ms)')
- if f == 1
- ylabel(muscles{m}, 'Interpreter','none', 'FontWeight','bold')
- end
- if m == 1
- title(tracefilt{f})
- end
- end
- end
- sgtitle(stim{s})
- end
- %% No-stim vs. stim comparison traces
- % Layout: rows = muscles, columns = stim conditions. Not saved.
- close all
- for f = 1:2
- T(f) = figure; hold on
- T(f).Name = sprintf('MEP traces %s', tracefilt{f});
- if f == 1
- traces2Plot = MEPtraces;
- else
- traces2Plot = filtMEP;
- end
- for s = 1:size(traces2Plot,1)
- for m = 1:size(traces2Plot,2)
- % figIdx maps (muscle, stim) to subplot index in a nMuscle × nStim grid
- figIdx = (m-1)*2 + s;
- Tx(figIdx) = subplot(size(traces2Plot,2), size(traces2Plot,1), figIdx); hold on
- for ii = 1:size(traces2Plot{s,m},1)
- plot(snipTime{s}, traces2Plot{s,m}(ii,:))
- end
- plot(snipTime{s}, mean(traces2Plot{s,m}), 'LineWidth',2, 'Color','k')
- xlabel('Time (ms)')
- ylabel(muscles{m}, 'Interpreter','none', 'FontWeight','bold')
- xlim([60 120])
- if m == 1
- title(stim{s})
- end
- end
- end
- % Link axes for each muscle across stim conditions so zoom/pan stays in sync
- nMuscle = size(traces2Plot,2);
- nStim = size(traces2Plot,1);
- for m = 1:nMuscle
- linkaxes(Tx((m-1)*nStim + (1:nStim)));
- end
- sgtitle(tracefilt{f})
- end
- %% Peak-to-peak and AUC within the MEP window
- close all
- for s = 1:size(filtMEP,1)
- for m = 1:size(filtMEP,2)
- % Find time indices corresponding to the MEP window
- [~, startIdx] = min(abs(snipTime{s} - TimeWindow(1)));
- [~, stopIdx] = min(abs(snipTime{s} - TimeWindow(2)));
- for ii = 1:size(filtMEP{s,m},1)
- peakwindow = filtMEP{s,m}(ii, startIdx:stopIdx);
- % Subtract the mean of the first 3 samples as a local baseline,
- % then take absolute value so peak-to-peak is always positive
- adj_peakwindow = abs(peakwindow - mean(peakwindow(1:3)));
- aucMat{s,m}(ii,:) = trapz(adj_peakwindow);
- p2pMat{s,m}(ii,:) = peak2peak(adj_peakwindow);
- end
- % Remove statistical outliers before plotting and computing group stats
- p2pCleaned{s,m} = rmoutliers(p2pMat{s,m});
- aucCleaned{s,m} = rmoutliers(aucMat{s,m});
- end
- end
- ColorMap = {'#0072BD','#D95319','#EDB120','#7E2F8E','#77AC30','#4DBEEE','#A2142F'};
- G(1) = figure;
- G(1).Name = sprintf('P2P %s', Trial2Load);
- for m = 1:size(p2pMat,2)
- Gx(m) = subplot(2,3,m); hold on
- myboxplot(p2pCleaned(:,m), 'box', ColorMap, 1, Gx(m))
- xticks(1:size(p2pMat,1))
- xticklabels(stim)
- title(muscles{m}, 'Interpreter','none')
- end
- sgtitle('Peak-to-Peak MEPs')
- G(2) = figure;
- G(2).Name = sprintf('AUC %s', Trial2Load);
- for m = 1:size(aucMat,2)
- Dx(m) = subplot(2,3,m); hold on
- myboxplot(aucCleaned(:,m), 'box', ColorMap, 1, Dx(m))
- xticks(1:size(aucMat,1))
- xticklabels(stim)
- title(muscles{m}, 'Interpreter','none')
- end
- sgtitle('AUC MEPs')
- %% Percentage increase in AUC from no-stim baseline (Fig 2B, 2C)
- close all
- % Compute mean AUC per (stim, muscle) for normalization
- for s = 1:size(aucCleaned,1)
- for m = 1:size(aucCleaned,2)
- meanAUC(s,m) = mean(aucCleaned{s,m});
- end
- end
- % Individual trial scatter with condition mean
- V(1) = figure;
- V(1).Name = sprintf('Percentage Increase %s pts', Trial2Load);
- for s = 1:size(aucCleaned,1)
- for m = 1:size(aucCleaned,2)
- baselineAUC = meanAUC(1,m); % No-stim mean as baseline
- varAUCmean = (meanAUC(s,m) - baselineAUC) / baselineAUC * 100;
- subplot(2,3,m); hold on
- plot(s, varAUCmean, '-o', 'Color', ColorMap{s})
- for r = 1:length(aucCleaned{s,m})
- varAUC{s,m}(r,1) = (aucCleaned{s,m}(r) - baselineAUC) / baselineAUC * 100;
- plot(s, varAUC{s,m}(r,1), '.', 'Color', ColorMap{s})
- end
- xticks(1:size(aucMat,1))
- xticklabels(stim)
- ylabel('Percentage Increase')
- title(muscles{m}, 'Interpreter','none')
- end
- end
- sgtitle('Percentage Increase TMS')
- % Summary boxplot with bootstrap statistics
- V(2) = figure;
- V(2).Name = sprintf('Percentage Increase %s Stats', Trial2Load);
- for m = 1:size(aucMat,2)
- Vx(m) = subplot(2,3,m); hold on
- myboxplot(varAUC(:,m), 'box', ColorMap, 1, Vx(m))
- xticks(1:size(aucMat,1))
- xticklabels(stim)
- title(muscles{m}, 'Interpreter','none')
- end
- sgtitle('Percentage Increase TMS')
- %% Save
- if savePlots
- if ~exist(savePATH,'dir'), mkdir(savePATH); end
- saveFigurePDF(V, fullfile(savePATH, Trial2Load))
- end
Fig2_B_C_TMS_MEP.m at commit 14655cc, under MIT · at the source
Overview
20 affiliations
- Rehab Neural Engineering Labs, University of Pittsburgh, 1622 Locust St., Floor 4, Pittsburgh, PA USA
- School of Medicine, University of Pittsburgh, 3550 Terrace St, Pittsburgh, PA USA
- Department of Physical Medicine and Rehabilitation, University of Pittsburgh, 3471 Fifth Avenue, Suite 910, Pittsburgh, PA USA
- Department of Neuroscience, University of Montreal, Pavillon Paul-G.-Desmarais, 2960, chemin de la Tour, Room 2140, Montreal, Quebec, Canada
- Department of Bioengineering, University of Pittsburgh, 151 Benedum Hall, Pittsburgh, PA USA
- Department of Neurosurgery, Johns Hopkins University, 1800 Orleans St Sheikh Zayed Tower, Baltimore, MD USA
- Department of Otolaryngology, University of Pittsburgh, Pittsburgh, PA USA
- Department of Neurological Surgery, University of Pittsburgh, Medical Center, 200 Lothrop Street, Suite B-400, Pittsburgh, PA USA
- Department of Psychology, University of Pittsburgh, Pittsburgh, PA USA
- UPMC Voice, Airway, & Swallow Center, UPMC Mercy Hospital, 1400 Locust St., Pittsburgh, PA USA
- Department of Communicative Disorders and Sciences, University at Buffalo, 122 Cary Hall, South Campus, Buffalo, NY USA
- University of Pittsburgh Clinical and Translational Science Institute (CTSI), Pittsburgh, PA USA
- Department of Neurology, University of Pittsburgh, 3471 Fifth Avenue Ste 802, Pittsburgh, PA USA
- TECH-GRECC & HERL, VA Pittsburgh Healthcare System, University Dr., Pittsburgh, PA USA
- Center for the Neural Basis of Cognition, 4400 Fifth Avenue, Suite 115, Pittsburgh, PA USA
- Department of Psychology, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA USA
- Neuroscience Institute, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA USA
- Department of Communication Sciences & Disorders, University of Pittsburgh, Pittsburgh, PA USA
- Department of Neuroscience, University of Pittsburgh, Pittsburgh, PA USA
- Department of Neurobiology, University of Pittsburgh, 200 Lothrop Street, Room E1440, Pittsburgh, PA USA
Abstract
The abstract is not reproduced here: the paper's license (CC BY-NC-ND) does not allow it. Read it in the paper, at the publisher or on Europe PMC.
Repository
Its files are read in the Code ↔ Paper reader above, with 9 matches between paragraphs and lines of code.
emg27/mThal_Face_2026
14655cc1b626eb0c5f44914a1fbb765e31782e89, 27 May 2026Availability: 1 check, the latest on 27 September 2026: the link answers
- 27 September 2026: the link answers
28 files
- +XLTEK/
export.m , MATLAB, 36 lines - Fig1_G_FrequencyDependen
tClassification.m , MATLAB, 112 lines - Fig1_intraOp_20230615_fa
ce.m , MATLAB, 167 lines - Fig1_intraOp_comparison_
contra_vs_ipsi_muscle.m , MATLAB, 348 lines, 1 match - Fig2_B_C_TMS_MEP.m, MATLAB, 311 lines, 2 matches
- Fig2_F_G_Amplitude.m, MATLAB, 253 lines, 1 match
- Fig2_H_plotDLC_area_2023
0630.m , MATLAB, 389 lines, 2 matches - Fig2_I_plotDLC_area_grou
p.m , MATLAB, 33 lines - Fig2_I_plotDLC_velocity_
group.m , MATLAB, 33 lines - Fig4_articulateFrequency
Phoneme_bySessions.m , MATLAB, 207 lines - Fig4_compare_cppData.m, MATLAB, 397 lines
- Fig4_plotIntensityScatte
rPlot.m , MATLAB, 157 lines - Fig4_plot_intensity.m, MATLAB, 122 lines
- Fig4_voiceBreaks.m, MATLAB, 179 lines
- Fig5_A_C_plotDLC_area_20
230630.m , MATLAB, 389 lines - InterraterReliabilityMBS
.m , MATLAB, 80 lines, 1 match - InterraterReliabilitySpe
ech.m , MATLAB, 55 lines - SupFig4_B_plotDLClateral
ity_20241204.m , MATLAB, 413 lines - fig4C_formantChangePlots
.m , MATLAB, 416 lines, 1 match - plotDLC_kinematics_Metri
cs.m , MATLAB, 1 line - utilities/
bootstrapCompMeans.m , MATLAB, 61 lines, 1 match - utilities/
calcFigureSize.m , MATLAB, 26 lines - utilities/
matchAxis.m , MATLAB, 97 lines - utilities/
myboxplot.m , MATLAB, 384 lines - utilities/
plotStatComparisons.m , MATLAB, 127 lines - utilities/
subplotSimple.m , MATLAB, 87 lines - LICENSE, License, 21 lines
- README.md, Text, 6 lines
Code availability statement
The paper has a code availability statement. Its license (CC BY-NC-ND) does not allow reproducing it here; in short, from what the harvester recognized in it:
- it points to the authors' code: emg27/
mThal_Face_2026
Read it in the paper: doi.org/10.1038/s41467-026-75588-3.
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;
- 26 scripts, each with its path and the digest of its content;
- 9 matches 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
Datasets cited
- zenodo:20091706, at Zenodo; found in “Data availability”
Data availability statement
The paper has a data availability statement. Its license (CC BY-NC-ND) does not allow reproducing it here; in short, from what the harvester recognized in it:
- it points to a dataset: Zenodo 20091706
- it says that the data are available on request
Read it in the paper: doi.org/10.1038/s41467-026-75588-3.
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, 22 authors, 2 keywords, 13 MeSH terms, 1 funder, 90 references.
Cite
This paper
Tang, L. W., Grigsby, E. M., Damiani, A., Ho, J. C., Montanaro, I. M., Nouduri, S., Ensel, S., Trant, S., Constantine, T., Adams, G. M., Balason, D. V., Thomas, T. L., Zdrowak, K., Ting, J., Wittenberg, G. F., Franzese, K., Mahon, B. Z., Fiez, J. A., Crammond, D. J., . . . Pirondini, E. (2026). Frequency-dependent effects of motor thalamus deep brain stimulation on speech and swallowing. Nature communications, 17(1), 8794. https://
BibTeX
@article{tang2026frequen
author = {Tang, Lilly W and Grigsby, Erinn M and Damiani, Arianna and Ho, Jonathan C and Montanaro, Isabella M and Nouduri, Sirisha and Ensel, Scott and Trant, Sara and Constantine, Theodora and Adams, Gregory M and Balason, Denise V and Thomas, Tracey L and Zdrowak, Kelly and Ting, Jordyn and Wittenberg, George F and Franzese, Kevin and Mahon, Bradford Z and Fiez, Julie A and Crammond, Donald J and Stipancic, Kaila L and Gonzalez-Martinez, Jorge A and Pirondini, Elvira},
title = {{Frequency-dependent effects of motor thalamus deep brain stimulation on speech and swallowing}},
journal = {Nature communications},
year = {2026},
month = jul,
volume = {17},
number = {1},
pages = {8794},
publisher = {Nature Publishing Group},
issn = {2041-1723},
doi = {10.1038/
url = {https://
pmid = {42471326},
pmcid = {PMC13493936}
}
RIS
TY - JOUR
AU - Tang, Lilly W
AU - Grigsby, Erinn M
AU - Damiani, Arianna
AU - Ho, Jonathan C
AU - Montanaro, Isabella M
AU - Nouduri, Sirisha
AU - Ensel, Scott
AU - Trant, Sara
AU - Constantine, Theodora
AU - Adams, Gregory M
AU - Balason, Denise V
AU - Thomas, Tracey L
AU - Zdrowak, Kelly
AU - Ting, Jordyn
AU - Wittenberg, George F
AU - Franzese, Kevin
AU - Mahon, Bradford Z
AU - Fiez, Julie A
AU - Crammond, Donald J
AU - Stipancic, Kaila L
AU - Gonzalez-Martinez, Jorge A
AU - Pirondini, Elvira
TI - Frequency-dependent effects of motor thalamus deep brain stimulation on speech and swallowing
T2 - Nature communications
J2 - Nat Commun
PY - 2026
DA - 2026/
VL - 17
IS - 1
SP - 8794
SN - 2041-1723
PB - Nature Publishing Group
DO - 10.1038/
UR - https://
LA - en
ER -
CSL-JSON
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