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Flexible ultrasound array for subcortical brain stimulation in humans: a simulation study.

Code ↔ Paper

4 matches between paragraphs of the paper and lines of its authors' code, computed by the harvester (lexical-v1). Click a colored paragraph or line to see its counterpart.

The 4 matches · 2 of them tie a paragraph to a whole file without given lines: weak matches, whose lines are not tinted
  1. [1] § Methods › Modeling tFUS wave propagation ↔ forwardSimulation.m, the whole file · a weak match · score 0.81 · pstdElastic3D, element position, sub elements, CFL, delay, medium · Report a mismatch
  2. [2] § Results › Numerical simulation setup ↔ FlexibleArray.m, lines 12 to 41 · score 0.73 · cerebrospinal fluid, human brain, slices, thickness, segmented, scalp · Report a mismatch
  3. [3] § Results › Numerical simulation setup ↔ forwardSimulation.m, the whole file · a weak match · score 0.55 · acoustic parameters, bone, signal, compression, cycles, water · Report a mismatch
  4. [4] § Results › Numerical simulation setup ↔ FlexibleArray.m, lines 12 to 41 · score 0.54 · cerebrospinal fluid, human brain, scalp, MRI, flexible, skull · Report a mismatch

Paper

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The authors' code

MATLAB · 90 lines · 3.2 KB · AGPL-3.0 · 2 matches

  1. function [sensorDataSumGPU, p_max_all_cut, target_point] = forwardSimulation(medium, Element, sim_vol, kgrid, sensor, input_args)
  2. %% Forward Simulation - Single Emission, Single Focusing
  3. % One transmit with all array elements focusing at a single target point
  5. Nx = kgrid.Nx;
  6. Ny = kgrid.Ny;
  7. Nz = kgrid.Nz;
  9. % Element positions
  10. CoorList = Element.CoorList;
  11. CoorSubList = Element.CoorSubList;
  12. NumSensors = size(CoorList, 1);
  13. SubElementNum = size(CoorSubList, 2);
  15. % Acoustic parameters
  16. sos = 1500; % speed of sound in water [m/s]
  17. sos_bone = 2820; % speed of sound in bone [m/s]
  18. cfl = 0.05;
  19. t_end = 1e-4; % [s]
  20. kgrid.makeTime(max(medium.sound_speed_compression(:)), cfl, t_end);
  22. %% Define focus target point
  23. center_inds = [5, floor(Ny/2), floor(Nz/2)];
  24. xc = find(sim_vol(:, center_inds(2), center_inds(3)) == 3, 1, 'first');
  25. yc = center_inds(2);
  26. zc = center_inds(3);
  28. targetDepth = floor(0.04 / kgrid.dx);
  29. target_point = [xc + targetDepth, yc, zc];
  31. %% Emit mask - all sensors participate in single transmission
  32. Emit_Mask_Grid = CoorList;
  33. Emit_Mask_Sub_Grid = CoorSubList;
  34. Emit_Mask_Sub_Idx = zeros(size(Emit_Mask_Sub_Grid));
  36. % Convert sub-element coordinates to linear indices
  37. for row = 1:size(Emit_Mask_Sub_Idx, 1)
  38. for col = 1:size(Emit_Mask_Sub_Idx, 2)
  39. ElemSub = cell2mat(Emit_Mask_Sub_Grid(row, col));
  40. Emit_Mask_Sub_Idx(row, col) = sub2ind(size(sensor.mask), ElemSub(1), ElemSub(2), ElemSub(3));
  41. end
  42. end
  44. source.u_mask = zeros(kgrid.Nx, kgrid.Ny, kgrid.Nz);
  45. source.u_mask(Emit_Mask_Sub_Idx(:)) = 1;
  47. %% Compute delay for each element (skull compensation)
  48. skull = zeros(size(sim_vol));
  49. wb = waitbar(0, 'Calculating delay for focusing...');
  51. DelayIdxList = zeros(1, NumSensors * SubElementNum);
  52. for idelay = 1:NumSensors
  53. EmitGrid = Emit_Mask_Grid(idelay, :);
  54. [SkullDepth, idx_near, idx_far] = CalculateSkullDepth(EmitGrid, target_point, sim_vol);
  55. dis_target_sensor = sqrt(sum((EmitGrid - target_point).^2));
  56. time1 = (dis_target_sensor - SkullDepth) * kgrid.dx / (sos * kgrid.dt);
  57. time2 = SkullDepth * kgrid.dx / (sos_bone * kgrid.dt);
  58. DelayIdxList((idelay-1)*SubElementNum + 1 : idelay*SubElementNum) = ceil(time1 + time2);
  59. skull(idx_near) = 1;
  60. skull(idx_far) = 1;
  61. waitbar(idelay / NumSensors, wb, sprintf('Calculating... %.0f%%', 100*idelay/NumSensors));
  62. end
  64. % Normalize delay (reverse for focusing)
  65. DelayIdxList = DelayIdxList - min(DelayIdxList);
  66. DelayIdxList = max(DelayIdxList) - DelayIdxList;
  68. [~, sort_idx] = sort(reshape(Emit_Mask_Sub_Idx.', 1, []));
  69. DelayIdxSorted = DelayIdxList(sort_idx);
  71. close(wb);
  73. %% Define source signal
  74. tone_burst_freq = sensor.frequency_response(1); % [Hz]
  75. tone_burst_cycles = 10;
  76. input_signal = toneBurst(1/kgrid.dt, tone_burst_freq, tone_burst_cycles, 'SignalOffset', DelayIdxSorted);
  78. source_mag = 0.15; % [m/s]
  79. source.ux = source_mag .* input_signal;
  80. source.uy = source_mag .* input_signal;
  81. source.uz = source_mag .* input_signal;
  83. %% Run elastic wave simulation
  84. sensor.record = {'p_max_all'};
  85. sensorDataSumGPU = pstdElastic3D(kgrid, medium, source, sensor, input_args{:});
  87. %% Post-process: mask to brain region
  88. p_max_all = gather(sensorDataSumGPU.p_max_all);
  89. mask_brain = (sim_vol ~= 0);
  90. p_max_all_cut = p_max_all .* mask_brain;

forwardSimulation.m at commit df3fe7b, under AGPL-3.0 · at the source

Overview

Authors: Haoming Huo1, Anthony DiSpirito1, Nanchao Wang1, Chenhang Li2, Sunho Moon3, Chaorui Qiu2, Kaiping Yin2, Huaiyu Wu3, Bin Sun1, Roarke Horstmeyer1, Wuwei Feng4, Xiaoning Jiang3,4, Xiaoyue Ni2, Junjie Yao1,4
ORCID iDs: Huaiyu Wu
  1. Department of Biomedical Engineering, Duke University, Durham, NC USA
  2. Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC USA
  3. Department of Mechanical and Aerospace Engineering, North Carolina State University, Raleigh, NC USA
  4. Department of Neurology, Duke University School of Medicine, Durham, NC USA
Institutions: Duke University (United States); North Carolina State University (United States)
Journal: NPJ acoustics, volume 2, issue 1, article 11
Dates: received 7 May 2025; accepted 10 February 2026; published online 30 March 2026; in print 2026
Type: Research article · Language: English
License: CC BY-NC-ND
Identifiers: DOI 10.1038/s44384-026-00046-9 · PMID 41924435 · PMCID PMC13035476 · OpenAlex W7143468789
Open access: hybrid, a free copy (OpenAlex)
Status: code verified (how the code is found and verified)
Categories: other (modality), human (organism), computational (subfield)
Methods: fMRI & imaging
Keywords: Electrical and electronic engineering, Neuroscience, Techniques and instrumentation
Topic: Ultrasound and Hyperthermia Applications (Biomedical Engineering, Engineering), according to OpenAlex
Funding: Duke University Pratt Beyond the Horizon Grant; National Science Foundation; Duke Coulter Translational Grant; North Carolina Biotechnology Center Triangle Research Grant; Eli Lilly Research Award Program; National Institutes of Health; American Heart Association Collaborative Science Award; Chan Zuckerberg Initiative Grant; Duke University DST Spark Seed Grant
Citations: cited by 1 paper (Europe PMC); 70 references in the paper

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 4 matches between paragraphs and lines of code.

gitlab.oit.duke.edu/pilab/flexible-array-simulation

License: AGPL-3.0
State: the link answers, verified on 30 September 2026
Evidence: files inventoried
Commit: df3fe7b569932e7a30c4e20f1bd7ad0a89055f4a, 17 February 2026
Languages: MATLAB (7)
Size: 14 files, 7 scripts
Software Heritage: not archived
Found in: “Code availability”
Holds: README, license file
Not found: CITATION.cff, environment file, tests, continuous integration, documentation
Tools: Image Processing Toolbox (1 file), Statistics and Machine Learning Toolbox (1 file)
Availability: 1 check, the latest on 30 September 2026: the link answers
  • 30 September 2026: the link answers
9 files
At the source: gitlab.oit.duke.edu/pilab/flexible-array-simulation

Code availability statement

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Read it in the paper: doi.org/10.1038/s44384-026-00046-9.

Tracing map

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

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Versions

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Version 1, 30 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 14 authors, 3 keywords, 8 funders, 60 references.

Cite

This paper

Huo, H., DiSpirito, A., Wang, N., Li, C., Moon, S., Qiu, C., Yin, K., Wu, H., Sun, B., Horstmeyer, R., Feng, W., Jiang, X., Ni, X., & Yao, J. (2026). Flexible ultrasound array for subcortical brain stimulation in humans: a simulation study. NPJ acoustics, 2(1), 11. https://doi.org/10.1038/s44384-026-00046-9

BibTeX

@article{huo2026flexible,
author = {Huo, Haoming and DiSpirito, Anthony and Wang, Nanchao and Li, Chenhang and Moon, Sunho and Qiu, Chaorui and Yin, Kaiping and Wu, Huaiyu and Sun, Bin and Horstmeyer, Roarke and Feng, Wuwei and Jiang, Xiaoning and Ni, Xiaoyue and Yao, Junjie},
title = {{Flexible ultrasound array for subcortical brain stimulation in humans: a simulation study}},
journal = {NPJ acoustics},
year = {2026},
month = mar,
volume = {2},
number = {1},
pages = {11},
publisher = {Springer Science+Business Media},
issn = {3005-141X},
doi = {10.1038/s44384-026-00046-9},
url = {https://doi.org/10.1038/s44384-026-00046-9},
pmid = {41924435},
pmcid = {PMC13035476}
}

RIS

TY - JOUR
AU - Huo, Haoming
AU - DiSpirito, Anthony
AU - Wang, Nanchao
AU - Li, Chenhang
AU - Moon, Sunho
AU - Qiu, Chaorui
AU - Yin, Kaiping
AU - Wu, Huaiyu
AU - Sun, Bin
AU - Horstmeyer, Roarke
AU - Feng, Wuwei
AU - Jiang, Xiaoning
AU - Ni, Xiaoyue
AU - Yao, Junjie
TI - Flexible ultrasound array for subcortical brain stimulation in humans: a simulation study
T2 - NPJ acoustics
J2 - NPJ Acoust
PY - 2026
DA - 2026/03/30
VL - 2
IS - 1
SP - 11
SN - 3005-141X
PB - Springer Science+Business Media
DO - 10.1038/s44384-026-00046-9
UR - https://doi.org/10.1038/s44384-026-00046-9
LA - en
ER -

CSL-JSON

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"container-title": "NPJ acoustics",
"author": [
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},
{
"family": "Wu",
"given": "Huaiyu"
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{
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"container-title-short": "NPJ Acoust",
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