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Multi-focal ultrasound neuromodulation to the dorsal anterior cingulate cortex disrupts behavioural and neural pain processing.

Code ↔ Paper

2 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 2 matches · all tie a paragraph to a whole file, not to given lines: weak matches, whose lines are not tinted
  1. [1] § Methods › Statistical analysis ↔ scripts_for_analysis/fmri_code_osf.sh, the whole file · a weak match · score 0.79 · Motion outliers, FSL, TE2, timeseries, mask, segmentations
  2. [2] § Methods › Statistical analysis ↔ scripts_for_analysis/mrs_output_analysis_osf.R, the whole file · a weak match · score 0.53 · Glx ratio, Gannet, GLM, GABA, fit, age

Paper

Loaded from Europe PMC by your browser, not stored by OSCR: doi.org · Europe PMC

The paper is loaded when this pane is shown.

The authors' code

Shell · 60 lines · 3.3 KB · no license · 1 match

  1. #!/bin/bash
  3. # insert code to loop through subjects, sessions and runs
  4. # STEP 1: RUN FEAT PREPROCESSING
  6. # navigate to subject and session directoy
  7. cd /media/STUDY-HP-FouE-TP-150823/TE2_analysis/${subj}/${ses}
  9. # run feat preprocessing
  10. # NOTE: example design.fsf listed here must have same parameters as the subj input - check TE
  11. cp /media/STUDY-HP-FouE-TP-150823/TE2_analysis/TUSPAIN01/session01/func_task-rest_run-01_e2.feat/design.fsf .
  12. sed -i "s|TUSPAIN01|${subj}|g" design.fsf
  13. sed -i "s|session01|${ses}|g" design.fsf
  14. feat design.fsf
  17. # insert code to loop through subjects, sessions and runs
  18. # STEP 2: CONFOUND REMOVAL
  20. # segment T1w image into tissue classes
  21. fast -g T1_biascorr_brain.nii.gz
  23. # identify outliers in fmri data
  24. fsl_motion_outliers -i func_task-rest_run-01_e2.nii.gz -o motionoutliers_run-01.dat --dummy=0
  25. fsl_motion_outliers -i func_task-rest_run-03_e2.nii.gz -o motionoutliers_run-03.dat --dummy=0
  27. # get avg CSF and WM timeseries_run-01
  28. flirt -in T1_biascorr_brain_pve_0.nii.gz -ref func_task-rest_run-01_e2.feat/example_func.nii.gz -applyxfm -init func_task-rest_run-01_e2.feat/reg/highres2example_func.mat -out csf_run-01.nii.gz
  29. flirt -in T1_biascorr_brain_pve_2.nii.gz -ref func_task-rest_run-01_e2.feat/example_func.nii.gz -applyxfm -init func_task-rest_run-01_e2.feat/reg/highres2example_func.mat -out wm_run-01.nii.gz
  30. fslmaths csf_run-01.nii.gz -thr 0.95 -bin csf_mask_run-01.nii.gz
  31. fslmaths wm_run-01.nii.gz -thr 0.95 -bin wm_mask_run-01.nii.gz
  32. fslmeants -i func_task-rest_run-01_e2.feat/filtered_func_data.nii.gz -o csfavg_run-01.dat -m csf_mask_run-01.nii.gz
  33. fslmeants -i func_task-rest_run-01_e2.feat/filtered_func_data.nii.gz -o wmavg_run-01.dat -m wm_mask_run-01.nii.gz
  35. # get avg CSF and WM timeseries_run-03
  36. flirt -in T1_biascorr_brain_pve_0.nii.gz -ref func_task-rest_run-03_e2.feat/example_func.nii.gz -applyxfm -init func_task-rest_run-03_e2.feat/reg/highres2example_func.mat -out csf_run-03.nii.gz
  37. flirt -in T1_biascorr_brain_pve_2.nii.gz -ref func_task-rest_run-03_e2.feat/example_func.nii.gz -applyxfm -init func_task-rest_run-03_e2.feat/reg/highres2example_func.mat -out wm_run-03.nii.gz
  38. fslmaths csf_run-03.nii.gz -thr 0.95 -bin csf_mask_run-03.nii.gz
  39. fslmaths wm_run-03.nii.gz -thr 0.95 -bin wm_mask_run-03.nii.gz
  40. fslmeants -i func_task-rest_run-03_e2.feat/filtered_func_data.nii.gz -o csfavg_run-03.dat -m csf_mask_run-03.nii.gz
  41. fslmeants -i func_task-rest_run-03_e2.feat/filtered_func_data.nii.gz -o wmavg_run-03.dat -m wm_mask_run-03.nii.gz
  44. # extract mean timeseries from dACC
  45. fslmeants -i func_task-rest_run-01_e2.feat/filtered_func_data.nii.gz -o clean_3dACC_func_meants_run-01.txt -m clean_3dACC_func.nii.gz
  46. fslmeants -i func_task-rest_run-03_e2.feat/filtered_func_data.nii.gz -o clean_3dACC_func_meants_run-03.txt -m clean_3dACC_func.nii.gz
  49. # insert code to loop through subjects, sessions and runs
  50. # STEP 3: RUN FEAT STATS
  52. # navigate to subject and session directoy
  53. cd /media/STUDY-HP-FouE-TP-150823/TE2_analysis/${subj}/${ses}/
  55. # run feat stats
  56. cp /media/STUDY-HP-FouE-TP-150823/TE2_analysis/TUSPAIN01/session01/func_task-rest_run-01_e2.feat/design.fsf .
  57. sed -i "s|TUSPAIN01|${subj}|g" design.fsf
  58. sed -i "s|session01|${ses}|g" design.fsf
  59. feat design.fsf

fmri_code_osf.sh, no license · at the source

Overview

Authors: Sophie Clarke1,2,3, Samuel Mugglestone1,2, Mathilde Lojkiewiez1,2, Joshua Marquez1,2, Nadège Bault1,2, Elsa Fouragnan1,2, Sam Hughes3
ORCID iDs: Sophie Clarke, Nadège Bault, Elsa Fouragnan, Sam Hughes
  1. School of Psychology, Faculty of Health, University of Plymouth, Plymouth, UK
  2. Brain Research and Imaging Centre, Faculty of Health, University of Plymouth, Plymouth, UK
  3. Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
Institutions: University of Exeter (United Kingdom); University of Plymouth (United Kingdom)
Journal: Nature communications, volume 17, issue 1, article 6269
Dates: received 22 August 2025; accepted 24 April 2026; published online 9 May 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1038/s41467-026-72934-3 · PMID 42106337 · PMCID PMC13376748 · OpenAlex W4414017017
Open access: gold, a free copy (OpenAlex)
Preprint: doi:10.1101/2025.09.04.674195
Status: code verified
Categories: structural MRI / diffusion (modality), fMRI (modality), other (modality), human (organism), pain (population), systems (subfield)
Methods: Statistics, Smoothing, state filtering, decompositions, fMRI & imaging, Preprocessing
Keywords: Neural circuits, Preclinical research
MeSH: Gyrus Cinguli*, Neuralgia*, Pain*, Adult, Double-Blind Method, Female, Humans, Magnetic Resonance Imaging, Magnetic Resonance Spectroscopy, Male, Pain Management, Pain Measurement, Young Adult (* major topic)
Topic: Pain Management and Treatment (Anesthesiology and Pain Medicine, Medicine), according to OpenAlex
Funding: Biotechnology and Biological Sciences Research Council (BB/Y001494/1)
Citations: not cited yet (Europe PMC); 60 references in the paper

Abstract

Transcranial ultrasound stimulation (TUS) is a promising non-invasive neuromodulation technique for pain-related deep brain regions. This study aimed to investigate neural mechanisms underlying TUS effects on pain processing using neuroimaging. Thirty-two healthy participants underwent two double-blind, randomised sessions (active or sham). A tonic cold stimulus was applied during multifocal TUS applied to the dorsal anterior cingulate cortex (dACC), and during functional magnetic resonance imaging (fMRI) and magnetic resonance spectroscopy (MRS). While no significant main effect on pain intensity was observed, active TUS showed a significantly greater reduction in pain ratings between 28- and 55-minutes post-stimulation, suggesting a delayed analgesic effect. Active TUS altered sensory encoding, disrupting the relationship between temperature and pain intensity. There was increased functional connectivity between the dACC and the supplementary motor area, pre-motor cortex, mid-ACC and supramarginal gyrus, and altered salience network connectivity. Overall, these findings suggest dACC-TUS has multidimensional effects across behavioural and neural aspects of pain processing, supporting its potential therapeutic value.

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 2 matches between paragraphs and lines of code.

OSF vp2gz

License: none: the authors keep all their rights
State: the link answers, verified on 28 September 2026
Evidence: files inventoried
Languages: R (2), Shell (1)
Size: 6 files, 3 scripts
Software Heritage: not checked
Found in: “Code availability”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: ggplot2 (2 files), lme4 (2 files), lmerTest (2 files), tidyverse (2 files), broom (1 file), car (1 file), emmeans (1 file), FSL (1 file), ggpubr (1 file), reshape2 (1 file), rstatix (1 file)
Availability: 1 check, the latest on 28 September 2026: the link answers (HTTP 200)
  • 28 September 2026: the link answers (HTTP 200)
3 files
At the source: osf.io/vp2gz/

Code availability

The code for running behavioural and neuroimaging data analysis presented in this study is also available at https://osf.io/vp2gz/.

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

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;
  • 3 scripts, each with its path and the digest of its content;
  • 2 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

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

Data availability

The behavioural, MRI and MRS data generated in this study are available on the Open Science Framework (OSF) at https://osf.io/vp2gz/. The data used to generate all figures in the paper are provided in the Source Data file. Source data are provided with this paper.

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, 28 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 7 authors, 2 keywords, 13 MeSH terms, 1 funder, 57 references.

Cite

This paper

Clarke, S., Mugglestone, S., Lojkiewiez, M., Marquez, J., Bault, N., Fouragnan, E., & Hughes, S. (2026). Multi-focal ultrasound neuromodulation to the dorsal anterior cingulate cortex disrupts behavioural and neural pain processing. Nature communications, 17(1), 6269. https://doi.org/10.1038/s41467-026-72934-3

BibTeX

@article{clarke2026multi,
author = {Clarke, Sophie and Mugglestone, Samuel and Lojkiewiez, Mathilde and Marquez, Joshua and Bault, Nadège and Fouragnan, Elsa and Hughes, Sam},
title = {{Multi-focal ultrasound neuromodulation to the dorsal anterior cingulate cortex disrupts behavioural and neural pain processing}},
journal = {Nature communications},
year = {2026},
month = may,
volume = {17},
number = {1},
pages = {6269},
publisher = {Nature Publishing Group},
issn = {2041-1723},
doi = {10.1038/s41467-026-72934-3},
url = {https://doi.org/10.1038/s41467-026-72934-3},
pmid = {42106337},
pmcid = {PMC13376748}
}

RIS

TY - JOUR
AU - Clarke, Sophie
AU - Mugglestone, Samuel
AU - Lojkiewiez, Mathilde
AU - Marquez, Joshua
AU - Bault, Nadège
AU - Fouragnan, Elsa
AU - Hughes, Sam
TI - Multi-focal ultrasound neuromodulation to the dorsal anterior cingulate cortex disrupts behavioural and neural pain processing
T2 - Nature communications
J2 - Nat Commun
PY - 2026
DA - 2026/05/09
VL - 17
IS - 1
SP - 6269
SN - 2041-1723
PB - Nature Publishing Group
DO - 10.1038/s41467-026-72934-3
UR - https://doi.org/10.1038/s41467-026-72934-3
LA - en
ER -

CSL-JSON

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"issued": {
"date-parts": [
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9
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}
}

The tracing map gets a citation of its own once an author has validated it and it has a DOI.

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