OSCR

Test-Retest Reliability of Sensorimotor Activity Measured With Spinal Cord fMRI.

Code ↔ Paper

8 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 8 matches · 4 of them tie a paragraph to a whole file, not to given lines: weak matches, whose lines are not tinted
  1. [1] § Material and Methods › Data Analysis › Imaging Data › Preprocessing ↔ 01_preprocessing/06_reg_rootlets.sh, the whole file · a weak match · score 0.83 · sct_deepseg, sct_register_multimodal, PAM50 template, cord template, rootlet, disc
  2. [2] § Material and Methods › Data Analysis › Imaging Data › Preprocessing ↔ code/01_preprocessing/03_reg.sh, lines 26–103 · score 0.83 · sct_register_multimodal, sct deepseg, PAM50 T2, cord template, FSLeyes, disc
  3. [3] § Material and Methods › Procedure › MRI Visits ↔ 01_preprocessing/phys_merge.m, lines 90–177 · score 0.63 · pulse oximeter, traces, Respiratory, positioned, triggers, scanner
  4. [4] § Material and Methods › Data Analysis › Imaging Data › Subject‐Level Modelling ↔ code/01_preprocessing/06_bandpass.sh, the whole file · a weak match · score 0.63 · temporal filtering, PNM regressors, motion, FSL
  5. [5] § Material and Methods › Data Analysis › Imaging Data › Preprocessing ↔ 01_preprocessing/03_neptune_moco.sh, lines 1–62 · score 0.55 · dWarpDrive, Neptune, AFNI, tools, FSL, slice
  6. [6] § Material and Methods › Data Analysis › Test–Retest Reliability › Intraclass Correlation Coefficient › Imaging Data ↔ code/05_tsnr/01_tsnr_cord.sh, the whole file · a weak match · score 0.55 · standard deviation, tSNR, temporal, masks, cord
  7. [7] § Material and Methods › Data Analysis › Test–Retest Reliability › Intraclass Correlation Coefficient › Imaging Data ↔ 04_reliability/tsnr/01_tsnr.sh, the whole file · a weak match · score 0.54 · standard deviation, tSNR, temporal, preprocessing, reliability, cord
  8. [8] § Material and Methods › Data Analysis › Imaging Data › Preprocessing ↔ 01_preprocessing/03_neptune_moco.sh, lines 1–62 · score 0.51 · dWarpDrive, AFNI, Matlab, FSL, slices, preprocessing

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 · 100 lines · 3.1 KB · MIT · 2 matches

  1. #!/bin/bash
  3. # Following taken (almost) entirely from Rob Barry's use of AFNI' 3dWarpDrive in Neptune (MATLAB tool)
  4. # 2022/05/09
  6. if [ $# -ne 3 ] ; then
  7. echo "Usage:" $(basename $0) "<input4D> <target> <mask>"
  8. exit
  9. fi
  11. fbase=$(basename $1 .nii.gz)
  12. numslices=$(fslval $1 dim3)
  13. oneless=$(echo "$numslices - 1" | bc)
  14. tpoints=$(fslval $1 dim4)
  15. endpoint=$(echo "$tpoints - 1" | bc)
  17. # dimensions of onepix
  18. xdim=$(fslval $1 dim1)
  19. ydim=$(fslval $1 dim2)
  20. xpixdim=$(fslval $1 pixdim1)
  21. ypixdim=$(fslval $1 pixdim2)
  22. zpixdim=$(fslval $1 pixdim3)
  23. tr=$(fslval $1 pixdim4)
  25. outxpixdim=$(awk -v v1="$xdim" -v v2="$xpixdim" 'BEGIN { printf "%6.5f", v1 * v2 }')
  26. outypixdim=$(awk -v v1="$ydim" -v v2="$ypixdim" 'BEGIN { printf "%6.5f", v1 * v2 }')
  27. outzpixdim=$zpixdim
  29. parfix="-parfix 3 0 -parfix 4 0 -parfix 5 0 -parfix 6 0 -parfix 7 1 -parfix 8 1 -parfix 9 1 -parfix 10 0 -parfix 11 0 -parfix 12 0"
  31. # nasty
  32. if [ -d mocotmp ] ; then
  33. \rm -rf mocotmp
  34. fi
  35. mkdir mocotmp
  37. # create onepix for later use
  38. $FSLDIR/bin/fslcreatehd 1 1 1 1 $outxpixdim $outypixdim $outzpixdim $tr 0 0 0 16 mocotmp/onepix
  40. # split according to slice
  41. fslsplit $1 mocotmp/slice -z
  42. fslsplit $2 mocotmp/target -z
  43. fslsplit $3 mocotmp/mask -z
  46. for pass in one two ; do
  47. for i in $(seq 0 ${oneless}) ; do
  48. slicepad=$(zeropad $i 4)
  49. echo "PASS $pass"
  50. if [ "${pass}" == "one" ] ; then
  51. baseim=target${slicepad}.nii.gz
  52. else
  53. baseim=target${slicepad}_MC_tmean.nii.gz
  54. fi
  56. 3dWarpDrive -affine_general $parfix -quintic -final quintic \
  57. -base mocotmp/$baseim \
  58. -prefix mocotmp/slice${slicepad}_MCnofilt.nii.gz \
  59. -weight mocotmp/mask${slicepad}.nii.gz \
  60. -1Dfile mocotmp/slice${slicepad}_MC_params.txt \
  61. -1Dmatrix_save mocotmp/slice${slicepad}_MC_xform.aff12.1D \
  62. mocotmp/slice${slicepad}.nii.gz
  65. # if on first pass create new mean image to register to
  66. if [ "${pass}" == "one" ] ; then
  67. fslmaths mocotmp/slice${slicepad}_MCnofilt -Tmean mocotmp/target${slicepad}_MC_tmean
  68. rm mocotmp/slice${slicepad}_MCnofilt.nii.gz
  69. else # we've completed second pass, now just need to create per slice motion regressor
  70. for dim in x y ; do
  71. for t in $(seq 0 ${endpoint}) ; do
  72. timeline=$(echo "$t + 4" | bc)
  73. zp_t=$(zeropad $t 4)
  74. if [ "${dim}" == "x" ] ; then
  75. val=$(cat mocotmp/slice${slicepad}_MC_params.txt | awk -v tp="${timeline}" '{if(NR==tp){print $1}}')
  76. else
  77. val=$(cat mocotmp/slice${slicepad}_MC_params.txt | awk -v tp="${timeline}" '{if(NR==tp){print $2}}')
  78. fi
  79. fslmaths mocotmp/onepix -add $val mocotmp/${dim}_${slicepad}_${zp_t}
  80. done
  81. $FSLDIR/bin/fslmerge -tr mocotmp/${dim}_${slicepad} mocotmp/${dim}_${slicepad}_????.nii.gz $tr
  82. done
  83. fi
  86. done
  88. done
  90. fslmerge -z ${fbase}_MCnofilt mocotmp/slice????_MCnofilt.nii.gz
  91. fslmerge -z ${fbase}_MCnofilt_x_params mocotmp/x_????.nii.gz
  92. fslmerge -z ${fbase}_MCnofilt_y_params mocotmp/y_????.nii.gz
  93. fslmaths ${fbase}_MCnofilt -Tmean ${fbase}_MCnofilt_tmean
  95. mkdir moco_params
  96. cp mocotmp/*MC_params.txt moco_params
  98. # tidy up (bit brutal)
  99. \rm -rf mocotmp

03_neptune_moco.sh at commit 19d029c, under MIT · at the source

Overview

Authors: Olivia S Kowalczyk1,2, Sonia Medina3, Alessandra Venezia1, Dimitra Tsivaka4, Aminul I Ahmed5,6, Steven C R Williams1, Jonathan C W Brooks7, David J Lythgoe1, Matthew A Howard1
ORCID iDs: Olivia S Kowalczyk, Steven C R Williams, David J Lythgoe, Matthew A Howard
  1. Department of Neuroimaging, Institute of Psychiatry, Psychology, & Neuroscience, King's College London, London, UK
  2. Functional Imaging Laboratory, Department of Imaging Neuroscience, UCL Queen Square Institute of Neurology, University College London, London, UK
  3. Department of Clinical and Biomedical Sciences, University of Exeter, Exeter, UK
  4. Medical Physics Department, Medical School, University of Thessaly, Volos, Greece
  5. Department of Neurosurgery, King's College Hospital NHS Foundation Trust, London, UK
  6. Wolfson Sensory, Pain and Regeneration Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
  7. Department of Psychology, University of Liverpool, Liverpool, UK
Institutions: King's College London (United Kingdom); UCL Queen Square Institute of Neurology (United Kingdom); University College London (United Kingdom); University of Exeter (United Kingdom); University of Thessaly (Greece); King's College Hospital NHS Foundation Trust (United Kingdom); King's College Hospital (United Kingdom); University of Liverpool (United Kingdom)
Journal: Human brain mapping, volume 47, issue 10, article e70593
Dates: received 25 February 2026; accepted 17 June 2026; published online 29 June 2026; in print July 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1002/hbm.70593 · PMID 42367071 · PMCID PMC13312036 · OpenAlex W7166546750
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: fMRI (modality), human (organism)
Methods: Statistics, Machine learning, fMRI & imaging
Keywords: motor function, spinal cord, spinal fMRI, test–retest reliability
MeSH: Magnetic Resonance Imaging*, Spinal Cord*, Adult, Evoked Potentials, Motor, Female, Hand Strength, Humans, Male, Reproducibility of Results, Young Adult (* major topic)
Topic: Transcranial Magnetic Stimulation Studies (Neurology, Neuroscience), according to OpenAlex
Funding: Medical Research Council (MR/N026969/1); King’s College London (King's Prize Fellowship); NIHR Maudsley Biomedical Research Centre
Citations: not cited yet (Europe PMC); 111 references in the paper

Abstract

Establishing the reliability of spinal cord functional magnetic resonance imaging (fMRI) is critical before employing it to assess experimental or clinical interventions. Previous studies have mapped human motor activity primarily to the ipsilateral ventral horn, aligning with myotomal and dermatomal projections. Despite these insights, the test–retest reliability of spinal fMRI remains under‐investigated. Here we assessed spinal cord activation during a sensorimotor paradigm involving right‐hand grasping and grip force estimation in 30 healthy volunteers. Participants completed two identical scanning visits, each time performing the same task twice, enabling the investigation of test–retest reliability both within a single experimental visit and between visits performed on different days. Aggregating all task runs, motor‐evoked activation was observed in ipsilateral ventro‐dorsal regions of spinal segmental levels C5–T1, as well as in medial regions of levels C2–C3. Despite highly reliable task performance (grip force) and fMRI signal quality (temporal signal‐to‐noise ratio), the reliability of motor activation was predominantly poor‐to‐fair both within and between visits, with notable variability in spatial distribution observed across task runs. Increasing the number of task runs per individual improved the robustness of group‐level activation, as indexed by higher activated voxel count, larger cluster spatial extent, and attenuated t‐statistic distribution. Although we demonstrated that motor‐evoked activation corresponds to the known neuroanatomical organisation of motor circuits, its low test–retest reliability presents a challenge for wider applications of spinal fMRI. Understanding the drivers of low reliability in functional imaging is warranted, but we suggest that looking beyond measurement error is required, including careful consideration of inherent within‐individual variability underpinned by neurophysiological and psychological factors.

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

Repositories

Its files are read in the Code ↔ Paper reader above, with 8 matches between paragraphs and lines of code.

oliviakowalczyk/spain_squeeze

License: MIT
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: 19d029c93c508aaf8ef48d30004f12aefb22b4e6, 8 May 2026
Languages: Shell (25), MATLAB (2), Python (1)
Size: 187 files, 28 scripts
Software Heritage: not archived
Found in: “Data Availability Statement”
Holds: README, license file
Not found: CITATION.cff, environment file, tests, continuous integration, documentation
Tools: FSL (11 files), AFNI (3 files), Image Processing Toolbox (1 file)
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
30 files
At the source: github.com/oliviakowalczyk/spain_squeeze/releases/tag/v1.0

OSF fjasd

License: none: the authors keep all their rights
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Languages: Shell (21), MATLAB (2), Python (1)
Size: 47 files, 24 scripts
Software Heritage: not checked
Found in: “Data Availability Statement”
Holds: README, license file
Not found: CITATION.cff, environment file, tests, continuous integration, documentation
Tools: FSL (26 files), AFNI (7 files), Image Processing Toolbox (2 files), NumPy (2 files), pandas (2 files), Matplotlib (1 file), SciPy (1 file), seaborn (1 file), statsmodels (1 file)
Availability: 1 check, the latest on 27 September 2026: the link answers (HTTP 200)
  • 27 September 2026: the link answers (HTTP 200)
59 files, to read at the source

This repository has no license: its authors keep all rights. Read it at the source.

At the source: osf.io/fjasd/

OSF u8rbq

License: none: the authors keep all their rights
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Size: 0 files, 0 scripts
Software Heritage: not checked
Found in: the references
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 27 September 2026: the link answers (HTTP 200)
  • 27 September 2026: the link answers (HTTP 200)
At the source:

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:

  • 3 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 85 scripts, each with its path and the digest of its content;
  • 8 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 Statement

The participants of this study did not give written consent for their data to be shared publicly; therefore, raw study data are not available. Spatial maps generated from group‐level models and reliability assessments are available on NeuroVault: https://identifiers.org/neurovault.collection:23114. Please note that currently NeuroVault does not support a spinal cord (PAM50) template for online visualisation of spatial maps. Consequently, we recommend downloading the maps and overlaying them on a PAM50 spinal cord template in your software of choice. All code used in the analysis of this data is openly accessible on GitHub: https://github.com/oliviakowalczyk/spain_squeeze/releases/tag/v1.0. The code, together with study preregistration and other study‐related information, can also be accessed through the project's Open Science Framework (OSF) repository: https://osf.io/fjasd/. Data that support the findings of this study are available on request from the corresponding author. The data are not publicly available due to privacy or ethical restrictions.

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, 4 keywords, 10 MeSH terms, 3 funders, 107 references.

Cite

This paper

Kowalczyk, O. S., Medina, S., Venezia, A., Tsivaka, D., Ahmed, A. I., Williams, S. C. R., Brooks, J. C. W., Lythgoe, D. J., & Howard, M. A. (2026). Test-Retest Reliability of Sensorimotor Activity Measured With Spinal Cord fMRI. Human brain mapping, 47(10), e70593. https://doi.org/10.1002/hbm.70593

BibTeX

@article{kowalczyk2026test,
author = {Kowalczyk, Olivia S and Medina, Sonia and Venezia, Alessandra and Tsivaka, Dimitra and Ahmed, Aminul I and Williams, Steven C R and Brooks, Jonathan C W and Lythgoe, David J and Howard, Matthew A},
title = {{Test-Retest Reliability of Sensorimotor Activity Measured With Spinal Cord fMRI}},
journal = {Human brain mapping},
year = {2026},
month = jul,
volume = {47},
number = {10},
pages = {e70593},
publisher = {Wiley},
issn = {1065-9471},
doi = {10.1002/hbm.70593},
url = {https://doi.org/10.1002/hbm.70593},
pmid = {42367071},
pmcid = {PMC13312036}
}

RIS

TY - JOUR
AU - Kowalczyk, Olivia S
AU - Medina, Sonia
AU - Venezia, Alessandra
AU - Tsivaka, Dimitra
AU - Ahmed, Aminul I
AU - Williams, Steven C R
AU - Brooks, Jonathan C W
AU - Lythgoe, David J
AU - Howard, Matthew A
TI - Test-Retest Reliability of Sensorimotor Activity Measured With Spinal Cord fMRI
T2 - Human brain mapping
J2 - Hum Brain Mapp
PY - 2026
DA - 2026/07/01
VL - 47
IS - 10
SP - e70593
SN - 1065-9471
PB - Wiley
DO - 10.1002/hbm.70593
UR - https://doi.org/10.1002/hbm.70593
LA - en
ER -

CSL-JSON

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