Handgrip weakness is associated with motor cortex atrophy in rheumatoid arthritis: a cross-sectional study with a hand exercise intervention.

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Paper

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The authors' code

Shell · 98 lines · 3.2 KB · BSD-3-Clause

#!/bin/sh
# This is set as the minimum number of arguments for the script to run
ndefargs=2
# Parameters go here, where optionally, you can specify a default value
max_iter=100
bc_order=4
# Check number of args
image=$1
mask=$2
# Check mandatory args
if [ ! -f $image ]; then
echo "The image '$image' to be segmented does not exist!"
exit
fi
if [ ! -f $mask ]; then
echo "The mask image '$mask' does not exist!"
exit
fi
# Parse remaining command line options after the mandatory ones.
shift $ndefargs
while [ "$#" -gt 0 ]
do
case $1 in
-max_iter)
max_iter=$2
shift 1
;;
-bc_order)
bc_order=$2
shift 1
;;
*)
echo "Error: option $1 not recognised"
exit
;;
esac
shift 1
done
# Create command line args for binary.
if [ "$max_iter" != "" ]; then
max_iter_arg=" -max_iter $max_iter "
fi
if [ "$bc_order" != "" ]; then
bc_order_arg=" -bc_order $bc_order "
fi
name=`echo $image | awk -F '.nii' {'print $1'}`
pathatlas=~/Source/nifty-seg/priors
atlas=${pathatlas}/T1.nii.gz
grey_prior=${pathatlas}/CGM_prior.nii.gz
white_prior=${pathatlas}/WM_prior.nii.gz
csf_prior=${pathatlas}/ECSF_prior.nii.gz
deep_grey_prior=${pathatlas}/DGM_prior.nii.gz
internal_csf_prior=${pathatlas}/ICSF_prior.nii.gz
seg_maths ${mask} -bin -dil 3 -ero 3 -fill -dil 1 ${name}__mask_filled.nii
if [ ! -f ${name}__affine.mat ]; then
echo Starting reg_aladin
linearArgs="-target ${image} -tmask ${name}__mask_filled.nii -source ${atlas} -aff ${name}__affine.mat -ln 3 -lp 2 -result ${name}__affine_result.nii.gz"
LinearExecutable=`which reg_aladin`
$LinearExecutable $linearArgs
fi
if [ ! -f ${name}__cpp.nii ]; then
echo Starting reg_f3d
nonLinearExecutable=`which reg_f3d`
nonLinearArgs=" -ln 3 -lp 2 -sx 5 -target ${image} -tmask ${name}__mask_filled.nii -source ${atlas} -aff ${name}__affine.mat -cpp ${name}__cpp.nii"
$nonLinearExecutable $nonLinearArgs
echo Finished reg_f3d
###############################################################
# Transform images from atlas space to native T1 space
################################################################
reg_resample -target ${image} -source $grey_prior -cpp ${name}__cpp.nii -result ${name}__registered_grey.nii -TRI
reg_resample -target ${image} -source $white_prior -cpp ${name}__cpp.nii -result ${name}__registered_white.nii -TRI
reg_resample -target ${image} -source $csf_prior -cpp ${name}__cpp.nii -result ${name}__registered_csf.nii -TRI
reg_resample -target ${image} -source $deep_grey_prior -cpp ${name}__cpp.nii -result ${name}__registered_deep_grey.nii -TRI
reg_resample -target ${image} -source $internal_csf_prior -cpp ${name}__cpp.nii -result ${name}__registered_internal_csf.nii -TRI
echo Finishing Resampling
fi
################################################################
# Run LoAd
################################################################
cmd="seg_LoAd -in ${image} -mask ${name}__mask_filled.nii -priors ${name}__registered_white.nii ${name}__registered_grey.nii ${name}__registered_csf.nii ${name}__registered_deep_grey.nii ${name}__registered_internal_csf.nii -out ${name}_segmentation.nii -v 1 $max_iter_arg $bc_order_arg"
echo "Running command:$cmd"
eval $cmd
rm ${name}__*

LoAd_brainonly.sh at commit e7404b9, under BSD-3-Clause · at the source

Overview

Authors: Amanda L Gustafsson¹, Rolf A Heckemann², Malin C Erlandsson^1,3, Victoria ME Lundgren¹, Zhao Dai⁴, Sofia T Silfverswärd⁵, Rille Pullerits^1,6, Maria I Bokarewa^1,3, Caroline Wasén^1,7

ORCID iDs: Caroline Wasén

Institutions: University of Gothenburg (Sweden); Sahlgrenska University Hospital (Sweden); Guangzhou University of Chinese Medicine (China); Karolinska University Hospital (Sweden)

Journal: BMC medicine, volume 24, issue 1, article 331

Dates: received 13 November 2025; accepted 21 May 2026; published online 26 May 2026

Type: Research article · Language: English

License: CC BY

Identifiers: DOI 10.1186/s12916-026-04956-z · PMID 42192374 · PMCID PMC13214063 · OpenAlex W7162416810

Open access: gold, a free copy (OpenAlex)

Status: code verified

Categories: genetics / omics (modality), structural MRI / diffusion (modality), human (organism)

Methods: Statistics, Preprocessing, Physiology & signal measures

Keywords: Arthritis, Rheumatoid, Hand Strength, Magnetic Resonance Imaging, Brain Mapping, Motor Cortex, CD4-Positive T-Lymphocytes, Monocytes, Cytokines, Gene Expression Profiling, Exercise Therapy

MeSH: Arthritis, Rheumatoid*, Exercise Therapy*, Hand Strength*, Motor Cortex*, Adult, Aged, Atrophy, Clinical Trials as Topic, Cross-Sectional Studies, Female, Humans, Magnetic Resonance Imaging, Middle Aged, Pilot Projects, Young Adult (* major topic)

Topic: Rheumatoid Arthritis Research and Therapies (Rheumatology, Medicine), according to OpenAlex

Funding: University of Gothenburg

Citations: not cited yet (Europe PMC); 61 references in the paper

Abstract

Background: Handgrip strength (HGS) in rheumatoid arthritis (RA) is commonly attributed to joint pathology, but may also reflect extra-articular manifestations, including atrophy of motor-related brain regions. We investigated HGS as a marker of peripheral joint status, systemic immune regulation, and central motor integrity.

Methods: Maximal HGS was assessed using a dynamometer. Joint pathology was evaluated using radiographic and clinical measures, and upper limb disability using questionnaire. Brain volumes were quantified using MRI and MAPER software. Transcriptome sequencing was performed on circulating CD4⁺ and CD14⁺ cells. In a six-month, single-arm pilot trial, a subgroup of patients performed daily hand exercises. Associations and longitudinal changes were analysed using linear mixed-effects models accounting for repeated measurements across hands and timepoints, with variable selection performed using LASSO regression.

Results: A total of 59 women with established RA were included in the cross-sectional analysis (median age 64 years [range 23–76], DAS28 2.46 [1.1–5.8], disease duration 11 years [0–45]). Lower HGS was associated with greater disability. HGS was also independently associated with premotor and supplementary motor cortex (PMA/SMA) volume after adjustment for age, hand dominance, and joint pathology. Among joint pathology measures, tender joint count showed a significant negative association with HGS. Transcriptome analyses of CD4⁺ and CD14⁺ cells indicated that lower HGS was associated with reduced immune responsiveness and altered cytokine signalling pathways. In a six-month pilot hand exercise trial (n = 12; median age 54 years [28–68], DAS28 2.87 [1.2–3.6], disease duration 14 years [1–40]), HGS increased at 3 months, with a non-significant trend at 6 months. Baseline PMA/SMA volume showed a non-significant trend towards predicting HGS improvement. Longitudinal analyses revealed region-specific brain changes, with a decrease in PMA/SMA volume and an increase in insular volume over time.

Conclusions: Handgrip weakness in RA may reflect both joint pathology and motor cortex atrophy in the PMA/SMA. Hand exercise improved HGS and induced certain structural changes in the brain, though effects on motor regions remain uncertain and warrant further study.

Trial registration: Clinical trial registration: ClinicalTrials.gov, NCT04378621. Registration date: May 5, 2020.

Supplementary Information: The online version contains supplementary material available at 10.1186/s12916-026-04956-z.

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

Repository

Its files are read in the Code ↔ Paper reader above.

KCL-BMEIS/NiftySeg

License: BSD-3-Clause

State: the link answers, verified on 28 September 2026

Evidence: files inventoried

Commit: e7404b9548d3362fef7de0f31339bd23c5e4f220, 24 August 2026

Languages: C/C++ (28), C++ (18), C (16), Shell (1)

Size: 85 files, 63 scripts

Software Heritage: not archived

Found in: the text, “MRI of the brain”

Holds: README, license file

Not found: CITATION.cff, environment file, tests, continuous integration, documentation

Availability: 1 check, the latest on 28 September 2026: the link answers

28 September 2026: the link answers

65 files

LoAd_brainonly.sh, Shell, 98 lines
nifti/nifti1.h, C/C++, 1,490 lines
nifti/nifti1_io.c, C, 5,567 lines
nifti/nifti1_io.h, C/C++, 551 lines
nifti/znzlib.c, C, 322 lines
nifti/znzlib.h, C/C++, 123 lines
seg-apps/seg_CalcTopNCC.cpp, C++, 161 lines
seg-apps/seg_EM.cpp, C++, 679 lines
seg-apps/seg_EM_CLIxml.h, C/C++, 355 lines
seg-apps/seg_FillLesions.cpp, C++, 515 lines
seg-apps/seg_LabFusion.cpp, C++, 906 lines
seg-apps/seg_LabFusion_CLIxml.h, C/C++, 49 lines
seg-apps/seg_LoAd.cpp, C++, 289 lines
seg-apps/seg_PatchMatch.cpp, C++, 583 lines
seg-apps/seg_Stats.cpp, C++, 1,932 lines
seg-apps/seg_maths.cpp, C++, 3,271 lines
seg-lib/NiftySegWinExportHeader.h, C/C++, 15 lines
seg-lib/_seg_EM.cpp, C++, 2,999 lines
seg-lib/_seg_EM.h, C/C++, 216 lines
seg-lib/_seg_FMM.cpp, C++, 651 lines
seg-lib/_seg_FMM.h, C/C++, 35 lines
seg-lib/_seg_LabFusion.cpp, C++, 2,172 lines
seg-lib/_seg_LabFusion.h, C/C++, 124 lines
seg-lib/_seg_LoAd.cpp, C++, 5,369 lines
seg-lib/_seg_LoAd.h, C/C++, 418 lines
seg-lib/_seg_PatchMatch.cpp, C++, 1,369 lines
seg-lib/_seg_PatchMatch.h, C/C++, 131 lines
seg-lib/_seg_PatchMatchResult.cpp, C++, 102 lines
seg-lib/_seg_PatchMatchResult.h, C/C++, 45 lines
seg-lib/_seg_common.h, C/C++, 330 lines
seg-lib/_seg_fill_lesions.cpp, C++, 855 lines
seg-lib/_seg_fill_lesions.h, C/C++, 84 lines
seg-lib/_seg_fill_lesions_other.cpp, C++, 568 lines
seg-lib/_seg_fill_lesions_other.h, C/C++, 68 lines
seg-lib/_seg_matrix.cpp, C++, 7 lines
seg-lib/_seg_matrix.h, C/C++, 425 lines
seg-lib/_seg_tools.cpp, C++, 4,039 lines
seg-lib/_seg_tools.h, C/C++, 137 lines
win32/dirent_win.h, C/C++, 372 lines
win32/printdir.c, C, 52 lines
zlib/adler32.c, C, 149 lines
zlib/compress.c, C, 79 lines
zlib/crc32.c, C, 423 lines
zlib/crc32.h, C/C++, 441 lines
zlib/deflate.c, C, 1,736 lines
zlib/deflate.h, C/C++, 331 lines
zlib/gzio.c, C, 1,026 lines
zlib/infback.c, C, 623 lines
zlib/inffast.c, C, 318 lines
zlib/inffast.h, C/C++, 11 lines
zlib/inffixed.h, C/C++, 94 lines
zlib/inflate.c, C, 1,368 lines
zlib/inflate.h, C/C++, 115 lines
zlib/inftrees.c, C, 329 lines
zlib/inftrees.h, C/C++, 55 lines
zlib/minigzip.c, C, 322 lines
zlib/trees.c, C, 1,219 lines
zlib/trees.h, C/C++, 128 lines
zlib/uncompr.c, C, 61 lines
zlib/zconf.h, C/C++, 334 lines
zlib/zlib.h, C/C++, 1,357 lines
zlib/zutil.c, C, 318 lines
zlib/zutil.h, C/C++, 269 lines
LICENSE.txt, License, 28 lines
README.md, Text, 126 lines

At the source: github.com/KCL-BMEIS/NiftySeg

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;
63 scripts, each with its path and the digest of its content;
no match between paragraphs and code yet;
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

Data links

ncbi.nlm.nih.gov/geo/query, NCBI; found in “Data availability”

Data availability

The RNA sequencing datasets generated and analysed during the current study are available in the NCBI GEO repository with accession [GSE201670](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi? acc=GSE201670) (CD14⁺) and [GSE201669](https:/www.ncbi.nlm.nih.gov/geo/query/acc.cgi? acc=GSE201669) (CD4⁺).Due to ethical and legal restrictions related to patient confidentiality and the handling of pseudonymised MRI data under GDPR, the imaging and associated clinical datasets are not publicly available. Data may be made available upon reasonable request to the corresponding author, subject to review of a research proposal, relevant ethical approval, and a data use agreement to ensure compliance with data protection and ethical requirements.

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, 9 authors, 10 keywords, 15 MeSH terms, 1 funder, 58 references.

Cite

This paper

Gustafsson, A. L., Heckemann, R. A., Erlandsson, M. C., Lundgren, V. M., Dai, Z., Silfverswärd, S. T., Pullerits, R., Bokarewa, M. I., & Wasén, C. (2026). Handgrip weakness is associated with motor cortex atrophy in rheumatoid arthritis: a cross-sectional study with a hand exercise intervention. BMC medicine, 24(1), 331. https://doi.org/10.1186/s12916-026-04956-z

BibTeX

@article{gustafsson2026handgrip, author = {Gustafsson, Amanda L and Heckemann, Rolf A and Erlandsson, Malin C and Lundgren, Victoria ME and Dai, Zhao and Silfverswärd, Sofia T and Pullerits, Rille and Bokarewa, Maria I and Wasén, Caroline}, title = {{Handgrip weakness is associated with motor cortex atrophy in rheumatoid arthritis: a cross-sectional study with a hand exercise intervention}}, journal = {BMC medicine}, year = {2026}, month = may, volume = {24}, number = {1}, pages = {331}, publisher = {BioMed Central}, issn = {1741-7015}, doi = {10.1186/s12916-026-04956-z}, url = {https://doi.org/10.1186/s12916-026-04956-z}, pmid = {42192374}, pmcid = {PMC13214063} }

RIS

TY - JOUR AU - Gustafsson, Amanda L AU - Heckemann, Rolf A AU - Erlandsson, Malin C AU - Lundgren, Victoria ME AU - Dai, Zhao AU - Silfverswärd, Sofia T AU - Pullerits, Rille AU - Bokarewa, Maria I AU - Wasén, Caroline TI - Handgrip weakness is associated with motor cortex atrophy in rheumatoid arthritis: a cross-sectional study with a hand exercise intervention T2 - BMC medicine J2 - BMC Med PY - 2026 DA - 2026/05/26 VL - 24 IS - 1 SP - 331 SN - 1741-7015 PB - BioMed Central DO - 10.1186/s12916-026-04956-z UR - https://doi.org/10.1186/s12916-026-04956-z LA - en ER -

CSL-JSON

{ "id": "10.1186/s12916-026-04956-z", "type": "article-journal", "title": "Handgrip weakness is associated with motor cortex atrophy in rheumatoid arthritis: a cross-sectional study with a hand exercise intervention", "container-title": "BMC medicine", "author": [ { "family": "Gustafsson", "given": "Amanda L" }, { "family": "Heckemann", "given": "Rolf A" }, { "family": "Erlandsson", "given": "Malin C" }, { "family": "Lundgren", "given": "Victoria ME" }, { "family": "Dai", "given": "Zhao" }, { "family": "Silfverswärd", "given": "Sofia T" }, { "family": "Pullerits", "given": "Rille" }, { "family": "Bokarewa", "given": "Maria I" }, { "family": "Wasén", "given": "Caroline" } ], "container-title-short": "BMC Med", "volume": "24", "issue": "1", "page": "331", "DOI": "10.1186/s12916-026-04956-z", "PMID": "42192374", "PMCID": "PMC13214063", "ISSN": "1741-7015", "publisher": "BioMed Central", "URL": "https://doi.org/10.1186/s12916-026-04956-z", "language": "en", "issued": { "date-parts": [ [ 2026, 5, 26 ] ] } }

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