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Heritable and experience-dependent cortical traits of reading ability.

Code ↔ Paper

5 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 5 matches · 3 of them tie a paragraph to a whole file, not to given lines: weak matches, whose lines are not tinted
  1. [1] § Materials and methods › MRI acquisition and processing ↔ scripts/tractography.sh, lines 115–162 · score 0.82 · preprocessing pipeline, diffusion space, Probabilistic, Trilinear, binarized, FSL
  2. [2] § Materials and methods › Genetic analyses ↔ scripts/run_ace_model.R, the whole file · a weak match · score 0.59 · Confidence intervals, CI, CSOLNP, AE, optimizer, fit
  3. [3] § Materials and methods › Statistical analyses ↔ scripts/run_ace_model.R, the whole file · a weak match · score 0.57 · handedness scaled, intracranial, gender, age, ROI, fitted
  4. [4] § Materials and methods › MRI acquisition and processing ↔ scripts/extract_areas.sh, the whole file · a weak match · score 0.54 · Connectome Workbench, surface area, S1200, TR, SPACE, Cortical
  5. [5] § Materials and methods › Participants and data source ↔ scripts/tractography.sh, lines 115–162 · score 0.53 · preprocessing pipeline, transformation, atlas, warp, ACPC, space

Paper

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

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The authors' code

Shell · 220 lines · 5.1 KB · MIT · 2 matches

  1. #!/usr/bin/env bash
  2. set -euo pipefail
  4. # ==============================
  5. # SETTINGS
  6. # ==============================
  8. AREAS=("AF" "IFO")
  10. DIFF_RAW="PATH_TO_DIFFUSION_DATA_SOURCE_DIRECTORY"
  11. STRUCT_RAW="PATH_TO_STRUCTURAL_DATA_SOURCE_DIRECTORY"
  12. WORK="PATH_TO_WORKING_DIRECTORY"
  13. DERIV="PATH_TO_DERIVATIVES_DIRECTORY"
  14. ATLAS="PATH_TO_ATLAS_DIRECTORY"
  16. THR=0.30
  18. mkdir -p "$WORK" "$DERIV"
  20. OUTCSV="$DERIV/tracts_FA_MD_RD_AD.csv"
  22. # ======================================
  23. # CSV HEADER
  24. # ======================================
  26. if [ ! -f "$OUTCSV" ]; then
  27. echo "Subject,\
  28. FA_AF_L,FA_AF_R,MD_AF_L,MD_AF_R,RD_AF_L,RD_AF_R,AD_AF_L,AD_AF_R,Vox_AF_L,Vox_AF_R,\
  29. FA_IFO_L,FA_IFO_R,MD_IFO_L,MD_IFO_R,RD_IFO_L,RD_IFO_R,AD_IFO_L,AD_IFO_R,Vox_IFO_L,Vox_IFO_R" \
  30. > "$OUTCSV"
  31. fi
  34. # ==============================
  35. # SUBJECT LOOP
  36. # ==============================
  38. for zip in "$DIFF_RAW"/*_Diffusion3TRecommended.zip; do
  40. subj="$(basename "$zip" | cut -d_ -f1)"
  42. echo "===================================="
  43. echo "Processing $subj"
  44. echo "===================================="
  46. TMP_WORK="$WORK/tmp_$subj"
  47. SUBJ_DERIV="$DERIV/$subj"
  49. rm -rf "$TMP_WORK"
  50. mkdir -p "$TMP_WORK" "$SUBJ_DERIV"
  53. # --------------------------------------
  54. # Unzip diffusion
  55. # --------------------------------------
  57. unzip -q "$zip" -d "$TMP_WORK" -x "*/Diffusion.bedpostX/*"
  59. DIFF="$TMP_WORK/$subj/T1w/Diffusion"
  61. if [ ! -d "$DIFF" ]; then
  62. echo "Diffusion folder missing — skipping"
  63. rm -rf "$TMP_WORK"
  64. continue
  65. fi
  67. cd "$DIFF"
  70. # --------------------------------------
  71. # Structural files from HCP preprocessing
  72. # --------------------------------------
  74. LOCAL_STRUCT="$STRUCT_RAW/$subj"
  76. T1="$LOCAL_STRUCT/T1w/T1w_acpc_dc_restore.nii.gz"
  77. WARP="$LOCAL_STRUCT/MNINonLinear/xfms/standard2acpc_dc.nii.gz"
  78. ACPC_MAT="$LOCAL_STRUCT/T1w/xfms/acpc.mat"
  81. # ======================================
  82. # DTI SCALARS
  83. # ======================================
  85. if [ -f "$SUBJ_DERIV/dti_FA.nii.gz" ]; then
  87. echo "Reusing DTI scalars"
  88. cp "$SUBJ_DERIV"/dti_*.nii.gz .
  90. else
  92. echo "Running dtifit"
  94. dtifit \
  95. -k data.nii.gz \
  96. -o dti \
  97. -m nodif_brain_mask.nii.gz \
  98. -r bvecs \
  99. -b bvals
  101. fslmaths dti_L2.nii.gz -add dti_L3.nii.gz -div 2 dti_RD.nii.gz
  102. cp dti_L1.nii.gz dti_AD.nii.gz
  104. cp dti_FA.nii.gz "$SUBJ_DERIV/"
  105. cp dti_MD.nii.gz "$SUBJ_DERIV/"
  106. cp dti_RD.nii.gz "$SUBJ_DERIV/"
  107. cp dti_AD.nii.gz "$SUBJ_DERIV/"
  109. fi
  112. METRICS=()
  115. # ======================================
  116. # TRACT PROCESSING
  117. # ======================================
  119. for AREA in "${AREAS[@]}"; do
  121. for side in left right; do
  123. IN_MASK="$ATLAS/${AREA}_${side}_MNI.nii.gz"
  125. TEMP_T1="${AREA}_${side}_T1.nii.gz"
  126. OUT_DIFF="${AREA}_${side}_diff.nii.gz"
  127. OUT_PROB="${AREA}_${side}_prob.nii.gz"
  128. OUT_BIN="${AREA}_${side}_thr.nii.gz"
  131. # --- MNI → T1
  133. applywarp \
  134. --in="$IN_MASK" \
  135. --ref="$T1" \
  136. --warp="$WARP" \
  137. --interp=trilinear \
  138. --out="$TEMP_T1"
  141. # --- T1 (ACPC space) → diffusion space
  142. # The acpc.mat transform from the HCP preprocessing pipeline maps
  143. # between structural ACPC space and diffusion space.
  145. flirt \
  146. -in "$TEMP_T1" \
  147. -ref data.nii.gz \
  148. -applyxfm \
  149. -init "$ACPC_MAT" \
  150. -interp trilinear \
  151. -out "$OUT_DIFF"
  154. # --- Threshold and binarize
  156. fslmaths "$OUT_DIFF" -thr "$THR" "$OUT_PROB"
  157. fslmaths "$OUT_PROB" -bin "$OUT_BIN"
  159. cp "$OUT_BIN" "$SUBJ_DERIV/"
  160. cp "$OUT_PROB" "$SUBJ_DERIV/"
  162. done
  165. # ======================================
  166. # METRIC EXTRACTION
  167. # ======================================
  169. VOX_L=$(fslstats ${AREA}_left_thr.nii.gz -V | awk '{print $1}')
  170. VOX_R=$(fslstats ${AREA}_right_thr.nii.gz -V | awk '{print $1}')
  172. if [ "$VOX_L" -lt 20 ] || [ "$VOX_R" -lt 20 ]; then
  173. echo "Too few voxels in $AREA for $subj — skipping subject"
  174. cd "$WORK"
  175. rm -rf "$TMP_WORK"
  176. continue 2
  177. fi
  180. FA_L=$(fslstats dti_FA.nii.gz -k ${AREA}_left_thr.nii.gz -M)
  181. FA_R=$(fslstats dti_FA.nii.gz -k ${AREA}_right_thr.nii.gz -M)
  183. MD_L=$(fslstats dti_MD.nii.gz -k ${AREA}_left_thr.nii.gz -M)
  184. MD_R=$(fslstats dti_MD.nii.gz -k ${AREA}_right_thr.nii.gz -M)
  186. RD_L=$(fslstats dti_RD.nii.gz -k ${AREA}_left_thr.nii.gz -M)
  187. RD_R=$(fslstats dti_RD.nii.gz -k ${AREA}_right_thr.nii.gz -M)
  189. AD_L=$(fslstats dti_AD.nii.gz -k ${AREA}_left_thr.nii.gz -M)
  190. AD_R=$(fslstats dti_AD.nii.gz -k ${AREA}_right_thr.nii.gz -M)
  193. METRICS+=("$FA_L" "$FA_R" \
  194. "$MD_L" "$MD_R" \
  195. "$RD_L" "$RD_R" \
  196. "$AD_L" "$AD_R" \
  197. "$VOX_L" "$VOX_R")
  199. done
  202. # ======================================
  203. # UPDATE CSV
  204. # ======================================
  206. grep -v "^$subj," "$OUTCSV" > "$OUTCSV.tmp" || true
  207. mv "$OUTCSV.tmp" "$OUTCSV"
  209. (IFS=,; echo "$subj,${METRICS[*]}") >> "$OUTCSV"
  212. cd "$WORK"
  213. rm -rf "$TMP_WORK"
  215. done
  218. echo "===================================="
  219. echo "All subjects processed successfully."
  220. echo "===================================="

tractography.sh at commit 2cf64d7, under MIT · at the source

Overview

Authors: Mikael Roll1
ORCID iDs: Mikael Roll
  1. Centre for Languages and Literature, Lund University, Helgonabacken 12, 223 62 Lund, Sweden
Institutions: Lund University (Sweden)
Journal: Cerebral cortex (New York, N.Y. : 1991), volume 36, issue 8, article bhag125
Dates: received 16 March 2026; accepted 21 July 2026; published online 22 August 2026; in print August 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1093/cercor/bhag125 · PMID 42632036 · PMCID PMC13575274 · OpenAlex W7203542131
Open access: hybrid, a free copy (OpenAlex)
Status: code verified
Categories: genetics / omics (modality), human (organism), other condition (population)
Methods: Connectivity, Statistics, Preprocessing, fMRI & imaging
Keywords: anterior temporal lobe, auditory cortex, cortical microstructure, heritability, reading
MeSH: Cerebral Cortex*, Reading*, Adult, Auditory Cortex, Brain Mapping, Dyslexia, Female, Humans, Magnetic Resonance Imaging, Male, Semantics, Young Adult (* major topic)
Topic: Reading and Literacy Development (Developmental and Educational Psychology, Psychology), according to OpenAlex
Funding: Crafoord Foundation (2017.0006); Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation) (2018.0454); Vetenskapsrådet (2018.00632)
Citations: not cited yet (Europe PMC); 106 references in the paper

Abstract

Reading ability emerges from interacting phonological and semantic skills. However, the cortical microstructure supporting these traits remains unclear. Multimodal cortical parcellation and diffusion analysis were performed in 1,068 participants, including a genetically informed twin subsample. We identified auditory and anterior temporal subregions predicting oral reading scores. In the left auditory cortex, myelin in a paralemniscal (belt) area was heritably linked to reading, whereas thickness in the lemniscal (core) region reflected experience-dependent contributions. Bilateral anterior temporal lobe (ATL) surface areas were genetically associated with reading and predicted semantic performance, providing novel cortical evidence for heritable semantic substrates of literacy. The left inferior fronto-occipital fasciculus and a left ATL region connected with the arcuate fasciculus predicted reading scores independent of genetic influences. The cortical traits were linked to reading continuously across the population, challenging categorical models of dyslexia. The findings suggest that genetic and experience-dependent mechanisms jointly shape the phonological and semantic foundations of literacy.

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 5 matches between paragraphs and lines of code.

mikaelroll/corticalreading

License: MIT
State: the link answers, verified on 26 September 2026
Evidence: files inventoried
Commit: 2cf64d76d37944d6e79d06bdbe08a910d5202231, 28 August 2026
Languages: Shell (2), R (1)
Size: 6 files, 3 scripts
Software Heritage: not archived
Found in: “Data availability”
Holds: README, license file, documentation
Not found: CITATION.cff, environment file, tests, continuous integration
Tools: FSL (1 file), Connectome Workbench (1 file)
Availability: 1 check, the latest on 26 September 2026: the link answers
  • 26 September 2026: the link answers
5 files
At the source: github.com/mikaelroll/corticalreading

The paper's code and data availability statement is in the Data section.

Tracing map

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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;
  • 5 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

Preprocessed HCP Young Adult MRI data are available from the BALSA repository (https://balsa.wustl.edu/reference/pkXDZ). The full dataset (1.57 GB) can be downloaded, or individual files can be selected as needed. Minimally preprocessed HCP Young Adult structural (1.5 TB) and diffusion (2.7 TB) MRI, as well as behavioral and demographic data, are available from the Human Connectome Project BALSA repository (https://balsa.wustl.edu/project?project=HCP_YA). Use the “Export CSV” option to download behavioral data (3.5 MB for unrestricted data, 4.3 MB including restricted variables), or select specific columns as required. All code and scripts used for the analyses are available on GitHub (https://github.com/mikaelroll/corticalreading).

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

Versions

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Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 1 author, 5 keywords, 12 MeSH terms, 3 funders, 103 references.

Cite

This paper

Roll, M. (2026). Heritable and experience-dependent cortical traits of reading ability. Cerebral cortex (New York, N.Y. : 1991), 36(8), bhag125. https://doi.org/10.1093/cercor/bhag125

BibTeX

@article{roll2026heritable,
author = {Roll, Mikael},
title = {{Heritable and experience-dependent cortical traits of reading ability}},
journal = {Cerebral cortex (New York, N.Y. : 1991)},
year = {2026},
month = aug,
volume = {36},
number = {8},
pages = {bhag125},
publisher = {Oxford University Press},
issn = {1047-3211},
doi = {10.1093/cercor/bhag125},
url = {https://doi.org/10.1093/cercor/bhag125},
pmid = {42632036},
pmcid = {PMC13575274}
}

RIS

TY - JOUR
AU - Roll, Mikael
TI - Heritable and experience-dependent cortical traits of reading ability
T2 - Cerebral cortex (New York, N.Y. : 1991)
J2 - Cereb Cortex
PY - 2026
DA - 2026/08/01
VL - 36
IS - 8
SP - bhag125
SN - 1047-3211
PB - Oxford University Press
DO - 10.1093/cercor/bhag125
UR - https://doi.org/10.1093/cercor/bhag125
LA - en
ER -

CSL-JSON

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"id": "10.1093/cercor/bhag125",
"type": "article-journal",
"title": "Heritable and experience-dependent cortical traits of reading ability",
"container-title": "Cerebral cortex (New York, N.Y. : 1991)",
"author": [
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"family": "Roll",
"given": "Mikael"
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"container-title-short": "Cereb Cortex",
"volume": "36",
"issue": "8",
"page": "bhag125",
"DOI": "10.1093/cercor/bhag125",
"PMID": "42632036",
"PMCID": "PMC13575274",
"ISSN": "1047-3211",
"publisher": "Oxford University Press",
"URL": "https://doi.org/10.1093/cercor/bhag125",
"language": "en",
"issued": {
"date-parts": [
[
2026,
8,
1
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]
}
}

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