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Sign language narrative reveals universal and modality-specific features of cortical timescale hierarchy.

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The authors' code

Jupyter notebook · 342 lines · 10 KB · no license

  1. # %%
  2. import os
  3. import glob
  4. import numpy as np
  5. import pandas as pd
  6. import matplotlib.pyplot as plt
  7. import seaborn as sns
  8. from nltools.stats import regress, zscore
  9. from nltools.data import Brain_Data, Design_Matrix
  10. from nltools.stats import find_spikes
  11. from nltools.mask import expand_mask
  12. # %%
  13. from nilearn import datasets
  14. from nilearn import image
  15. dataset_ho = datasets.fetch_atlas_harvard_oxford("cort-maxprob-thr25-2mm", data_dir=None, symmetric_split=True, resume=True, verbose=1)
  16. dataset_ju = datasets.fetch_atlas_juelich("maxprob-thr0-2mm")
  17. dataset_ju=datasets.fetch_atlas_juelich("maxprob-thr0-2mm", data_dir=None, symmetric_split=True, resume=True, verbose=1)
  18. atlas_ho_filename = dataset_ho.filename
  19. atlas_ju_filename = dataset_ju.filename
  20. labels = dataset_ho["labels"]
  21. print(f"Atlas ROIs are located at: {atlas_ho_filename}")
  22. print(f"Atlas ROIs are located at: {atlas_ju_filename}")
  23. from nilearn import plotting
  24. plotting.plot_roi(
  25. atlas_ho_filename, view_type="contours", title="Juelich atlas in contours"
  26. )
  27. plotting.show()
  28. # %%
  29. atlas_filename =dataset_ho["maps"]
  30. print(atlas_filename.shape)
  31. # Loading atlas dadataset_juta stored in 'labels'
  32. labels = dataset_ho["labels"]
  33. print(len(labels))
  34. print(labels)
  35. # %%
  36. from nilearn.datasets import fetch_atlas_harvard_oxford
  37. from nilearn.maskers import NiftiLabelsMasker
  38. from nilearn.image import load_img, index_img, resample_to_img
  39. ho = dataset_ju
  40. ho_img = ho.maps
  41. ho_img_resampled = resample_to_img(ho_img, nii_img, interpolation='nearest')
  42. ho_data = ho_img_resampled.get_fdata()
  43. ho_labels = ho.labels
  44. data_dictionary = {}
  45. for index,label in enumerate(ho_labels):
  46. print(index,label)
  47. if index == 0: # Skip background
  48. continue
  49. ho_region = (ho_data==index)
  50. nii_data_in_region = nii_data[ho_region,:]
  51. data_dictionary[label] = nii_data_in_region
  52. # %%
  53. # Load Image
  54. from nilearn import image
  55. #bilateral_mask_path = '/path/to/mask.nii.gz'
  56. bilateral_mask = image.load_img(atlas_ju_filename)
  57. mask_data = bilateral_mask.get_fdata()
  58. affine = bilateral_mask.affine
  59. # %%
  60. # Get center X-coord
  61. import os
  62. x_dim = mask_data.shape[0]
  63. x_center = int(x_dim/2)
  64. plotting.plot_img(bilateral_mask, title='Bilateral Mask')
  65. plotting.show()
  66. # Get left mask
  67. mask_data_left = mask_data.copy()
  68. mask_data_left[0:x_center,:,:] = 0
  69. mask_left = image.new_img_like(bilateral_mask, mask_data_left, affine=affine, copy_header=True)
  70. plotting.plot_img(mask_left, title='Left Mask')
  71. plotting.show()
  72. os.chdir('/Users/marysia/dropbox/PJM/masks')
  73. mask_left.to_filename('left_mask.nii.gz')
  74. # Get right mask
  75. mask_data_right = mask_data.copy()
  76. mask_data_right[x_center:,:,:] = 0
  77. mask_right = image.new_img_like(bilateral_mask, mask_data_right, affine=affine, copy_header=True)
  78. plotting.plot_img(mask_right, title='Right Mask')
  79. plotting.show()
  80. bilateral_mask.to_filename('mask_J.nii.gz')
  81. # %%
  82. def get_file_names1(data_dir_, task_name_, verbose = False):
  83. """
  84. Get all the participant file names
  85. Parameters
  86. ----------
  87. data_dir_ [str]: the data root dir
  88. task_name_ [str]: the name of the task
  89. Return
  90. ----------
  91. fnames_ [list]: file names for all subjs
  92. """
  93. upper_limit_n_subjs=22
  94. c_ = 0
  95. fnames_ = []
  96. # Collect all file names
  97. #these are natives
  98. #for subj in [1,2,5,6,7,8,9,10,11,13,14,15,16,23,24,25,26,27,29,30]:
  99. for subj in [1,2,3,4,5,6,8,9,10,11,12,13,14,15,16,17,18,19,20,21]:
  100. #late signers
  101. #
  102. #for subj in [2,3,4,6,5,6,8,9,12,13,14,15,16,17,18,20,21]:
  103. #
  104. #for subj in range(1, n_subjs_total):
  105. #fname = os.path.join(
  106. #data_dir_, 'sub-%.2d/func/sub-%.2d_run-6_denoise_smooth6mm_task-%s_desc-preproc_bold.nii.gz' % (subj, subj, task_name_))
  107. fname = os.path.join(
  108. #data_dir_, 'sub-deaf%.2d/func/sub-deaf%.2d_denoise_smooth6mm_task-%s_MNI152NLin2009cAsym_desc-preproc_bold.nii.gz' % (subj, subj, task_name_))
  109. data_dir_, 'sub-deaf%.2d/func/sub-deaf%.2d_denoise_smooth6mm_task-%s_MNI152NLin2009cAsym_desc-preproc_bold.nii.gz' % (subj, subj, task_name_))
  110. #data_dir_, 'sub-%.3d/sub-%.3d-task-%s.nii.gz' % (subj, subj, task_name_))
  111. print(fname)
  112. # If the file exists
  113. if os.path.exists(fname):
  114. # Add to the list of file names
  115. fnames_.append(fname)
  116. if verbose:
  117. print(fname)
  118. c_+= 1
  119. if c_ >= upper_limit_n_subjs:
  120. break
  121. return fnames_
  122. # %%
  123. my_list=[]
  124. from nilearn import plotting
  125. from brainiak import io
  126. from nilearn.image import resample_to_img
  127. dir_mask='/Users/marysia/dropbox/PJM/masks'
  128. mask_name = os.path.join(dir_mask, 'MNI152_T1_3mm_Brain_mask.nii')
  129. import nibabel.processing
  130. isrsa_nn2=np.load('/Users/marysia/dropbox/PJM/results/whole_brain_isc/isc/Correlations/rs_pseudo.npy')
  131. brain_mask = nib.load(mask_name)
  132. brain_mask = io.load_boolean_mask(mask_name)
  133. # Get the list of nonzero voxel coordinates
  134. coords = np.where(brain_mask)
  135. # Load the brain nii image
  136. brain_nii = nib.load(mask_name)
  137. print(brain_nii.shape)
  138. import os
  139. base_dir='/Users/marysia/dropbox/PJM/fmriprep/'
  140. #datad = image.load_img(atlas_ho_filename)
  141. import nibabel as nib
  142. datad= nib.load(os.path.join('/Users/marysia/dropbox/PJM/masks/','FFA2.nii.gz'))
  143. print(datad.shape)
  144. datad= resample_to_img(datad, brain_nii)
  145. mask=Brain_Data(datad)
  146. file_list = glob.glob(os.path.join(base_dir, '*', 'func', f'*denoise_smooth6mm_task-intact22_MNI152NLin2009cAsym_desc-preproc_bold.nii.gz'))
  147. print(file_list)
  148. for f in file_list:
  149. sub = os.path.basename(f).split('_')[0]
  150. data = Brain_Data(f)
  151. roi = data.extract_roi(mask)
  152. pd.DataFrame(roi.T).to_csv(os.path.join(os.path.dirname(f),'ffa2_intact2.csv'), index=False)
  153. # %%
  154. my_list=[]
  155. import os
  156. base_dir='/Users/marysia/dropbox/PJM/fmriprep/'
  157. datad = image.load_img(atlas_ho_filename)
  158. datad= nib.load(FFA1.nii.gz)
  159. mask=Brain_Data(datad)
  160. print(mask)
  161. mask_x = expand_mask(mask)
  162. file_list = glob.glob(os.path.join(base_dir, '*', 'func', f'*denoise_smooth6mm_task-intact22_MNI152NLin2009cAsym_desc-preproc_bold.nii.gz'))
  163. print(file_list)
  164. for f in file_list:
  165. sub = os.path.basename(f).split('_')[0]
  166. data = Brain_Data(f)
  167. roi = data.extract_roi(mask)
  168. pd.DataFrame(roi.T).to_csv(os.path.join(os.path.dirname(f),'harvard_intact2.csv'), index=False)
  169. # %%
  170. my_list=[]
  171. import os
  172. base_dir='/Users/marysia/dropbox/PJM/fmriprep/'
  173. datad = image.load_img(atlas_ho_filename)
  174. mask=Brain_Data(datad)
  175. mask_x = expand_mask(mask)
  176. file_list = glob.glob(os.path.join(base_dir, '*', 'func', f'*denoise_smooth6mm_task-sentences2_MNI152NLin2009cAsym_desc-preproc_bold.nii.gz'))
  177. print(file_list)
  178. for f in file_list:
  179. sub = os.path.basename(f).split('_')[0]
  180. data = Brain_Data(f)
  181. roi = data.extract_roi(mask)
  182. pd.DataFrame(roi.T).to_csv(os.path.join(os.path.dirname(f),'harvard_sentences2.csv'), index=False)
  183. # %%
  184. my_list=[]
  185. import os
  186. base_dir='/Users/marysia/dropbox/PJM/fmriprep/'
  187. datad = image.load_img(atlas_ho_filename)
  188. mask=Brain_Data(datad)
  189. mask_x = expand_mask(mask)
  190. file_list = glob.glob(os.path.join(base_dir, '*', 'func', f'*denoise_smooth6mm_task-words2_MNI152NLin2009cAsym_desc-preproc_bold.nii.gz'))
  191. print(file_list)
  192. for f in file_list:
  193. sub = os.path.basename(f).split('_')[0]
  194. data = Brain_Data(f)
  195. roi = data.extract_roi(mask)
  196. pd.DataFrame(roi.T).to_csv(os.path.join(os.path.dirname(f),'harvard_words2.csv'), index=False)
  197. # %%
  198. my_list=[]
  199. import os
  200. base_dir='/Users/marysia/dropbox/PJM/fmriprep/'
  201. datad = image.load_img(atlas_ho_filename)
  202. mask=Brain_Data(datad)
  203. mask_x = expand_mask(mask)
  204. file_list = glob.glob(os.path.join(base_dir, '*', 'func', f'*denoise_smooth6mm_task-pseudo2_MNI152NLin2009cAsym_desc-preproc_bold.nii.gz'))
  205. print(file_list)
  206. for f in file_list:
  207. sub = os.path.basename(f).split('_')[0]
  208. data = Brain_Data(f)
  209. roi = data.extract_roi(mask)
  210. pd.DataFrame(roi.T).to_csv(os.path.join(os.path.dirname(f),'harvard_pseudo2.csv'), index=False)
  211. # %%
  212. from brainiak import isc
  213. time_series={}
  214. aa=[]
  215. file_list = glob.glob(os.path.join(base_dir, '*', 'func', f'*denoise_smooth6mm_task-pseudo_MNI152NLin2009cAsym_desc-preproc_bold.nii.gz'))
  216. print(file_list)
  217. for f in file_list:
  218. sub = os.path.basename(f).split('_')[0]
  219. part4 = pd.read_csv(os.path.join(base_dir, sub ,'func', 'ffa1_intact2.csv' ))
  220. part4.reset_index(inplace=True, drop=True)
  221. aa.append(part4)
  222. time_series[sub] = part4
  223. print(len(aa))
  224. np.stack((aa))
  225. print(np.shape(aa))
  226. roi_new=np.transpose(aa, (1, 2, 0))
  227. print(np.shape(roi_new))
  228. isc1 = isc.isc(roi_new, summary_statistic=None, pairwise=False)
  229. os.chdir('/Users/marysia/dropbox/PJM/')
  230. np.save('ffa1_ISC_pseudo2',isc1)
  231. df = pd.DataFrame(isc1)
  232. #labels = dataset_ho["labels"]
  233. #print(labels)
  234. ##df.columns = labels[1:97]
  235. #df.insert(loc=0, column='SUB', value=[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20])
  236. df.to_csv('ISC_ffa1.csv', index=[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20])
  237. # %%
  238. import numpy as np
  239. import pandas as pd
  240. import os
  241. os.chdir('/Users/marysia/dropbox/PJM/')
  242. a=pd.read_csv('ISC_harvard_words2.csv')
  243. b=pd.read_csv('ISC_harvard_sentences2.csv')
  244. c=pd.read_csv('ISC_harvard_pseudo2.csv')
  245. d=pd.read_csv('ISC_harvard_intact2.csv')
  246. cond= ['intact'] * 20
  247. cond1= ['sentences'] * 20
  248. cond2= ['words'] * 20
  249. cond3= ['pseudo'] * 20
  250. cond4=cond+cond1+cond2+cond3
  251. print(cond4)
  252. df.to_csv('ISC_ho_words.csv', index=None)
  253. df= pd.concat([d,b,a,c])
  254. new_labels = list(range(1, 97))
  255. new_labels1=[]
  256. for i in new_labels:
  257. new_labels1.append(str(i))
  258. df.insert(loc=0, column='cond', value=cond4)
  259. #new_labels=['cond','no','SUB']+new_labels
  260. #df.columns = new_labels
  261. print(df)
  262. df.to_csv('ISC_ho_all_rois123.csv', index=None)
  263. # %%
  264. print(labels[1:97])
  265. print(df)
  266. # %%
  267. new_labels = list(range(1, 97))
  268. new_labels1=[]
  269. for i in new_labels:
  270. new_labels1.append(str(i))
  271. print(labels)
  272. print(new_labels1[1:97])
  273. df=pd.melt(df, id_vars=['SUB','cond'], value_vars=labels[1:97])
  274. #df = pd.melt(df, id_vars='SUB')
  275. df.to_csv('ISC_ho_all_long.csv', index=None)
  276. # %%
  277. #view updated DataFrame
  278. df
  279. cond= ['words'] * 1920
  280. df.insert(loc=0, column='cond', value=cond)
  281. df.to_csv('ISC_ho_words.csv', index=None)
  282. # %%
  283. import os
  284. import pandas as pd
  285. os.chdir('/Users/marysia/dropbox/PJM/ROI')
  286. df = pd.read_csv("ISC_lang.csv", sep=';')
  287. print(df)
  288. df1 = df[df["ROI"] == "Mask07"]
  289. print(df1)
  290. df2=df1.pivot(index='Subject', columns='Condition', values='ISC')
  291. print(df2)
  292. df2.to_csv('ISC_lang_06.csv', index=None)

ROI_analysis.ipynb, no license · at the source

Overview

Authors: Maria Zimmermann1,2, Piotr Tomaszewski1, Artur Marchewka3, Marcin Szwed4, Marina Bedny2
  1. Department of Psychology, University of Warsaw,Warsaw, Poland
  2. Department of Psychological and Brain Sciences, Johns Hopkins University,Baltimore, US
  3. Laboratory of Brain Imaging, Nencki Institute for Experimental Biology,Warsaw, Poland
  4. Institute of Psychology, Jagiellonian University,Kraków, Poland
Journal: Nature communications, volume 17, issue 1, article 7126
Dates: received 22 May 2025; accepted 18 May 2026; published online 3 June 2026
Type: Research article · Language: English
License: CC BY-NC-ND
Identifiers: DOI 10.1038/s41467-026-73895-3 · PMID 42236497 · PMCID PMC13396480 · OpenAlex W7163345805
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: fMRI (modality), human (organism), cognitive (subfield)
Methods: Connectivity, Statistics, Smoothing, state filtering, decompositions, Machine learning, fMRI & imaging
Keywords: Human behaviour, Cognitive neuroscience
MeSH: Cerebral Cortex*, Narration*, Sign Language*, Adult, Brain Mapping, Comprehension, Female, Humans, Magnetic Resonance Imaging, Male, Occipital Lobe, Parietal Lobe, Speech, Young Adult (* major topic)
Topic: Hearing Impairment and Communication (Developmental and Educational Psychology, Psychology), according to OpenAlex
Funding: Narodowe Centrum Nauki (2018/30/A/HS6/00595, 2024/52/C/HS6/00207)
Citations: not cited yet (Europe PMC); 94 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.

OSF n8sv3

License: none: the authors keep all their rights
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Languages: Jupyter (6)
Size: 65 files, 6 scripts
Software Heritage: not checked
Found in: “Code availability”
Holds: 6 notebooks
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: NiBabel (2 files), Nilearn (2 files), NumPy (2 files), pandas (2 files), BrainIAK (1 file), Matplotlib (1 file), nltools (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)
2 files
At the source:

Code availability statement

The paper has a code availability statement. Its license (CC BY-NC-ND) does not allow reproducing it here; in short, from what the harvester recognized in it:

  • it points to the authors' code: OSF n8sv3

Read it in the paper: doi.org/10.1038/s41467-026-73895-3.

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.

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  • 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 2 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

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Data availability statement

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  • no repository, dataset or request procedure was recognized in it

Read it in the paper: doi.org/10.1038/s41467-026-73895-3.

Versions

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Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 5 authors, 2 keywords, 14 MeSH terms, 1 funder, 71 references.

Cite

This paper

Zimmermann, M., Tomaszewski, P., Marchewka, A., Szwed, M., & Bedny, M. (2026). Sign language narrative reveals universal and modality-specific features of cortical timescale hierarchy. Nature communications, 17(1), 7126. https://doi.org/10.1038/s41467-026-73895-3

BibTeX

@article{zimmermann2026sign,
author = {Zimmermann, Maria and Tomaszewski, Piotr and Marchewka, Artur and Szwed, Marcin and Bedny, Marina},
title = {{Sign language narrative reveals universal and modality-specific features of cortical timescale hierarchy}},
journal = {Nature communications},
year = {2026},
month = jun,
volume = {17},
number = {1},
pages = {7126},
publisher = {Nature Publishing Group},
issn = {2041-1723},
doi = {10.1038/s41467-026-73895-3},
url = {https://doi.org/10.1038/s41467-026-73895-3},
pmid = {42236497},
pmcid = {PMC13396480}
}

RIS

TY - JOUR
AU - Zimmermann, Maria
AU - Tomaszewski, Piotr
AU - Marchewka, Artur
AU - Szwed, Marcin
AU - Bedny, Marina
TI - Sign language narrative reveals universal and modality-specific features of cortical timescale hierarchy
T2 - Nature communications
J2 - Nat Commun
PY - 2026
DA - 2026/06/03
VL - 17
IS - 1
SP - 7126
SN - 2041-1723
PB - Nature Publishing Group
DO - 10.1038/s41467-026-73895-3
UR - https://doi.org/10.1038/s41467-026-73895-3
LA - en
ER -

CSL-JSON

{
"id": "10.1038/s41467-026-73895-3",
"type": "article-journal",
"title": "Sign language narrative reveals universal and modality-specific features of cortical timescale hierarchy",
"container-title": "Nature communications",
"author": [
{
"family": "Zimmermann",
"given": "Maria"
},
{
"family": "Tomaszewski",
"given": "Piotr"
},
{
"family": "Marchewka",
"given": "Artur"
},
{
"family": "Szwed",
"given": "Marcin"
},
{
"family": "Bedny",
"given": "Marina"
}
],
"container-title-short": "Nat Commun",
"volume": "17",
"issue": "1",
"page": "7126",
"DOI": "10.1038/s41467-026-73895-3",
"PMID": "42236497",
"PMCID": "PMC13396480",
"ISSN": "2041-1723",
"publisher": "Nature Publishing Group",
"URL": "https://doi.org/10.1038/s41467-026-73895-3",
"language": "en",
"issued": {
"date-parts": [
[
2026,
6,
3
]
]
}
}

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Journal: Research Square (preprint)
In common: Nilearn, NiBabel, seaborn, 4 other tools, fMRI, cognitive, 4 references
[8] doi:10.64898/2026.03.09.710558 [code]
Multi-task fMRI outperforms resting-state fMRI for revealing task-invariant organization of the human brain
Journal: bioRxiv (preprint)
In common: Nilearn, NiBabel, seaborn, 4 other tools, fMRI, cognitive, 4 references
[9] doi:10.7554/elife.107933 [code]
Modality-agnostic decoding of vision and language from fMRI.
Journal: eLife
In common: Nilearn, NiBabel, statsmodels, 5 other tools, fMRI, cognitive, 2 references
[10] doi:10.1038/s41467-026-75745-8 [code]
A language network in the individualized functional connectomes of 1199 human brains doing arbitrary tasks.
Journal: Nature communications
In common: Nilearn, NiBabel, seaborn, 4 other tools, cognitive, 4 references

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