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
- # %%
- import os
- import glob
- import numpy as np
- import pandas as pd
- import matplotlib.pyplot as plt
- import seaborn as sns
- from nltools.stats import regress, zscore
- from nltools.data import Brain_Data, Design_Matrix
- from nltools.stats import find_spikes
- from nltools.mask import expand_mask
- # %%
- from nilearn import datasets
- from nilearn import image
- dataset_ho = datasets.fetch_atlas_harvard_oxford("cort-maxprob-thr25-2mm", data_dir=None, symmetric_split=True, resume=True, verbose=1)
- dataset_ju = datasets.fetch_atlas_juelich("maxprob-thr0-2mm")
- dataset_ju=datasets.fetch_atlas_juelich("maxprob-thr0-2mm", data_dir=None, symmetric_split=True, resume=True, verbose=1)
- atlas_ho_filename = dataset_ho.filename
- atlas_ju_filename = dataset_ju.filename
- labels = dataset_ho["labels"]
- print(f"Atlas ROIs are located at: {atlas_ho_filename}")
- print(f"Atlas ROIs are located at: {atlas_ju_filename}")
- from nilearn import plotting
- plotting.plot_roi(
- atlas_ho_filename, view_type="contours", title="Juelich atlas in contours"
- )
- plotting.show()
- # %%
- atlas_filename =dataset_ho["maps"]
- print(atlas_filename.shape)
- # Loading atlas dadataset_juta stored in 'labels'
- labels = dataset_ho["labels"]
- print(len(labels))
- print(labels)
- # %%
- from nilearn.datasets import fetch_atlas_harvard_oxford
- from nilearn.maskers import NiftiLabelsMasker
- from nilearn.image import load_img, index_img, resample_to_img
- ho = dataset_ju
- ho_img = ho.maps
- ho_img_resampled = resample_to_img(ho_img, nii_img, interpolation='nearest')
- ho_data = ho_img_resampled.get_fdata()
- ho_labels = ho.labels
- data_dictionary = {}
- for index,label in enumerate(ho_labels):
- print(index,label)
- if index == 0: # Skip background
- continue
- ho_region = (ho_data==index)
- nii_data_in_region = nii_data[ho_region,:]
- data_dictionary[label] = nii_data_in_region
- # %%
- # Load Image
- from nilearn import image
- #bilateral_mask_path = '/path/to/mask.nii.gz'
- bilateral_mask = image.load_img(atlas_ju_filename)
- mask_data = bilateral_mask.get_fdata()
- affine = bilateral_mask.affine
- # %%
- # Get center X-coord
- import os
- x_dim = mask_data.shape[0]
- x_center = int(x_dim/2)
- plotting.plot_img(bilateral_mask, title='Bilateral Mask')
- plotting.show()
- # Get left mask
- mask_data_left = mask_data.copy()
- mask_data_left[0:x_center,:,:] = 0
- mask_left = image.new_img_like(bilateral_mask, mask_data_left, affine=affine, copy_header=True)
- plotting.plot_img(mask_left, title='Left Mask')
- plotting.show()
- os.chdir('/Users/marysia/dropbox/PJM/masks')
- mask_left.to_filename('left_mask.nii.gz')
- # Get right mask
- mask_data_right = mask_data.copy()
- mask_data_right[x_center:,:,:] = 0
- mask_right = image.new_img_like(bilateral_mask, mask_data_right, affine=affine, copy_header=True)
- plotting.plot_img(mask_right, title='Right Mask')
- plotting.show()
- bilateral_mask.to_filename('mask_J.nii.gz')
- # %%
- def get_file_names1(data_dir_, task_name_, verbose = False):
- """
- Get all the participant file names
- Parameters
- ----------
- data_dir_ [str]: the data root dir
- task_name_ [str]: the name of the task
- Return
- ----------
- fnames_ [list]: file names for all subjs
- """
- upper_limit_n_subjs=22
- c_ = 0
- fnames_ = []
- # Collect all file names
- #these are natives
- #for subj in [1,2,5,6,7,8,9,10,11,13,14,15,16,23,24,25,26,27,29,30]:
- for subj in [1,2,3,4,5,6,8,9,10,11,12,13,14,15,16,17,18,19,20,21]:
- #late signers
- #
- #for subj in [2,3,4,6,5,6,8,9,12,13,14,15,16,17,18,20,21]:
- #
- #for subj in range(1, n_subjs_total):
- #fname = os.path.join(
- #data_dir_, 'sub-%.2d/func/sub-%.2d_run-6_denoise_smooth6mm_task-%s_desc-preproc_bold.nii.gz' % (subj, subj, task_name_))
- fname = os.path.join(
- #data_dir_, 'sub-deaf%.2d/func/sub-deaf%.2d_denoise_smooth6mm_task-%s_MNI152NLin2009cAsym_desc-preproc_bold.nii.gz' % (subj, subj, task_name_))
- data_dir_, 'sub-deaf%.2d/func/sub-deaf%.2d_denoise_smooth6mm_task-%s_MNI152NLin2009cAsym_desc-preproc_bold.nii.gz' % (subj, subj, task_name_))
- #data_dir_, 'sub-%.3d/sub-%.3d-task-%s.nii.gz' % (subj, subj, task_name_))
- print(fname)
- # If the file exists
- if os.path.exists(fname):
- # Add to the list of file names
- fnames_.append(fname)
- if verbose:
- print(fname)
- c_+= 1
- if c_ >= upper_limit_n_subjs:
- break
- return fnames_
- # %%
- my_list=[]
- from nilearn import plotting
- from brainiak import io
- from nilearn.image import resample_to_img
- dir_mask='/Users/marysia/dropbox/PJM/masks'
- mask_name = os.path.join(dir_mask, 'MNI152_T1_3mm_Brain_mask.nii')
- import nibabel.processing
- isrsa_nn2=np.load('/Users/marysia/dropbox/PJM/results/whole_brain_isc/isc/Correlations/rs_pseudo.npy')
- brain_mask = nib.load(mask_name)
- brain_mask = io.load_boolean_mask(mask_name)
- # Get the list of nonzero voxel coordinates
- coords = np.where(brain_mask)
- # Load the brain nii image
- brain_nii = nib.load(mask_name)
- print(brain_nii.shape)
- import os
- base_dir='/Users/marysia/dropbox/PJM/fmriprep/'
- #datad = image.load_img(atlas_ho_filename)
- import nibabel as nib
- datad= nib.load(os.path.join('/Users/marysia/dropbox/PJM/masks/','FFA2.nii.gz'))
- print(datad.shape)
- datad= resample_to_img(datad, brain_nii)
- mask=Brain_Data(datad)
- file_list = glob.glob(os.path.join(base_dir, '*', 'func', f'*denoise_smooth6mm_task-intact22_MNI152NLin2009cAsym_desc-preproc_bold.nii.gz'))
- print(file_list)
- for f in file_list:
- sub = os.path.basename(f).split('_')[0]
- data = Brain_Data(f)
- roi = data.extract_roi(mask)
- pd.DataFrame(roi.T).to_csv(os.path.join(os.path.dirname(f),'ffa2_intact2.csv'), index=False)
- # %%
- my_list=[]
- import os
- base_dir='/Users/marysia/dropbox/PJM/fmriprep/'
- datad = image.load_img(atlas_ho_filename)
- datad= nib.load(FFA1.nii.gz)
- mask=Brain_Data(datad)
- print(mask)
- mask_x = expand_mask(mask)
- file_list = glob.glob(os.path.join(base_dir, '*', 'func', f'*denoise_smooth6mm_task-intact22_MNI152NLin2009cAsym_desc-preproc_bold.nii.gz'))
- print(file_list)
- for f in file_list:
- sub = os.path.basename(f).split('_')[0]
- data = Brain_Data(f)
- roi = data.extract_roi(mask)
- pd.DataFrame(roi.T).to_csv(os.path.join(os.path.dirname(f),'harvard_intact2.csv'), index=False)
- # %%
- my_list=[]
- import os
- base_dir='/Users/marysia/dropbox/PJM/fmriprep/'
- datad = image.load_img(atlas_ho_filename)
- mask=Brain_Data(datad)
- mask_x = expand_mask(mask)
- file_list = glob.glob(os.path.join(base_dir, '*', 'func', f'*denoise_smooth6mm_task-sentences2_MNI152NLin2009cAsym_desc-preproc_bold.nii.gz'))
- print(file_list)
- for f in file_list:
- sub = os.path.basename(f).split('_')[0]
- data = Brain_Data(f)
- roi = data.extract_roi(mask)
- pd.DataFrame(roi.T).to_csv(os.path.join(os.path.dirname(f),'harvard_sentences2.csv'), index=False)
- # %%
- my_list=[]
- import os
- base_dir='/Users/marysia/dropbox/PJM/fmriprep/'
- datad = image.load_img(atlas_ho_filename)
- mask=Brain_Data(datad)
- mask_x = expand_mask(mask)
- file_list = glob.glob(os.path.join(base_dir, '*', 'func', f'*denoise_smooth6mm_task-words2_MNI152NLin2009cAsym_desc-preproc_bold.nii.gz'))
- print(file_list)
- for f in file_list:
- sub = os.path.basename(f).split('_')[0]
- data = Brain_Data(f)
- roi = data.extract_roi(mask)
- pd.DataFrame(roi.T).to_csv(os.path.join(os.path.dirname(f),'harvard_words2.csv'), index=False)
- # %%
- my_list=[]
- import os
- base_dir='/Users/marysia/dropbox/PJM/fmriprep/'
- datad = image.load_img(atlas_ho_filename)
- mask=Brain_Data(datad)
- mask_x = expand_mask(mask)
- file_list = glob.glob(os.path.join(base_dir, '*', 'func', f'*denoise_smooth6mm_task-pseudo2_MNI152NLin2009cAsym_desc-preproc_bold.nii.gz'))
- print(file_list)
- for f in file_list:
- sub = os.path.basename(f).split('_')[0]
- data = Brain_Data(f)
- roi = data.extract_roi(mask)
- pd.DataFrame(roi.T).to_csv(os.path.join(os.path.dirname(f),'harvard_pseudo2.csv'), index=False)
- # %%
- from brainiak import isc
- time_series={}
- aa=[]
- file_list = glob.glob(os.path.join(base_dir, '*', 'func', f'*denoise_smooth6mm_task-pseudo_MNI152NLin2009cAsym_desc-preproc_bold.nii.gz'))
- print(file_list)
- for f in file_list:
- sub = os.path.basename(f).split('_')[0]
- part4 = pd.read_csv(os.path.join(base_dir, sub ,'func', 'ffa1_intact2.csv' ))
- part4.reset_index(inplace=True, drop=True)
- aa.append(part4)
- time_series[sub] = part4
- print(len(aa))
- np.stack((aa))
- print(np.shape(aa))
- roi_new=np.transpose(aa, (1, 2, 0))
- print(np.shape(roi_new))
- isc1 = isc.isc(roi_new, summary_statistic=None, pairwise=False)
- os.chdir('/Users/marysia/dropbox/PJM/')
- np.save('ffa1_ISC_pseudo2',isc1)
- df = pd.DataFrame(isc1)
- #labels = dataset_ho["labels"]
- #print(labels)
- ##df.columns = labels[1:97]
- #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])
- 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])
- # %%
- import numpy as np
- import pandas as pd
- import os
- os.chdir('/Users/marysia/dropbox/PJM/')
- a=pd.read_csv('ISC_harvard_words2.csv')
- b=pd.read_csv('ISC_harvard_sentences2.csv')
- c=pd.read_csv('ISC_harvard_pseudo2.csv')
- d=pd.read_csv('ISC_harvard_intact2.csv')
- cond= ['intact'] * 20
- cond1= ['sentences'] * 20
- cond2= ['words'] * 20
- cond3= ['pseudo'] * 20
- cond4=cond+cond1+cond2+cond3
- print(cond4)
- df.to_csv('ISC_ho_words.csv', index=None)
- df= pd.concat([d,b,a,c])
- new_labels = list(range(1, 97))
- new_labels1=[]
- for i in new_labels:
- new_labels1.append(str(i))
- df.insert(loc=0, column='cond', value=cond4)
- #new_labels=['cond','no','SUB']+new_labels
- #df.columns = new_labels
- print(df)
- df.to_csv('ISC_ho_all_rois123.csv', index=None)
- # %%
- print(labels[1:97])
- print(df)
- # %%
- new_labels = list(range(1, 97))
- new_labels1=[]
- for i in new_labels:
- new_labels1.append(str(i))
- print(labels)
- print(new_labels1[1:97])
- df=pd.melt(df, id_vars=['SUB','cond'], value_vars=labels[1:97])
- #df = pd.melt(df, id_vars='SUB')
- df.to_csv('ISC_ho_all_long.csv', index=None)
- # %%
- #view updated DataFrame
- df
- cond= ['words'] * 1920
- df.insert(loc=0, column='cond', value=cond)
- df.to_csv('ISC_ho_words.csv', index=None)
- # %%
- import os
- import pandas as pd
- os.chdir('/Users/marysia/dropbox/PJM/ROI')
- df = pd.read_csv("ISC_lang.csv", sep=';')
- print(df)
- df1 = df[df["ROI"] == "Mask07"]
- print(df1)
- df2=df1.pivot(index='Subject', columns='Condition', values='ISC')
- print(df2)
- df2.to_csv('ISC_lang_06.csv', index=None)
ROI_analysis.ipynb, no license · at the source
Overview
- Department of Psychology, University of Warsaw,Warsaw, Poland
- Department of Psychological and Brain Sciences, Johns Hopkins University,Baltimore, US
- Laboratory of Brain Imaging, Nencki Institute for Experimental Biology,Warsaw, Poland
- Institute of Psychology, Jagiellonian University,Kraków, Poland
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
Availability: 1 check, the latest on 27 September 2026: the link answers (HTTP 200)
- 27 September 2026: the link answers (HTTP 200)
2 files
- code/
ROI_analysis.ipynb , Jupyter, 342 lines - code/
lateralization_analysis. , Jupyter, 802 linesipynb
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:
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Read it in the paper: doi.org/10.1038/s41467-026-73895-3.
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- 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.
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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.
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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://
BibTeX
@article{zimmermann2026s
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/
url = {https://
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/
VL - 17
IS - 1
SP - 7126
SN - 2041-1723
PB - Nature Publishing Group
DO - 10.1038/
UR - https://
LA - en
ER -
CSL-JSON
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"id": "10.1038/
"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":
"volume": "17",
"issue": "1",
"page": "7126",
"DOI": "10.1038/
"PMID": "42236497",
"PMCID": "PMC13396480",
"ISSN": "2041-1723",
"publisher": "Nature Publishing Group",
"URL": "https://
"language": "en",
"issued": {
"date-parts": [
[
2026,
6,
3
]
]
}
}
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