OSCR

An open-access multi-site fMRI dataset for investigating conscious visual perception.

Code ↔ Paper

7 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 7 matches
  1. [1] § Technical Validation › Functional scans ↔ qc/01_analyze_MRIQC_IQMs.py, lines 1–44 · score 0.82 · framewise displacement, temporal SNR, MRIQC, DVARS, tsnr, fd
  2. [2] § Methods › Eye tracking data acquisition ↔ coglib/beh_et/eyetracking/DataParser.py, lines 739–833 · score 0.64 · EyeLink, eye tracker, Plus, pupil, position
  3. [3] § Technical Validation › Quality control ↔ coglib/beh_et/behavior/quality_checks.py, lines 833–903 · score 0.56 · alarm rates, hit rate, behavioral, Quality
  4. [4] § Methods › Experiment design ↔ logfiles_and_checks/01_exp1_create_events_tsv_file.py, lines 89–223 · score 0.55 · stimulus orientation, stimulus category, identities, block, irrelevant, letters
  5. [5] § Methods › Site-specific equipment differences ↔ coglib/beh_et/eyetracking/ET_param_manager.py, lines 241–296 · score 0.53 · eye trackers, viewing distances, setup
  6. [6] § Methods › Experiment procedure ↔ coglib/beh_et/behavior/data_reader.py, lines 350–416 · score 0.52 · stimulus onset, task irrelevant, manipulated, behavioral, fixation, block
  7. [7] § Data Records › Bundles › Subject-specific data ↔ decoding/searchlight_orientation_decoding_subject_level.py, lines 46–86 · score 0.51 · Dur_run, stimulus orientation, tsv, ses, sub

Paper

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The authors' code

Python · 221 lines · 8.7 KB · MIT · 1 match

  1. #!/usr/bin/env python3
  2. # -*- coding: utf-8 -*-
  3. """
  4. The code is used for QC motion threshold.
  5. It checks MRI data quality using IQMs from MRIQC.
  6. Takes MRIQC outputs, assuming bids specifications (bids_dir).
  7. Calculates mean FD, FD_perc, DVARS and tsnr per run. Uses FD_perc and DVARS
  8. to reject bad participants exceeding X SD above (FD_perc, DVARS) the group
  9. mean (X defined in SdThreshold).
  10. Utilized metrics are specified in more detail here:
  11. https://mriqc.readthedocs.io/en/latest/measures.html
  12. FD = Framewise Displacement: expresses instantaneous head-motion.
  13. MRIQC reports the average FD, labeled as fd_mean.
  14. Rotational displacements are calculated as the displacement on the surface
  15. of a sphere of radius 50 mm [Power2012]:
  16. FD_perc = the percent of FDs above the FD threshold w.r.t. the full timeseries
  17. FD threshold is set at 0.20mm.
  18. DVARS = D: temporal derivative of timecourses. VARS: RMS variance over voxels
  19. ([Power2012] dvars_nstd). Indexes the rate of change of BOLD signal across
  20. the entire brain at each frame of data.
  21. TSNR = Temporal SNR is a simplified interpretation of the tSNR definition
  22. [Kruger2001]. Reports the median value of the tSNR map calculated by:
  23. average BOLD signal (across time) divided by the corresponding temporal
  24. standard-deviation map.
  25. Writes 3 output csv files:
  26. 2 csv files with subjects rejected per session, averaged over runs
  27. (IQM-summary-ses).
  28. 1 csv file with rows per run, allowing for run specific rejection (IQM-allRuns)
  29. Each csv file contains subject IDs, session labels if applicable and 4 IQMs
  30. (FD, FD_perc, DVARS and tsnr), and a rejection flag, indicating if the
  31. run/subject should be rejected from analysis. Outputs are written to the MRIQC
  32. directory (mriQcSubdir).
  33. @author: David Richter, first created 01/27/2021
  34. @ Modified by Urszula Gorska ([email hidden])
  35. Last modified 06/15/2023
  36. """
  37. import os, sys, json
  38. import numpy as np
  39. import pandas as pd
  40. #%% Paths and Parameters
  41. # root project path
  42. root_dir = '/mnt/beegfs/XNAT/COGITATE/fMRI/phase_2/processed'
  43. # threshold to mark subjects as rejected if they exceed X SD above group mean
  44. SdThreshold = 2
  45. ###############################################################################
  46. # bids path
  47. bids_dir = root_dir + '/bids'
  48. # mri qc sub dir
  49. mriQcSubdir = '/derivatives/mriqc'
  50. # sub dir pattern with sub and ses key-value pairs
  51. dataDirPattern = bids_dir + mriQcSubdir + os.sep + '%(sub)s' + os.sep + '%(ses)s' + os.sep + 'func' + os.sep
  52. # session labels
  53. sesLabels = ['ses-V1']
  54. participants_dir = bids_dir
  55. subject_list_type = 'demo'
  56. # load helper functions / code dir
  57. code_dir_with_helperfunctions = bids_dir + '/coglib/fmri'
  58. sys.path.append(code_dir_with_helperfunctions)
  59. from helper_functions_MRI import get_subject_list
  60. # %% support functions
  61. def getJsonFnames(fPath):
  62. """
  63. Get MRIQC output json files for current subject and session
  64. fPath: file path + name
  65. Returns: jsonFiles per run
  66. """
  67. jsonFiles = []
  68. for root, dirs, files in os.walk(fPath):
  69. for file in files:
  70. if file.endswith(".json"):
  71. jsonFiles.append(os.path.join(root, file))
  72. return jsonFiles
  73. def saveIQMs(df, ses=None):
  74. """
  75. Save summary IQM as csv file, either per session with data averaged across
  76. runs if ses arg is passed or for all runs separately if ses arg is not
  77. passed
  78. df: data frame with IQMs to be written as csv file
  79. ses: session label
  80. """
  81. outputDir = bids_dir + mriQcSubdir
  82. # outputDir = bids_dir + mriQcSubdir
  83. if ses is None:
  84. fname = outputDir + os.sep + 'IQM-perRun_' + subject_list_type + '.csv'
  85. else:
  86. fname = outputDir + os.sep + 'IQM-summary_' + ses + '_' + subject_list_type + '.csv'
  87. df.to_csv(fname, sep=',', index=False)
  88. # %% data processing functions
  89. def getDataFromJson(jsonFiles):
  90. """
  91. Get relevant IQM data from json files (output of MRIQC) per run
  92. jsonFiles: json file paths + names
  93. Returns: df_sub pandas data frame with relevant IQMs per run
  94. """
  95. sub_id = []
  96. ses_label = []
  97. run_label = []
  98. fd_mean = []
  99. fd_perc = []
  100. dvars_nstd = []
  101. tsnr = []
  102. for fname in jsonFiles:
  103. sub_id.append(fname[fname.find('sub-')+4:fname.find('sub-')+9])
  104. ses_label.append(fname[fname.find('ses-')+4:fname.find('ses-')+6])
  105. run_label.append(fname[fname.find('task-')+5:fname.find('run-')+5])
  106. with open(fname) as json_file:
  107. data = json.load(json_file)
  108. fd_mean.append(data['fd_mean'])
  109. fd_perc.append(data['fd_perc'])
  110. dvars_nstd.append(data['dvars_nstd'])
  111. tsnr.append(data['tsnr'])
  112. df_sub = pd.DataFrame({"sub_id":sub_id, "session":ses_label, "run":run_label, "fd_mean":fd_mean, "fd_perc":fd_perc, "dvars_nstd":dvars_nstd, "tsnr":tsnr, "rejected":[False]*len(sub_id)})
  113. return df_sub
  114. def processQMs(df):
  115. """
  116. Process IQMs by adding the mean and adding a rejection flag per subject
  117. based on the subject's IQM being x SD (defined in SdThreshold) worse than
  118. the group mean.
  119. IQMs used for rejection are:
  120. fd_perc = the percent of FDs above the FD threshold w.r.t. the full
  121. timeseries FD threshold is set at 0.20mm (MRI QC default).
  122. dvars_nstd = D: temporal derivative of timecourses. VARS: RMS variance over
  123. voxels ([Power2012] dvars_nstd). Indexes the rate of change of BOLD
  124. signal across the entire brain at each frame of data.
  125. tsnr = Temporal SNR is a simplified interpretation of the tSNR definition
  126. [Kruger2001]. Reports the median value of the tSNR map calculated by:
  127. average BOLD signal (across time) divided by the corresponding
  128. temporal standard-deviation map.
  129. df: data frame to be processed containing the IQMs
  130. Returns df with added mean and rejection flags (rejected == 1 indicating
  131. rejected participants/runs)
  132. """
  133. # add mean
  134. sd = df.std().copy()
  135. df.loc['mean'] = df.mean().copy()
  136. df.loc['mean', ['subIDs']]='average'
  137. # add rejection flag for 'bad' subjects if any IQM does not pass check
  138. # fd percentage
  139. rejThresh_fd_perc = df.fd_perc['mean'] + SdThreshold * sd['fd_perc']
  140. df.loc[df.fd_perc > rejThresh_fd_perc,['rejected']] = 1
  141. # dvars
  142. rejThresh_dvars = df.dvars_nstd['mean'] + SdThreshold * sd['dvars_nstd']
  143. df.loc[df.dvars_nstd > rejThresh_dvars,['rejected']] = 1
  144. ## tsnr (add lines below back in if tsnr is also to be used to reject data)
  145. #rejThresh_tsnr = df.tsnr['mean'] - SdThreshold * sd['tsnr']
  146. #df.loc[df.tsnr < rejThresh_tsnr,['rejected']] = 1
  147. return df
  148. #%%
  149. if __name__ == '__main__':
  150. """
  151. Gather IQMs (image quality metrics) from MRIQC output per subject
  152. (averaging over runs) and session.
  153. Write output csv file containing IQMs of interest
  154. subjects: list of subjects to be processed (MRI QC must be finished for all
  155. sessions for these subjects)
  156. """
  157. # subjects = get_subject_list(bids_dir,subject_list_type)
  158. subjects = get_subject_list(participants_dir,subject_list_type)
  159. df_all = pd.DataFrame()
  160. # loop over sessions
  161. for sesIdx in range(len(sesLabels)):
  162. ses = sesLabels[sesIdx]
  163. subIDs = []
  164. av_fd_mean = []
  165. av_fd_perc = []
  166. av_dvars_nstd =[]
  167. av_tsnr = []
  168. # loop over subjects
  169. for sub in subjects:
  170. print('Processing | subject: ' + sub + ' | session: ' + ses)
  171. fPath = dataDirPattern%{'sub':sub, 'ses':ses}
  172. # get json files
  173. jsonFiles = getJsonFnames(fPath)
  174. print(fPath)
  175. # check if json files exist; otherwise throw warning and skip sub
  176. if not jsonFiles:
  177. print('! CAUTION: No MRIQC json files found for subject: ' + sub + ' | session: ' + ses + ' ! Skipping ! Make sure to run MRIQC for all subjects first !')
  178. continue
  179. df_sub = getDataFromJson(jsonFiles)
  180. # append sub df to df with all runs and sessions
  181. df_all = df_all.append(df_sub, ignore_index=True)
  182. # calc mean over runs and add to list
  183. av_fd_mean.append(np.mean(df_sub['fd_mean']))
  184. av_fd_perc.append(np.mean(df_sub['fd_perc']))
  185. av_dvars_nstd.append(np.mean(df_sub['dvars_nstd']))
  186. av_tsnr.append(np.mean(df_sub['tsnr']))
  187. subIDs.append(sub)
  188. # gather data to df (QMs averaged over runs per subject)
  189. df = pd.DataFrame({"subIDs":subIDs, "fd_mean":av_fd_mean, "fd_perc":av_fd_perc, "dvars_nstd":av_dvars_nstd, "tsnr":av_tsnr, "rejected":[False]*len(av_tsnr)})
  190. df = processQMs(df)
  191. saveIQMs(df, ses)
  192. # process data frame containing all subjects & session IQMs per run
  193. df_all = processQMs(df_all)
  194. saveIQMs(df_all)

01_analyze_MRIQC_IQMs.py at commit 179b917, under MIT · at the source

Overview

Authors: Aya Khalaf1, David Richter2,3, Yamil Vidal2, Urszula Gorska-Klimowska4, Rony Hirschhorn5, Diptyajit Das6, Kyle Sinan Taylan Kahraman6, Praveen Sripad6, Fatemeh Taheriyan6, Liad Mudrik5,7,8, Michael Pitts9, Hal Blumenfeld10, Floris P de Lange2, Niccolò Bonacchi11, Tanya Brown6, Lucia Melloni6,7,12
  1. Department of Neurology, Yale School of Medicine, New Haven, CT USA
  2. Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, Nijmegen, the Netherlands
  3. Mind, Brain and Behavior Research Center (CIMCYC), University of Granada, Granada, Spain
  4. Department of Psychiatry, University of Wisconsin-Madison, Madison, WI 53719 USA
  5. Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
  6. Neural Circuits, Consciousness and Cognition Research Group, Max Planck Institute for Empirical Aesthetics, Frankfurt am Main, 60322 Germany
  7. Program for Brain, Mind, and Consciousness, Canadian Institute for Advanced Research, Toronto, Ontario Canada
  8. School of Psychological Sciences, Tel Aviv University, Tel Aviv, Israel
  9. Psychology Department, Reed College, Portland, OR 97202 USA
  10. Departments of Neurology, Neuroscience and Neurosurgery, Yale University School of Medicine, New Haven, CT USA
  11. William James Center for Research (WJCR), ISPA - Instituto Universitário, Rua Jardim do Tabaco, 34, 1149-041 Lisbon, Portugal
  12. Department of Neurology, New York University Grossman School of Medicine, New York, NY 10016 USA
Journal: Scientific data, volume 13, issue 1, article 779
Dates: received 25 August 2025; accepted 28 April 2026; published online 7 May 2026
Type: Data paper · Language: English
License: CC BY
Identifiers: DOI 10.1038/s41597-026-07377-y · PMID 42115661 · PMCID PMC13213011 · OpenAlex W7160823495
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: fMRI (modality), human (organism)
Methods: Physiology & signal measures, Statistics
Keywords: Perception, Consciousness
MeSH: Consciousness*, Magnetic Resonance Imaging*, Visual Perception*, Brain, Humans (* major topic)
Topic: Face Recognition and Perception (Cognitive Neuroscience, Neuroscience), according to OpenAlex
Funding: Max-Planck-Gesellschaft; Templeton World Charity Foundation (TWCF0389)
Citations: not cited yet (Europe PMC); 54 references in the paper

Abstract

We present a functional magnetic resonance (fMRI) dataset collected as part of an adversarial collaboration aimed at arbitrating between the Global Neuronal Workspace theory (GNWT) and the Integrated Information Theory (IIT) of consciousness. Participants (N = 118) were presented with suprathreshold visual stimuli belonging to four different categories (faces, objects, letters, false fonts) with three orientations (front, left, right view), and three durations (0.5, 1.0, 1.5 seconds). Participants were asked to identify infrequent targets that changed in each block, thereby rendering two categories task-relevant and two task-irrelevant. The simplicity of the experimental design and of the task given to the participants ensures that these data are broadly reusable. Besides testing predictions from other theories of consciousness, these data can be used to examine various aspects of visual processing. The anonymized data were converted to Brain Imaging Data Structure (BIDS), and can be easily accessed through a web platform or an API. The dataset contains quality reports, demographics, behavioral performance, and eye-tracking data. We also provide code for preprocessing and analyzing the data.

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 7 matches between paragraphs and lines of code.

cogitate-consortium/cogitate-experiment-code

License: MIT
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Evidence: files inventoried
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Cogitate-consortium/cogitate-fmri-analysis

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Commit: 179b9177ec599e9f928f31fa04357f5804c4b89d, 26 July 2024
Languages: Python (44), MATLAB (16), Shell (1)
Size: 128 files, 61 scripts
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cogitate-consortium/cogitate-msp1

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Not found: CITATION.cff, continuous integration, documentation
Tools: NumPy (134 files), pandas (89 files), Matplotlib (84 files), MNE-Python (78 files), SciPy (60 files), MNE-BIDS (38 files), seaborn (28 files), scikit-learn (22 files), NiBabel (15 files), Nilearn (12 files), statsmodels (12 files), scikit-image (8 files), Pingouin (6 files), MNE-Connectivity (5 files), autoreject (4 files), FreeSurfer (4 files), PyPREP (4 files), SPM (4 files), afex (2 files), BayesFactor (2 files), easystats (2 files), emmeans (2 files), FSL (2 files), ggplot2 (2 files), lmerTest (2 files), tidyverse (2 files), xarray (2 files), AFNI (1 file), car (1 file), Statistics and Machine Learning Toolbox (1 file)
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Zenodo 14020043

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Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: NumPy (36 files), pandas (23 files), Nilearn (12 files), NiBabel (11 files), Matplotlib (6 files), scikit-learn (6 files), SciPy (5 files), MNE-Python (4 files), SPM (4 files), FSL (2 files), Pingouin (2 files), AFNI (1 file)
Availability: 1 check, the latest on 28 September 2026: the link answers (HTTP 200)
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63 files
At the source:

Code availability

The codebase is implemented in Python and MATLAB. For an overview of the code and environment setup instructions, please refer to the README file in the repository. The code can be accessed through the following links:

• Experiment Code50: GitHub - Experiment Code (https://github.com/Cogitate-consortium/cogitate-experiment-code/tree/FMRI-Exp1)

• Preprocessing and Analysis Code51: GitHub - Analysis Code (https://github.com/Cogitate-consortium/cogitate-fmri-analysis)

For more information, please visit the COGITATE Data wiki (https://cogitate-consortium.github.io/cogitate-data), and the COGITATE website (https://www.arc-cogitate.com/).

Sample data and code demo. Sample data from four participants (two per testing site) can be found here (https://github.com/Cogitate-consortium/cogitate-msp1/tree/main/coglib/fmri#sample-data-and-demo). We provide bids converted data (./bids/) as well as preprocessed data (./bids/derivatives/fmriprep/ and ./bids/derivatives/freesurfer/). We also provide data quality measures that can be found in ./bids/derivatives/mriqc/. At the link, instructions can be found to try out the analyses using these data.

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

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:

  • 4 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 384 scripts, each with its path and the digest of its content;
  • 7 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

Datasets cited

Data availability

The data can be accessed through the following links:

• Data Terms of Use: PDF file (https://s.gwdg.de/NMyO8Y)

• Raw47 and BIDS48 fMRI Data (Bundle Format): Data Bundles (https://www.arc-cogitate.com/data-bundles-active)

• Raw and BIDS fMRI Data (XNAT49): XNAT Portal (https://cogitate-data.ae.mpg.de/)

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, 16 authors, 2 keywords, 5 MeSH terms, 2 funders, 44 references.

Cite

This paper

Khalaf, A., Richter, D., Vidal, Y., Gorska-Klimowska, U., Hirschhorn, R., Das, D., Kahraman, K. S. T., Sripad, P., Taheriyan, F., Mudrik, L., Pitts, M., Blumenfeld, H., de Lange, F. P., Bonacchi, N., Brown, T., & Melloni, L. (2026). An open-access multi-site fMRI dataset for investigating conscious visual perception. Scientific data, 13(1), 779. https://doi.org/10.1038/s41597-026-07377-y

BibTeX

@article{khalaf2026open,
author = {Khalaf, Aya and Richter, David and Vidal, Yamil and Gorska-Klimowska, Urszula and Hirschhorn, Rony and Das, Diptyajit and Kahraman, Kyle Sinan Taylan and Sripad, Praveen and Taheriyan, Fatemeh and Mudrik, Liad and Pitts, Michael and Blumenfeld, Hal and de Lange, Floris P and Bonacchi, Niccolò and Brown, Tanya and Melloni, Lucia},
title = {{An open-access multi-site fMRI dataset for investigating conscious visual perception}},
journal = {Scientific data},
year = {2026},
month = may,
volume = {13},
number = {1},
pages = {779},
publisher = {Nature Publishing Group},
issn = {2052-4463},
doi = {10.1038/s41597-026-07377-y},
url = {https://doi.org/10.1038/s41597-026-07377-y},
pmid = {42115661},
pmcid = {PMC13213011}
}

RIS

TY - JOUR
AU - Khalaf, Aya
AU - Richter, David
AU - Vidal, Yamil
AU - Gorska-Klimowska, Urszula
AU - Hirschhorn, Rony
AU - Das, Diptyajit
AU - Kahraman, Kyle Sinan Taylan
AU - Sripad, Praveen
AU - Taheriyan, Fatemeh
AU - Mudrik, Liad
AU - Pitts, Michael
AU - Blumenfeld, Hal
AU - de Lange, Floris P
AU - Bonacchi, Niccolò
AU - Brown, Tanya
AU - Melloni, Lucia
TI - An open-access multi-site fMRI dataset for investigating conscious visual perception
T2 - Scientific data
J2 - Sci Data
PY - 2026
DA - 2026/05/07
VL - 13
IS - 1
SP - 779
SN - 2052-4463
PB - Nature Publishing Group
DO - 10.1038/s41597-026-07377-y
UR - https://doi.org/10.1038/s41597-026-07377-y
LA - en
ER -

CSL-JSON

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"PMCID": "PMC13213011",
"ISSN": "2052-4463",
"publisher": "Nature Publishing Group",
"URL": "https://doi.org/10.1038/s41597-026-07377-y",
"language": "en",
"issued": {
"date-parts": [
[
2026,
5,
7
]
]
}
}

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