An open-access multi-site fMRI dataset for investigating conscious visual perception.
The 7 matches
- [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] § Methods › Eye tracking data acquisition ↔ coglib/beh_et/eyetracking/DataParser.py, lines 739–833 · score 0.64 · EyeLink, eye tracker, Plus, pupil, position
- [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] § 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] § 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] § 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] § 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
- #!/usr/bin/env python3
- # -*- coding: utf-8 -*-
- """
- The code is used for QC motion threshold.
- It checks MRI data quality using IQMs from MRIQC.
- Takes MRIQC outputs, assuming bids specifications (bids_dir).
- Calculates mean FD, FD_perc, DVARS and tsnr per run. Uses FD_perc and DVARS
- to reject bad participants exceeding X SD above (FD_perc, DVARS) the group
- mean (X defined in SdThreshold).
- Utilized metrics are specified in more detail here:
- https://mriqc.readthedocs.io/en/latest/measures.html
- FD = Framewise Displacement: expresses instantaneous head-motion.
- MRIQC reports the average FD, labeled as fd_mean.
- Rotational displacements are calculated as the displacement on the surface
- of a sphere of radius 50 mm [Power2012]:
- FD_perc = the percent of FDs above the FD threshold w.r.t. the full timeseries
- FD threshold is set at 0.20mm.
- DVARS = D: temporal derivative of timecourses. VARS: RMS variance over voxels
- ([Power2012] dvars_nstd). Indexes the rate of change of BOLD signal across
- the entire brain at each frame of data.
- TSNR = Temporal SNR is a simplified interpretation of the tSNR definition
- [Kruger2001]. Reports the median value of the tSNR map calculated by:
- average BOLD signal (across time) divided by the corresponding temporal
- standard-deviation map.
- Writes 3 output csv files:
- 2 csv files with subjects rejected per session, averaged over runs
- (IQM-summary-ses).
- 1 csv file with rows per run, allowing for run specific rejection (IQM-allRuns)
- Each csv file contains subject IDs, session labels if applicable and 4 IQMs
- (FD, FD_perc, DVARS and tsnr), and a rejection flag, indicating if the
- run/subject should be rejected from analysis. Outputs are written to the MRIQC
- directory (mriQcSubdir).
- @author: David Richter, first created 01/27/2021
- @ Modified by Urszula Gorska ([email hidden])
- Last modified 06/15/2023
- """
- import os, sys, json
- import numpy as np
- import pandas as pd
- #%% Paths and Parameters
- # root project path
- root_dir = '/mnt/beegfs/XNAT/COGITATE/fMRI/phase_2/processed'
- # threshold to mark subjects as rejected if they exceed X SD above group mean
- SdThreshold = 2
- ###############################################################################
- # bids path
- bids_dir = root_dir + '/bids'
- # mri qc sub dir
- mriQcSubdir = '/derivatives/mriqc'
- # sub dir pattern with sub and ses key-value pairs
- dataDirPattern = bids_dir + mriQcSubdir + os.sep + '%(sub)s' + os.sep + '%(ses)s' + os.sep + 'func' + os.sep
- # session labels
- sesLabels = ['ses-V1']
- participants_dir = bids_dir
- subject_list_type = 'demo'
- # load helper functions / code dir
- code_dir_with_helperfunctions = bids_dir + '/coglib/fmri'
- sys.path.append(code_dir_with_helperfunctions)
- from helper_functions_MRI import get_subject_list
- # %% support functions
- def getJsonFnames(fPath):
- """
- Get MRIQC output json files for current subject and session
- fPath: file path + name
- Returns: jsonFiles per run
- """
- jsonFiles = []
- for root, dirs, files in os.walk(fPath):
- for file in files:
- if file.endswith(".json"):
- jsonFiles.append(os.path.join(root, file))
- return jsonFiles
- def saveIQMs(df, ses=None):
- """
- Save summary IQM as csv file, either per session with data averaged across
- runs if ses arg is passed or for all runs separately if ses arg is not
- passed
- df: data frame with IQMs to be written as csv file
- ses: session label
- """
- outputDir = bids_dir + mriQcSubdir
- # outputDir = bids_dir + mriQcSubdir
- if ses is None:
- fname = outputDir + os.sep + 'IQM-perRun_' + subject_list_type + '.csv'
- else:
- fname = outputDir + os.sep + 'IQM-summary_' + ses + '_' + subject_list_type + '.csv'
- df.to_csv(fname, sep=',', index=False)
- # %% data processing functions
- def getDataFromJson(jsonFiles):
- """
- Get relevant IQM data from json files (output of MRIQC) per run
- jsonFiles: json file paths + names
- Returns: df_sub pandas data frame with relevant IQMs per run
- """
- sub_id = []
- ses_label = []
- run_label = []
- fd_mean = []
- fd_perc = []
- dvars_nstd = []
- tsnr = []
- for fname in jsonFiles:
- sub_id.append(fname[fname.find('sub-')+4:fname.find('sub-')+9])
- ses_label.append(fname[fname.find('ses-')+4:fname.find('ses-')+6])
- run_label.append(fname[fname.find('task-')+5:fname.find('run-')+5])
- with open(fname) as json_file:
- data = json.load(json_file)
- fd_mean.append(data['fd_mean'])
- fd_perc.append(data['fd_perc'])
- dvars_nstd.append(data['dvars_nstd'])
- tsnr.append(data['tsnr'])
- 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)})
- return df_sub
- def processQMs(df):
- """
- Process IQMs by adding the mean and adding a rejection flag per subject
- based on the subject's IQM being x SD (defined in SdThreshold) worse than
- the group mean.
- IQMs used for rejection are:
- fd_perc = the percent of FDs above the FD threshold w.r.t. the full
- timeseries FD threshold is set at 0.20mm (MRI QC default).
- dvars_nstd = D: temporal derivative of timecourses. VARS: RMS variance over
- voxels ([Power2012] dvars_nstd). Indexes the rate of change of BOLD
- signal across the entire brain at each frame of data.
- tsnr = Temporal SNR is a simplified interpretation of the tSNR definition
- [Kruger2001]. Reports the median value of the tSNR map calculated by:
- average BOLD signal (across time) divided by the corresponding
- temporal standard-deviation map.
- df: data frame to be processed containing the IQMs
- Returns df with added mean and rejection flags (rejected == 1 indicating
- rejected participants/runs)
- """
- # add mean
- sd = df.std().copy()
- df.loc['mean'] = df.mean().copy()
- df.loc['mean', ['subIDs']]='average'
- # add rejection flag for 'bad' subjects if any IQM does not pass check
- # fd percentage
- rejThresh_fd_perc = df.fd_perc['mean'] + SdThreshold * sd['fd_perc']
- df.loc[df.fd_perc > rejThresh_fd_perc,['rejected']] = 1
- # dvars
- rejThresh_dvars = df.dvars_nstd['mean'] + SdThreshold * sd['dvars_nstd']
- df.loc[df.dvars_nstd > rejThresh_dvars,['rejected']] = 1
- ## tsnr (add lines below back in if tsnr is also to be used to reject data)
- #rejThresh_tsnr = df.tsnr['mean'] - SdThreshold * sd['tsnr']
- #df.loc[df.tsnr < rejThresh_tsnr,['rejected']] = 1
- return df
- #%%
- if __name__ == '__main__':
- """
- Gather IQMs (image quality metrics) from MRIQC output per subject
- (averaging over runs) and session.
- Write output csv file containing IQMs of interest
- subjects: list of subjects to be processed (MRI QC must be finished for all
- sessions for these subjects)
- """
- # subjects = get_subject_list(bids_dir,subject_list_type)
- subjects = get_subject_list(participants_dir,subject_list_type)
- df_all = pd.DataFrame()
- # loop over sessions
- for sesIdx in range(len(sesLabels)):
- ses = sesLabels[sesIdx]
- subIDs = []
- av_fd_mean = []
- av_fd_perc = []
- av_dvars_nstd =[]
- av_tsnr = []
- # loop over subjects
- for sub in subjects:
- print('Processing | subject: ' + sub + ' | session: ' + ses)
- fPath = dataDirPattern%{'sub':sub, 'ses':ses}
- # get json files
- jsonFiles = getJsonFnames(fPath)
- print(fPath)
- # check if json files exist; otherwise throw warning and skip sub
- if not jsonFiles:
- print('! CAUTION: No MRIQC json files found for subject: ' + sub + ' | session: ' + ses + ' ! Skipping ! Make sure to run MRIQC for all subjects first !')
- continue
- df_sub = getDataFromJson(jsonFiles)
- # append sub df to df with all runs and sessions
- df_all = df_all.append(df_sub, ignore_index=True)
- # calc mean over runs and add to list
- av_fd_mean.append(np.mean(df_sub['fd_mean']))
- av_fd_perc.append(np.mean(df_sub['fd_perc']))
- av_dvars_nstd.append(np.mean(df_sub['dvars_nstd']))
- av_tsnr.append(np.mean(df_sub['tsnr']))
- subIDs.append(sub)
- # gather data to df (QMs averaged over runs per subject)
- 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)})
- df = processQMs(df)
- saveIQMs(df, ses)
- # process data frame containing all subjects & session IQMs per run
- df_all = processQMs(df_all)
- saveIQMs(df_all)
01_analyze_MRIQC_IQMs.py at commit 179b917, under MIT · at the source
Overview
- Department of Neurology, Yale School of Medicine, New Haven, CT USA
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, Nijmegen, the Netherlands
- Mind, Brain and Behavior Research Center (CIMCYC), University of Granada, Granada, Spain
- Department of Psychiatry, University of Wisconsin-Madison, Madison, WI 53719 USA
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
- Neural Circuits, Consciousness and Cognition Research Group, Max Planck Institute for Empirical Aesthetics, Frankfurt am Main, 60322 Germany
- Program for Brain, Mind, and Consciousness, Canadian Institute for Advanced Research, Toronto, Ontario Canada
- School of Psychological Sciences, Tel Aviv University, Tel Aviv, Israel
- Psychology Department, Reed College, Portland, OR 97202 USA
- Departments of Neurology, Neuroscience and Neurosurgery, Yale University School of Medicine, New Haven, CT USA
- William James Center for Research (WJCR), ISPA - Instituto Universitário, Rua Jardim do Tabaco, 34, 1149-041 Lisbon, Portugal
- Department of Neurology, New York University Grossman School of Medicine, New York, NY 10016 USA
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
6b935f0cea81acc66c1d9cb6a9b35cf044faa743, 9 September 2025Availability: 1 check, the latest on 28 September 2026: the link answers
- 28 September 2026: the link answers
Cogitate-consortium/cogitate-fmri-analysis
179b9177ec599e9f928f31fa04357f5804c4b89d, 26 July 2024Availability: 1 check, the latest on 28 September 2026: the link answers
- 28 September 2026: the link answers
63 files
- decoding/
MSP1_roi_decoding_plots. , Python, 103 linespy - decoding/
MSP1_searchlight_decodin , Python, 97 linesg_plots.py - decoding/
config.py , Python, 63 lines - decoding/
plotters.py , Python, 1,010 lines - decoding/
rename_confounds_tsv_fil , MATLAB, 36 lineses.m - decoding/
roi_category_decoding_su , Python, 298 linesbject_level.py - decoding/
roi_category_decoding_te , Python, 282 linessting_IIT_predictions_co mbined_features.py - decoding/
roi_decoding_group_analy , Python, 69 linessis.py - decoding/
roi_decoding_group_analy , Python, 47 linessis_IIT_predictions.py - decoding/
roi_orientation_decoding , Python, 269 lines_subject_level.py - decoding/
searchlight_category_dec , Python, 243 linesoding_subject_level.py - decoding/
searchlight_decoding_gro , Python, 162 linesup_analysis.py - decoding/
searchlight_group_level_ , Python, 214 linestables.py - decoding/
searchlight_orientation_ , Python, 212 lines, 1 matchdecoding_subject_level.p y - decoding/
searchlight_stim_baselin , Python, 221 linese_decoding_subject_level .py - decoding_rois/
01_create_decoding_rois_ , Python, 351 linesall_runs.py - decoding_rois/
02_create_decoding_rois_ , Python, 353 linesleave_one_run_out.py - dicom_to_bids/
01_convert_dicom_to_bids , Python, 242 lines.py - glm/
01_create_confound_regre , Python, 202 linesssor_ev_file.py - glm/
02_run_fsf_feat_analyses , Python, 1,043 lines.py - gppi/
MSP1_gppi_plots.py , Python, 43 lines - gppi/
config.py , Python, 63 lines - gppi/
glm_subject_level.m , MATLAB, 173 lines - gppi/
glm_subject_level_combin , MATLAB, 149 linesed.m - gppi/
gppi_analysis.m , MATLAB, 164 lines - gppi/
gppi_analysis_combined.m , MATLAB, 121 lines - gppi/
gppi_group_analysis.py , Python, 142 lines - gppi/
gppi_group_level_tables. , Python, 187 linespy - gppi/
gppi_subject_level.m , MATLAB, 21 lines - gppi/
gppi_subject_level_combi , MATLAB, 21 linesned.m - gppi/
nifti3D_conversion.m , MATLAB, 49 lines - gppi/
plotters.py , Python, 1,010 lines - gppi/
smoothing.m , MATLAB, 51 lines - helper_functions_MRI.py, Python, 186 lines
- logfiles_and_checks/
01_exp1_create_events_ts , Python, 373 lines, 1 matchv_file.py - logfiles_and_checks/
02_exp1_create_regressor , Python, 213 lines_txt_files.py - masks/
01_create_ROI_masks.py , Python, 525 lines - masks/
02_resample_ROI_masks_to , Python, 162 lines_target_space.py - masks/
03_create_theory_ROI_mas , Python, 286 linesks.py - masks/
04_resample_MNI152_ROIs. , Shell, 21 linessh - masks/
05_create_theory_ROI_mas , Python, 255 linesks_MNI152.py - putative_ncc/
01_putative_ncc_analysis , Python, 621 lines_on_FEAT_copes.py - putative_ncc/
02_putative_ncc_create_C , Python, 90 lines_not_A_or_B_maps.py - putative_ncc/
03_putative_ncc_analysis , Python, 619 lines_on_FEAT_copes_subject_l evel.py - putative_ncc/
04_putative_ncc_subject_ , Python, 95 lineslevel_create_C_not_A_or_ B_maps.py - putative_ncc/
05_multivariate_putative , Python, 142 lines_ncc_analysis.py - putative_ncc/
06_multivariate_putative , Python, 75 lines_ncc_create_C_not_A_or_B _maps.py - putative_ncc/
07_putative_ncc_merge_ph , Python, 112 linesases.py - putative_ncc/
10_putative_ncc_merge_su , Python, 105 linesbject_level.py - putative_ncc_plotting/
CustomColor.m , MATLAB, 27 lines - putative_ncc_plotting/
CustomColor_zMaps.m , MATLAB, 13 lines - putative_ncc_plotting/
Putative_NCC_01_univaria , MATLAB, 100 lineste.m - putative_ncc_plotting/
Putative_NCC_02_AB.m , MATLAB, 98 lines - putative_ncc_plotting/
Putative_NCC_03_multivar , MATLAB, 89 linesiate.m - putative_ncc_plotting/
Putative_NCC_04_z_maps.m , MATLAB, 106 lines - putative_ncc_plotting/
SaveFigures.m , MATLAB, 6 lines - putative_ncc_tables/
01_putative_ncc_group_le , Python, 203 linesvel_tables.py - putative_ncc_tables/
02_putative_ncc_subject_ , Python, 213 lineslevel_tables.py - putative_ncc_tables/
03_multivariate_putative , Python, 194 lines_ncc_group_level_tables. py - qc/
01_analyze_MRIQC_IQMs.py , Python, 221 lines, 1 match - seeds_for_gppi/
01_create_gppi_seeds.py , Python, 189 lines - LICENSE, License, 21 lines
- README.md, Text, 557 lines
cogitate-consortium/cogitate-msp1
e60764df21ab63d39ffa726a0dd38c2b6f1e3e9a, 29 August 2026Availability: 1 check, the latest on 28 September 2026: the link answers
- 28 September 2026: the link answers
264 files
- coglib/
bayesFactor/ , Jupyter, 561 linesHowToUse.ipynb - coglib/
bayesFactor/ , Python, 797 linesbayes_factor_fun.py - coglib/
bayesFactor/ , Jupyter, 89 linesbayesfactor_additionalin fo.ipynb - coglib/
beh_et/ , Python, 486 lines, 1 matchbehavior/ data_reader.py - coglib/
beh_et/ , Python, 149 linesbehavior/ data_saver.py - coglib/
beh_et/ , R, 592 linesbehavior/ exp1_lmms.R - coglib/
beh_et/ , Python, 1,044 lines, 1 matchbehavior/ quality_checks.py - coglib/
beh_et/ , Python, 90 linesbehavior/ quality_checks_criteria. py - coglib/
beh_et/ , Python, 89 lineseyetracking/ AnalysisHelpers.py - coglib/
beh_et/ , Python, 946 lines, 1 matcheyetracking/ DataParser.py - coglib/
beh_et/ , Python, 899 lineseyetracking/ ET_data_extraction.py - coglib/
beh_et/ , Python, 2,531 lineseyetracking/ ET_data_processing.py - coglib/
beh_et/ , Python, 297 lines, 1 matcheyetracking/ ET_param_manager.py - coglib/
beh_et/ , Python, 228 lineseyetracking/ ET_qc_manager.py - coglib/
beh_et/ , Python, 173 lineseyetracking/ based_noise_blinks_detec tion.py - coglib/
beh_et/ , Python, 226 lineseyetracking/ data_reader.py - coglib/
beh_et/ , R, 310 lineseyetracking/ exp1_et_lmms.R - coglib/
beh_et/ , Python, 499 lineseyetracking/ plotter.py - coglib/
beh_et/ , Python, 304 lineseyetracking/ tobii_et_handler_matlab_ limited.py - coglib/
fmri/ , Python, 103 linesdecoding/ MSP1_roi_decoding_plots. py - coglib/
fmri/ , Python, 97 linesdecoding/ MSP1_searchlight_decodin g_plots.py - coglib/
fmri/ , Python, 63 linesdecoding/ config.py - coglib/
fmri/ , Python, 1,010 linesdecoding/ plotters.py - coglib/
fmri/ , MATLAB, 36 linesdecoding/ rename_confounds_tsv_fil es.m - coglib/
fmri/ , Python, 298 linesdecoding/ roi_category_decoding_su bject_level.py - coglib/
fmri/ , Python, 282 linesdecoding/ roi_category_decoding_te sting_IIT_predictions_co mbined_features.py - coglib/
fmri/ , Python, 69 linesdecoding/ roi_decoding_group_analy sis.py - coglib/
fmri/ , Python, 47 linesdecoding/ roi_decoding_group_analy sis_IIT_predictions.py - coglib/
fmri/ , Python, 269 linesdecoding/ roi_orientation_decoding _subject_level.py - coglib/
fmri/ , Python, 243 linesdecoding/ searchlight_category_dec oding_subject_level.py - coglib/
fmri/ , Python, 162 linesdecoding/ searchlight_decoding_gro up_analysis.py - coglib/
fmri/ , Python, 214 linesdecoding/ searchlight_group_level_ tables.py - coglib/
fmri/ , Python, 212 linesdecoding/ searchlight_orientation_ decoding_subject_level.p y - coglib/
fmri/ , Python, 221 linesdecoding/ searchlight_stim_baselin e_decoding_subject_level .py - coglib/
fmri/ , Python, 351 linesdecoding_rois/ 01_create_decoding_rois_ all_runs.py - coglib/
fmri/ , Python, 353 linesdecoding_rois/ 02_create_decoding_rois_ leave_one_run_out.py - coglib/
fmri/ , Python, 242 linesdicom_to_bids/ 01_convert_dicom_to_bids .py - coglib/
fmri/ , Python, 202 linesglm/ 01_create_confound_regre ssor_ev_file.py - coglib/
fmri/ , Python, 1,043 linesglm/ 02_run_fsf_feat_analyses .py - coglib/
fmri/ , Python, 43 linesgppi/ MSP1_gppi_plots.py - coglib/
fmri/ , Python, 63 linesgppi/ config.py - coglib/
fmri/ , MATLAB, 173 linesgppi/ glm_subject_level.m - coglib/
fmri/ , MATLAB, 149 linesgppi/ glm_subject_level_combin ed.m - coglib/
fmri/ , MATLAB, 164 linesgppi/ gppi_analysis.m - coglib/
fmri/ , MATLAB, 121 linesgppi/ gppi_analysis_combined.m - coglib/
fmri/ , Python, 142 linesgppi/ gppi_group_analysis.py - coglib/
fmri/ , Python, 187 linesgppi/ gppi_group_level_tables. py - coglib/
fmri/ , MATLAB, 21 linesgppi/ gppi_subject_level.m - coglib/
fmri/ , MATLAB, 21 linesgppi/ gppi_subject_level_combi ned.m - coglib/
fmri/ , MATLAB, 49 linesgppi/ nifti3D_conversion.m - coglib/
fmri/ , Python, 1,010 linesgppi/ plotters.py - coglib/
fmri/ , MATLAB, 51 linesgppi/ smoothing.m - coglib/
fmri/ , Python, 186 lineshelper_functions_MRI.py - coglib/
fmri/ , Python, 373 lineslogfiles_and_checks/ 01_exp1_create_events_ts v_file.py - coglib/
fmri/ , Python, 213 lineslogfiles_and_checks/ 02_exp1_create_regressor _txt_files.py - coglib/
fmri/ , Python, 525 linesmasks/ 01_create_ROI_masks.py - coglib/
fmri/ , Python, 162 linesmasks/ 02_resample_ROI_masks_to _target_space.py - coglib/
fmri/ , Python, 286 linesmasks/ 03_create_theory_ROI_mas ks.py - coglib/
fmri/ , Shell, 21 linesmasks/ 04_resample_MNI152_ROIs. sh - coglib/
fmri/ , Python, 255 linesmasks/ 05_create_theory_ROI_mas ks_MNI152.py - coglib/
fmri/ , Python, 621 linesputative_ncc/ 01_putative_ncc_analysis _on_FEAT_copes.py - coglib/
fmri/ , Python, 90 linesputative_ncc/ 02_putative_ncc_create_C _not_A_or_B_maps.py - coglib/
fmri/ , Python, 619 linesputative_ncc/ 03_putative_ncc_analysis _on_FEAT_copes_subject_l evel.py - coglib/
fmri/ , Python, 95 linesputative_ncc/ 04_putative_ncc_subject_ level_create_C_not_A_or_ B_maps.py - coglib/
fmri/ , Python, 142 linesputative_ncc/ 05_multivariate_putative _ncc_analysis.py - coglib/
fmri/ , Python, 75 linesputative_ncc/ 06_multivariate_putative _ncc_create_C_not_A_or_B _maps.py - coglib/
fmri/ , Python, 112 linesputative_ncc/ 07_putative_ncc_merge_ph ases.py - coglib/
fmri/ , Python, 105 linesputative_ncc/ 10_putative_ncc_merge_su bject_level.py - coglib/
fmri/ , MATLAB, 27 linesputative_ncc_plotting/ CustomColor.m - coglib/
fmri/ , MATLAB, 13 linesputative_ncc_plotting/ CustomColor_zMaps.m - coglib/
fmri/ , MATLAB, 100 linesputative_ncc_plotting/ Putative_NCC_01_univaria te.m - coglib/
fmri/ , MATLAB, 98 linesputative_ncc_plotting/ Putative_NCC_02_AB.m - coglib/
fmri/ , MATLAB, 89 linesputative_ncc_plotting/ Putative_NCC_03_multivar iate.m - coglib/
fmri/ , MATLAB, 106 linesputative_ncc_plotting/ Putative_NCC_04_z_maps.m - coglib/
fmri/ , MATLAB, 6 linesputative_ncc_plotting/ SaveFigures.m - coglib/
fmri/ , Python, 203 linesputative_ncc_tables/ 01_putative_ncc_group_le vel_tables.py - coglib/
fmri/ , Python, 213 linesputative_ncc_tables/ 02_putative_ncc_subject_ level_tables.py - coglib/
fmri/ , Python, 194 linesputative_ncc_tables/ 03_multivariate_putative _ncc_group_level_tables. py - coglib/
fmri/ , Python, 221 linesqc/ 01_analyze_MRIQC_IQMs.py - coglib/
fmri/ , Python, 189 linesseeds_for_gppi/ 01_create_gppi_seeds.py - coglib/
ieeg/ , Python, 67 linesExperiment1ActivationAna lysis/ activation_analysis_batc h_runner.py - coglib/
ieeg/ , Python, 706 linesExperiment1ActivationAna lysis/ activation_analysis_help er_function.py - coglib/
ieeg/ , Python, 117 linesExperiment1ActivationAna lysis/ activation_analysis_para meters_class.py - coglib/
ieeg/ , Shell, 35 linesExperiment1ActivationAna lysis/ duration_decoding_job.sh - coglib/
ieeg/ , Python, 214 linesExperiment1ActivationAna lysis/ duration_decoding_master .py - coglib/
ieeg/ , Shell, 35 linesExperiment1ActivationAna lysis/ duration_tracking_job.sh - coglib/
ieeg/ , Python, 229 linesExperiment1ActivationAna lysis/ duration_tracking_master .py - coglib/
ieeg/ , Python, 218 linesExperiment1ActivationAna lysis/ linear_mixed_model_maste r.py - coglib/
ieeg/ , Shell, 35 linesExperiment1ActivationAna lysis/ lmm_job.sh - coglib/
ieeg/ , Shell, 35 linesExperiment1ActivationAna lysis/ onset_offset_job.sh - coglib/
ieeg/ , Python, 225 linesExperiment1ActivationAna lysis/ onset_offset_master.py - coglib/
ieeg/ , Python, 279 linesExperiment1ActivationAna lysis/ plot_duration_decoding_r esults.py - coglib/
ieeg/ , Python, 279 linesExperiment1ActivationAna lysis/ plot_duration_tracking_r esults.py - coglib/
ieeg/ , Python, 407 linesExperiment1ActivationAna lysis/ plot_lmm_results.py - coglib/
ieeg/ , Python, 75 linesExperiment1ActivationAna lysis/ plot_onset_offset_result s.py - coglib/
ieeg/ , Python, 1,669 linesPreprocessing/ PreprocessingHelperFunct ions.py - coglib/
ieeg/ , Python, 922 linesPreprocessing/ PreprocessingMaster.py - coglib/
ieeg/ , Python, 96 linesPreprocessing/ PreprocessingParametersC lass.py - coglib/
ieeg/ , Python, 188 linesPreprocessing/ SubjectInfo.py - coglib/
ieeg/ , Python, 125 linesPreprocessing/ test/ generate_simulated_raw.p y - coglib/
ieeg/ , Python, 67 linesPreprocessing/ test/ high_gamma_test.py - coglib/
ieeg/ , Python, 444 linesPreprocessing/ test/ test.py - coglib/
ieeg/ , Python, 65 linesanalysis_pipeline.py - coglib/
ieeg/ , Python, 32 linescategory_selectivity_ana lysis/ category_selectivity_bat ch_runner.py - coglib/
ieeg/ , Python, 333 linescategory_selectivity_ana lysis/ category_selectivity_hel per_function.py - coglib/
ieeg/ , Shell, 36 linescategory_selectivity_ana lysis/ category_selectivity_job .sh - coglib/
ieeg/ , Python, 240 linescategory_selectivity_ana lysis/ category_selectivity_mas ter.py - coglib/
ieeg/ , Python, 121 linescategory_selectivity_ana lysis/ category_selectivity_par ameters_class.py - coglib/
ieeg/ , Python, 427 linescategory_selectivity_ana lysis/ plot_category_selectivit y_results.py - coglib/
ieeg/ , Python, 55 linesdata_preparation/ DataPreparationParameter s.py - coglib/
ieeg/ , Python, 516 linesdata_preparation/ Experiment1_data_prepara tion.py - coglib/
ieeg/ , Python, 448 linesdata_preparation/ mne_bids_converter.py - coglib/
ieeg/ , Python, 1,292 linesdata_preparation/ trigger_alignment.py - coglib/
ieeg/ , Python, 675 linesdecoding/ calibration.py - coglib/
ieeg/ , Python, 116 linesdecoding/ decoding_analysis_parame ters_class.py - coglib/
ieeg/ , Python, 52 linesdecoding/ decoding_batch_runner.py - coglib/
ieeg/ , Python, 387 linesdecoding/ decoding_control_iit_vs_ iitgnw.py - coglib/
ieeg/ , Python, 789 linesdecoding/ decoding_helper_function s.py - coglib/
ieeg/ , Shell, 21 linesdecoding/ decoding_iitgnw_control_ job.sh - coglib/
ieeg/ , Python, 413 linesdecoding/ decoding_master.py - coglib/
ieeg/ , Shell, 36 linesdecoding/ decoding_master_job.sh - coglib/
ieeg/ , Shell, 35 linesdecoding/ decoding_robustness_job. sh - coglib/
ieeg/ , Python, 319 linesdecoding/ decoding_robustness_test .py - coglib/
ieeg/ , Python, 32 linesfreesurfer/ 0.recon_all_batch_runner .py - coglib/
ieeg/ , Python, 27 linesfreesurfer/ 1.fix_SE_recon.py - coglib/
ieeg/ , Python, 32 linesfreesurfer/ 2.wang_mapping_batch_run ner.py - coglib/
ieeg/ , Shell, 41 linesfreesurfer/ SE_recon_fix_job.sh - coglib/
ieeg/ , Shell, 45 linesfreesurfer/ recon_all_job.sh - coglib/
ieeg/ , Python, 80 linesfreesurfer/ wang_labels.py - coglib/
ieeg/ , Shell, 49 linesfreesurfer/ wang_mapping_job.sh - coglib/
ieeg/ , Python, 88 linesgeneral_helper_functions / channel_annot_to_bids.py - coglib/
ieeg/ , Python, 798 linesgeneral_helper_functions / data_general_utilities.p y - coglib/
ieeg/ , Python, 211 linesgeneral_helper_functions / ied_detection.py - coglib/
ieeg/ , Python, 101 linesgeneral_helper_functions / pathHelperFunctions.py - coglib/
ieeg/ , Python, 842 linesgeneral_helper_functions / plotters.py - coglib/
ieeg/ , Python, 131 linesgeneral_helper_functions / semi_automated_laplace_m apping.py - coglib/
ieeg/ , Python, 438 linesgeneral_helper_functions / test/ test_data_general_utilit ies.py - coglib/
ieeg/ , MATLAB, 461 linesplotting_uniformization/ BrewerMap-master/ brewermap.m - coglib/
ieeg/ , MATLAB, 52 linesplotting_uniformization/ BrewerMap-master/ brewermap_plot.m - coglib/
ieeg/ , MATLAB, 392 linesplotting_uniformization/ BrewerMap-master/ brewermap_view.m - coglib/
ieeg/ , MATLAB, 70 linesplotting_uniformization/ BrewerMap-master/ preset_colormap.m - coglib/
ieeg/ , Python, 395 linesplotting_uniformization/ MEG_activation/ plot_spectral_activation .py - coglib/
ieeg/ , Python, 473 linesplotting_uniformization/ MEG_synchrony/ plot_ppc_connectivity.py - coglib/
ieeg/ , Python, 335 linesplotting_uniformization/ category_selectivity/ plot_category_selectivit y.py - coglib/
ieeg/ , Python, 64 linesplotting_uniformization/ config.py - coglib/
ieeg/ , Python, 891 linesplotting_uniformization/ ecog_plotters.py - coglib/
ieeg/ , MATLAB, 942 linesplotting_uniformization/ findROIboundaries.m - coglib/
ieeg/ , MATLAB, 10 linesplotting_uniformization/ fs_fread3.m - coglib/
ieeg/ , Python, 368 linesplotting_uniformization/ general_utilities.py - coglib/
ieeg/ , MATLAB, 62 linesplotting_uniformization/ graphComponents.m - coglib/
ieeg/ , MATLAB, 77 linesplotting_uniformization/ handlePlotBrain.m - coglib/
ieeg/ , MATLAB, 17 linesplotting_uniformization/ iEEG_activation_analysis / activation_analysis_plot ting.m - coglib/
ieeg/ , Python, 151 linesplotting_uniformization/ iEEG_activation_analysis / duration_decoding.py - coglib/
ieeg/ , Python, 151 linesplotting_uniformization/ iEEG_activation_analysis / duration_decoding_brain. py - coglib/
ieeg/ , Python, 128 linesplotting_uniformization/ iEEG_activation_analysis / gnw_brain.py - coglib/
ieeg/ , Python, 745 linesplotting_uniformization/ iEEG_activation_analysis / iEEG_activation_plotting .py - coglib/
ieeg/ , Python, 209 linesplotting_uniformization/ iEEG_activation_analysis / onset_offset_brain.py - coglib/
ieeg/ , Python, 709 linesplotting_uniformization/ iEEG_rsa/ iEEG_rsa_plotting.py - coglib/
ieeg/ , Python, 182 linesplotting_uniformization/ iEEG_visual_responsivene ss/ brain_plots.py - coglib/
ieeg/ , MATLAB, 45 linesplotting_uniformization/ iEEG_visual_responsivene ss/ plot_ncc.m - coglib/
ieeg/ , Python, 396 linesplotting_uniformization/ iEEG_visual_responsivene ss/ plot_visual_responsivene ss.py - coglib/
ieeg/ , Python, 141 linesplotting_uniformization/ iEEG_visual_responsivene ss/ pncc_plotter.py - coglib/
ieeg/ , MATLAB, 45 linesplotting_uniformization/ iEEG_visual_responsivene ss/ putative_ncc.m - coglib/
ieeg/ , MATLAB, 863 linesplotting_uniformization/ plotBrain.m - coglib/
ieeg/ , MATLAB, 38 linesplotting_uniformization/ plotBrain_demo.m - coglib/
ieeg/ , MATLAB, 120 linesplotting_uniformization/ plot_electrodes_demo.m - coglib/
ieeg/ , Python, 848 linesplotting_uniformization/ plotters.py - coglib/
ieeg/ , Python, 126 linesplotting_uniformization/ plotting_examples.py - coglib/
ieeg/ , Python, 133 linesplotting_uniformization/ plotting_examples_ecog.p y - coglib/
ieeg/ , Python, 72 linesplotting_uniformization/ summaries/ channels_counts.py - coglib/
ieeg/ , MATLAB, 243 linesplotting_uniformization/ summaries/ plot_summaries_on_brain. m - coglib/
ieeg/ , Python, 1,449 linesplotting_uniformization/ summaries/ summaries_script.py - coglib/
ieeg/ , Python, 64 linesplotting_uniformization/ summaries/ tbl_parser.py - coglib/
ieeg/ , Python, 21 linesplotting_uniformization/ summaries/ venn_diagram.py - coglib/
ieeg/ , Python, 64 linesplotting_uniformization/ theories_rois.py - coglib/
ieeg/ , Python, 36 linesrsa/ rsa_batch_runner.py - coglib/
ieeg/ , Python, 1,182 linesrsa/ rsa_helper_functions.py - coglib/
ieeg/ , Python, 222 linesrsa/ rsa_master.py - coglib/
ieeg/ , Python, 120 linesrsa/ rsa_parameters_class.py - coglib/
ieeg/ , Shell, 36 linesrsa/ rsa_robustness_job.sh - coglib/
ieeg/ , Python, 196 linesrsa/ rsa_robustness_test.py - coglib/
ieeg/ , Shell, 36 linesrsa/ rsa_super_subject_job.sh - coglib/
ieeg/ , Python, 199 linesrsa/ rsa_super_subject_statis tics.py - coglib/
ieeg/ , Python, 108 linesrsa/ summarize_rsa_results.py - coglib/
ieeg/ , Python, 392 linesrsa/ theories_correlations.py - coglib/
ieeg/ , Python, 444 linessimulations/ data_simulation_master.p y - coglib/
ieeg/ , Python, 114 linessynchrony/ synchrony_analysis_param eters_class.py - coglib/
ieeg/ , Python, 52 linessynchrony/ synchrony_batch_runner.p y - coglib/
ieeg/ , Python, 630 linessynchrony/ synchrony_helper_functio ns.py - coglib/
ieeg/ , Python, 823 linessynchrony/ synchrony_master.py - coglib/
ieeg/ , Shell, 37 linessynchrony/ synchrony_master_job.sh - coglib/
ieeg/ , Python, 650 linesvisual_responsiveness_an alysis/ plot_visual_responsivene ss_results.py - coglib/
ieeg/ , Python, 32 linesvisual_responsiveness_an alysis/ visual_responsiveness_ba tch_runner.py - coglib/
ieeg/ , Python, 580 linesvisual_responsiveness_an alysis/ visual_responsiveness_he lper_functions.py - coglib/
ieeg/ , Shell, 36 linesvisual_responsiveness_an alysis/ visual_responsiveness_jo b.sh - coglib/
ieeg/ , Python, 458 linesvisual_responsiveness_an alysis/ visual_responsiveness_ma ster.py - coglib/
ieeg/ , Python, 123 linesvisual_responsiveness_an alysis/ visual_responsivness_par ameters_class.py - coglib/
meeg/ , Python, 399 linesactivation/ S01_source_loc.py - coglib/
meeg/ , Python, 255 linesactivation/ S02_source_loc_ga.py - coglib/
meeg/ , Python, 331 linesactivation/ S03a_source_dur_spectral .py - coglib/
meeg/ , Python, 330 linesactivation/ S03b_source_dur_erf.py - coglib/
meeg/ , Python, 272 linesactivation/ S04a_source_dur_spectral _ga.py - coglib/
meeg/ , Python, 191 linesactivation/ S04b_source_dur_erf_ga.p y - coglib/
meeg/ , Python, 893 linesactivation/ S05a_source_dur_spectral _lmm.py - coglib/
meeg/ , Python, 606 linesactivation/ S05b_source_dur_erf_lmm. py - coglib/
meeg/ , Python, 349 linesactivation/ S06_source_dur_onsetoffs et_control.py - coglib/
meeg/ , Python, 72 linesactivation/ S07_source_dur_lmm_table .py - coglib/
meeg/ , Python, 92 linesactivation/ S08_source_dur_lmm_BF.py - coglib/
meeg/ , Python, 130 linesconfig/ config.py - coglib/
meeg/ , Python, 547 linesconnectivity/ Co01_connect_ppc.py - coglib/
meeg/ , Python, 571 linesconnectivity/ Co01c_connect_dfc.py - coglib/
meeg/ , Python, 513 linesconnectivity/ Co02_connect_ppc_ga.py - coglib/
meeg/ , Python, 311 linesconnectivity/ Co02c_connect_dfc_ga.py - coglib/
meeg/ , Python, 632 linesged/ Co01_ged_selectivity.py - coglib/
meeg/ , Python, 564 linesged/ Co02_ged_pfc.py - coglib/
meeg/ , Python, 330 linesged/ Co03_ged_selectivity_ga. py - coglib/
meeg/ , Python, 318 linespreprocessing/ P01_maxwell_filtering.py - coglib/
meeg/ , Python, 271 linespreprocessing/ P02_find_bad_eeg.py - coglib/
meeg/ , Python, 241 linespreprocessing/ P03_artifact_annotation. py - coglib/
meeg/ , Python, 278 linespreprocessing/ P04_extract_events.py - coglib/
meeg/ , Python, 265 linespreprocessing/ P05_run_ica.py - coglib/
meeg/ , Python, 231 linespreprocessing/ P06_apply_ica.py - coglib/
meeg/ , Python, 288 linespreprocessing/ P07_make_epochs.py - coglib/
meeg/ , Python, 123 linespreprocessing/ P99_run_preproc.py - coglib/
meeg/ , Python, 386 linesqc/ P00_bids_conversion.py - coglib/
meeg/ , Python, 82 linesqc/ P00_run_qc.py - coglib/
meeg/ , Python, 82 linesqc/ P00_run_qc_epochs.py - coglib/
meeg/ , Python, 231 linesqc/ QC_epochs.py - coglib/
meeg/ , Python, 463 linesqc/ QC_processing.py - coglib/
meeg/ , Python, 331 linesqc/ QC_processing_eeg.py - coglib/
meeg/ , Python, 115 linesqc/ qc/ extract_events.py - coglib/
meeg/ , Python, 49 linesqc/ qc/ maxwell_filtering.py - coglib/
meeg/ , Python, 26 linesqc/ qc/ viz_psd.py - coglib/
meeg/ , Python, 30 linesqc/ srun_bids.py - coglib/
meeg/ , Python, 502 linesroi_mvpa/ D01_ROI_MVPA_Cat.py - coglib/
meeg/ , Python, 450 linesroi_mvpa/ D01_ROI_MVPA_Cat_PFC.py - coglib/
meeg/ , Python, 231 linesroi_mvpa/ D01_ROI_MVPA_Cat_subROI. py - coglib/
meeg/ , Python, 334 linesroi_mvpa/ D02_ROI_MVPA_Ori.py - coglib/
meeg/ , Python, 480 linesroi_mvpa/ D02_ROI_MVPA_Ori_PFC.py - coglib/
meeg/ , Python, 553 linesroi_mvpa/ D03_ROI_MVPA_GAT_Cat.py - coglib/
meeg/ , Python, 353 linesroi_mvpa/ D04_ROI_MVPA_GAT_Ori.py - coglib/
meeg/ , Python, 357 linesroi_mvpa/ D05_ROI_MVPA_RSA_Cat.py - coglib/
meeg/ , Python, 299 linesroi_mvpa/ D06_ROI_MVPA_RSA_Ori.py - coglib/
meeg/ , Python, 316 linesroi_mvpa/ D07_ROI_MVPA_RSA_ID.py - coglib/
meeg/ , Python, 426 linesroi_mvpa/ D98_group_stat_bayes_fac tors.py - coglib/
meeg/ , Python, 1,053 linesroi_mvpa/ D98_group_stat_sROI_plot .py - coglib/
meeg/ , Python, 603 linesroi_mvpa/ D98_group_stat_sROI_plot _GAT.py - coglib/
meeg/ , Python, 626 linesroi_mvpa/ D98_group_stat_sROI_plot _RSA.py - coglib/
meeg/ , Python, 629 linesroi_mvpa/ D98_group_stat_sROI_plot _RSA_phaseII.py - coglib/
meeg/ , Python, 1,116 linesroi_mvpa/ D98_group_stat_sROI_plot _phaseII.py - coglib/
meeg/ , Python, 1,373 linesroi_mvpa/ D98_group_stat_sROI_plot _subROI_phaseII.py - coglib/
meeg/ , Python, 202 linesroi_mvpa/ D99_group_data_pkl.py - coglib/
meeg/ , Python, 208 linesroi_mvpa/ D99_group_data_pkl_phase II.py - coglib/
meeg/ , Python, 939 linesroi_mvpa/ D_MEG_function.py - coglib/
meeg/ , Python, 259 linesroi_mvpa/ config.py - coglib/
meeg/ , Python, 1,153 linesroi_mvpa/ rsa_helper_functions_meg .py - coglib/
meeg/ , Python, 37 linesroi_mvpa/ sublist.py - coglib/
meeg/ , Python, 31 linesroi_mvpa/ sublist_phase2.py - coglib/
meeg/ , Python, 231 linessource_modelling/ S00_bem.py - coglib/
meeg/ , Python, 173 linessource_modelling/ S01_forward_model.py - coglib/
meeg/ , Python, 109 linessource_modelling/ S01b_forward_model_templ ate.py - coglib/
xnat/ , Python, 76 linesdownload_sample_datasets .py - LICENSE, License, 21 lines
- README.md, Text, 34 lines
Zenodo 14020043
Availability: 1 check, the latest on 28 September 2026: the link answers (HTTP 200)
- 28 September 2026: the link answers (HTTP 200)
63 files
- decoding/
MSP1_roi_decoding_plots. , Python, 103 linespy - decoding/
MSP1_searchlight_decodin , Python, 97 linesg_plots.py - decoding/
config.py , Python, 63 lines - decoding/
plotters.py , Python, 1,010 lines - decoding/
rename_confounds_tsv_fil , MATLAB, 36 lineses.m - decoding/
roi_category_decoding_su , Python, 298 linesbject_level.py - decoding/
roi_category_decoding_te , Python, 282 linessting_IIT_predictions_co mbined_features.py - decoding/
roi_decoding_group_analy , Python, 69 linessis.py - decoding/
roi_decoding_group_analy , Python, 47 linessis_IIT_predictions.py - decoding/
roi_orientation_decoding , Python, 269 lines_subject_level.py - decoding/
searchlight_category_dec , Python, 243 linesoding_subject_level.py - decoding/
searchlight_decoding_gro , Python, 162 linesup_analysis.py - decoding/
searchlight_group_level_ , Python, 214 linestables.py - decoding/
searchlight_orientation_ , Python, 212 linesdecoding_subject_level.p y - decoding/
searchlight_stim_baselin , Python, 221 linese_decoding_subject_level .py - decoding_rois/
01_create_decoding_rois_ , Python, 351 linesall_runs.py - decoding_rois/
02_create_decoding_rois_ , Python, 353 linesleave_one_run_out.py - dicom_to_bids/
01_convert_dicom_to_bids , Python, 242 lines.py - glm/
01_create_confound_regre , Python, 202 linesssor_ev_file.py - glm/
02_run_fsf_feat_analyses , Python, 1,043 lines.py - gppi/
MSP1_gppi_plots.py , Python, 43 lines - gppi/
config.py , Python, 63 lines - gppi/
glm_subject_level.m , MATLAB, 173 lines - gppi/
glm_subject_level_combin , MATLAB, 149 linesed.m - gppi/
gppi_analysis.m , MATLAB, 164 lines - gppi/
gppi_analysis_combined.m , MATLAB, 121 lines - gppi/
gppi_group_analysis.py , Python, 142 lines - gppi/
gppi_group_level_tables. , Python, 187 linespy - gppi/
gppi_subject_level.m , MATLAB, 21 lines - gppi/
gppi_subject_level_combi , MATLAB, 21 linesned.m - gppi/
nifti3D_conversion.m , MATLAB, 49 lines - gppi/
plotters.py , Python, 1,010 lines - gppi/
smoothing.m , MATLAB, 51 lines - helper_functions_MRI.py, Python, 186 lines
- logfiles_and_checks/
01_exp1_create_events_ts , Python, 373 linesv_file.py - logfiles_and_checks/
02_exp1_create_regressor , Python, 213 lines_txt_files.py - masks/
01_create_ROI_masks.py , Python, 525 lines - masks/
02_resample_ROI_masks_to , Python, 162 lines_target_space.py - masks/
03_create_theory_ROI_mas , Python, 286 linesks.py - masks/
04_resample_MNI152_ROIs. , Shell, 21 linessh - masks/
05_create_theory_ROI_mas , Python, 255 linesks_MNI152.py - putative_ncc/
01_putative_ncc_analysis , Python, 621 lines_on_FEAT_copes.py - putative_ncc/
02_putative_ncc_create_C , Python, 90 lines_not_A_or_B_maps.py - putative_ncc/
03_putative_ncc_analysis , Python, 619 lines_on_FEAT_copes_subject_l evel.py - putative_ncc/
04_putative_ncc_subject_ , Python, 95 lineslevel_create_C_not_A_or_ B_maps.py - putative_ncc/
05_multivariate_putative , Python, 142 lines_ncc_analysis.py - putative_ncc/
06_multivariate_putative , Python, 75 lines_ncc_create_C_not_A_or_B _maps.py - putative_ncc/
07_putative_ncc_merge_ph , Python, 112 linesases.py - putative_ncc/
10_putative_ncc_merge_su , Python, 105 linesbject_level.py - putative_ncc_plotting/
CustomColor.m , MATLAB, 27 lines - putative_ncc_plotting/
CustomColor_zMaps.m , MATLAB, 13 lines - putative_ncc_plotting/
Putative_NCC_01_univaria , MATLAB, 100 lineste.m - putative_ncc_plotting/
Putative_NCC_02_AB.m , MATLAB, 98 lines - putative_ncc_plotting/
Putative_NCC_03_multivar , MATLAB, 89 linesiate.m - putative_ncc_plotting/
Putative_NCC_04_z_maps.m , MATLAB, 106 lines - putative_ncc_plotting/
SaveFigures.m , MATLAB, 6 lines - putative_ncc_tables/
01_putative_ncc_group_le , Python, 203 linesvel_tables.py - putative_ncc_tables/
02_putative_ncc_subject_ , Python, 213 lineslevel_tables.py - putative_ncc_tables/
03_multivariate_putative , Python, 194 lines_ncc_group_level_tables. py - qc/
01_analyze_MRIQC_IQMs.py , Python, 221 lines - seeds_for_gppi/
01_create_gppi_seeds.py , Python, 189 lines - LICENSE, License, 21 lines
- README.md, Text, 557 lines
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://
• Preprocessing and Analysis Code51: GitHub - Analysis Code (https://
For more information, please visit the COGITATE Data wiki (https://
Sample data and code demo. Sample data from four participants (two per testing site) can be found here (https://
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
- cogitate-consortium.gith
ub.io/ , at cogitate-consortium.github.io; found in the text, “Usage Notes”cogitate-data
Data availability
The data can be accessed through the following links:
• Data Terms of Use: PDF file (https://
• Raw47 and BIDS48 fMRI Data (Bundle Format): Data Bundles (https://
• Raw and BIDS fMRI Data (XNAT49): XNAT Portal (https://
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://
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/
url = {https://
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/
VL - 13
IS - 1
SP - 779
SN - 2052-4463
PB - Nature Publishing Group
DO - 10.1038/
UR - https://
LA - en
ER -
CSL-JSON
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"container-title": "Scientific data",
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{
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{
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"issue": "1",
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"PMID": "42115661",
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"URL": "https://
"language": "en",
"issued": {
"date-parts": [
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2026,
5,
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}
}
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