Sustained Attention Task (gradCPT) Dataset using simultaneous EEG-fMRI and DTI.
The 15 matches
- [1] § Methods › DWI › Structural connectivity ↔ scripts/dwi/Structural_Connectivity.sh, lines 66–154 · score 0.89 · Probabilistic tractography, seed2all_length_roi, structural connectivity, PROBTRACKX2, BEDPOSTX, ROIs
- [2] § Methods › DWI › Structural connectivity ↔ scripts/dwi/Structural_Connectivity.sh, lines 66–154 · score 0.88 · Desikan Killiany, DWI space, FreeSurfer, T1 space, structural connectivity, atlas
- [3] § Methods › MRI preprocessing ↔ fmri/preprocessing/ccs_bids_04_funcnuisance.sh, lines 72–158 · score 0.80 · nuisance regression, global signal, motion parameters, components, derivatives, CSF
- [4] § Methods › DWI preprocessing ↔ scripts/dwi/MRtrix_DWI_Preproc.sh, lines 22–110 · score 0.79 · distortion correction, MRtrix, dwibiascorrect, dwidenoise, dwifslpreproc, eddy
- [5] § Technical Validation › fMRI: Measure for sustained attention lapse ↔ experiement_code folder/ CPT_withinSubject1_v2.m, lines 802–875 · score 0.79 · commission errors, omission errors, correct commissions, correct omissions, rejection, city
- [6] § Methods › DWI › Structural connectivity ↔ scripts/dwi/connectome_csv.m, lines 35–93 · score 0.77 · seed2all_length_roi, streamline lengths, symmetric, atlas, Probabilistic, Connectivity
- [7] § Methods › DWI › Structural connectivity ↔ scripts/dwi/connectome_csv.m, lines 35–93 · score 0.77 · connection probability, seed2all length, Streamline lengths, symmetrized, ROI, voxel
- [8] § Technical Validation › fMRI: Measure for sustained attention lapse ↔ experiement_code folder/ CPT_withinSubject1_v2.m, lines 802–875 · score 0.70 · Omission error, commission error, correct commissions, correct omissions, CPT
- [9] § Technical Validation › Limitations and technical challenges ↔ eeg/natview_eeg_preprocess_pipeline.m, lines 121–175 · score 0.69 · QRS detection, ECG channel, EEG channels, EEGLAB, FMRIB, median
- [10] § Methods › DWI preprocessing ↔ scripts/dwi/MRtrix_DWI_Preproc.sh, lines 22–110 · score 0.69 · fiber orientation, MRtrix, tractography, denoising, streamline, bias
- [11] § Methods › MRI preprocessing ↔ fmri/ccs_preproc_bids_docker.sh, lines 102–153 · score 0.63 · nuisance regression, FWHM, BIDS, smoothed, slice, pipeline
- [12] § Methods › EEG preprocessing ↔ eeg/natview_eeg_preprocess_pipeline.m, lines 121–175 · score 0.63 · QRS complexes, ECG channel, detection, EEGLAB, median, preprocessing
- [13] § Methods › EEG preprocessing ↔ eeg/natview_eeg_preprocess_pipeline.m, lines 177–187 · score 0.60 · pulse artifacts, artifact removal, QRS, FMRIB, template, preprocessing
- [14] § Methods › Gradient artifact removal ↔ eeg/natview_eeg_preprocess_pipeline.m, lines 96–117 · score 0.54 · remove gradient artifacts, FASTR, FMRIB, removal, EEG
- [15] § Technical Validation › fMRI data correlations ↔ fmri/preprocessing/ccs_bids_04_funcnuisance.sh, lines 72–158 · score 0.52 · temporal derivative, motion parameters, signal, fMRI
Paper
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The authors' code
MATLAB · 303 lines · 10 KB · CC-BY-SA-4.0 · 4 matches
- function EEG = natview_eeg_preprocess_pipeline(fileNameSET,outputDir,saveIntermediates,options)
- %% PURPOSE: This script preprocesses EEG data using EEGLAB functions
- % Simultaneously EEG and fMRI data was collected for the
- % NATVIEW_EEGFMRI dataset in a Siemens TrioTim 3T MRI scanner and
- % with Brain Products BrainCap MR at the Nathan Kline Institute
- % in Orangeburg, NY.
- %
- % This script utilizes the following toolboxes/plugins:
- %
- % EEGLAB (https://sccn.ucsd.edu/eeglab/index.php)
- % FMRIB Plug-In (https://fsl.fmrib.ox.ac.uk/eeglab/fmribplugin/)
- %
- % The toolbox and plugins above remove various artificats
- % (gradient artifact, pulse artifact, etc.) and performs other
- % preprocessing steps to prepare EEG data for secondary analysis.
- %
- % NOTE: This function uses the SET file format for file input
- %
- %--------------------------------------------------------------------------
- % INPUT:
- % fileNameSET - Filename of SET file
- %
- % outputDir - Output directory for preprocessed EEG file(s)
- %
- % saveIntermediates - Flag to save intermediate preprocessing steps
- % (Default: 0)
- %
- % options - Input STRUCT for saving specific intermediate steps
- % (Default: options.final = 1)
- %
- %--------------------------------------------------------------------------
- %% Error Checking
- % Output directory (Default: current working directory)
- if(nargin < 2 || isempty(outputDir))
- outputDir = pwd;
- end
- % Save intermediate preprocessing files (Default: 0)
- if(nargin < 3 || isempty(saveIntermediates))
- saveIntermediates = 0;
- end
- % Options STRUCT (Default: Only save final output)
- % NOTE: User can edit default flags here to save specific intermediate steps
- if(nargin < 4 || isempty(options))
- options.step1_gradient = 0;
- options.step2a_qrs = 0;
- options.step2b_pulse = 0;
- options.step3_downsample = 0;
- options.step4_nonEEG = 0;
- options.step5_bandpass = 0;
- options.step6_bad = 0;
- options.step7_asr = 0;
- options.step8_reference = 0;
- options.step9_ica = 0;
- options.final = 1;
- end
- % Create 'final' flag if not included with input options
- if(~isfield(options,'final'))
- options.final = 1;
- end
- %% STEP 0: Load data into EEGLAB
- [~,fileName] = fileparts(fileNameSET);
- EEG = pop_loadset(fileNameSET); % Load SET file into MATLAB
- EEG.data = double(EEG.data);
- underscore_idx = strfind(fileName,'_');
- fileInfo = cell(length(underscore_idx),1);
- for ii = 1:length(underscore_idx)
- if(ii==1)
- fileInfo{ii} = fileName(1:underscore_idx(1)-1);
- else
- fileInfo{ii} = fileName(underscore_idx(ii-1)+1:underscore_idx(ii)-1);
- end
- end
- subject = fileInfo{1}; % Participant ID
- session = fileInfo{2}; % Session
- task = fileInfo{3}; % Task Name
- if(length(fileInfo) > 3)
- runNum = fileInfo{4}; % Run
- output_fileName = [subject,'_',session,'_',task,'_',runNum];
- else
- output_fileName = [subject,'_',session,'_',task];
- end
- %% Non-EEG Channel specification
- ECGChan = find(strcmp({EEG.chanlocs.labels},'ECG'));
- EOGLChan = find(strcmp({EEG.chanlocs.labels},'EOGL'));
- EOGUChan = find(strcmp({EEG.chanlocs.labels},'EOGU'));
- electrodeExclude = [ECGChan,EOGLChan,EOGUChan];
- %% STEP 1: Gradient Artifact Removal
- % This step performs gradient artifact removal using FMRIB Toolbox
- % Link: https://fsl.fmrib.ox.ac.uk/eeglab/fmribplugin/
- if(strcmp(task,'task-checker') || ...
- strcmp(task,'task-dme') || ...
- strcmp(task,'task-dmh') || ...
- strcmp(task,'task-inscapes') || ...
- strcmp(task,'task-monkey1') || ...
- strcmp(task,'task-monkey2') || ...
- strcmp(task,'task-monkey5') || ...
- strcmp(task,'task-peer') || ...
- strcmp(task,'task-rest') || ...
- strcmp(task,'task-tp'))
- EEG = pop_fmrib_fastr(EEG,[],[],[],'R128',1,0,[],[],[],[],electrodeExclude,'auto'); % Remove gradient artifact
- % Save intermediate
- if(saveIntermediates == 1 && isfield(options, 'step1_gradient'))
- if(options.step1_gradient == 1)
- pop_saveset(EEG,'filename',[output_fileName,'_preprocess-1gradient_eeg'],'filepath',outputDir);
- end
- end
- end
- %% STEP 2a: QRS Detection
- % This step detects QRS complexes in the ECG channel. If the function fails
- % to find QRS complexes, QRS detection is performed on every EEG channel;
- % the channel chosen for QRS detection equals the mode of QRS counts
- try
- EEG = pop_fmrib_qrsdetect(EEG,ECGChan,'QRS','no'); % FMRIB Toolbox QRS Detection
- catch
- nChannels = EEG.nbchan;
- channelEEG = 1:nChannels;
- QRSCount = zeros(nChannels,1);
- channelError = zeros(nChannels,1);
- for nn = 1:nChannels
- try
- EEG_QRS = pop_fmrib_qrsdetect(EEG,channelEEG(nn),'QRS','no');
- eventLatency = extract_eventLatency(EEG_QRS,'QRS');
- if(length(eventLatency) > (EEG.xmax - 50) || nn ~= 32)
- QRSCount(nn) = length(eventLatency);
- end
- catch
- channelError(nn) = 1;
- end
- end
- channelEEG(QRSCount == 0) = [];
- QRSCount(QRSCount == 0) = [];
- [QRSCount_mode, QRSCount_modeNum] = mode(QRSCount);
- [QRSCount_sort, QRSCount_sort_idx] = sort(QRSCount);
- % Select mode of QRS count if 3 or more, else select median QRS count
- if(QRSCount_modeNum >= 3)
- QRSCount_mode_idx = find(QRSCount == QRSCount_mode);
- else
- if(length(QRSCount) == 1)
- QRSCount_mode_idx = 1;
- else
- QRSCount_mode_idx = QRSCount_sort_idx(find(diff(QRSCount_sort > median(QRSCount)))); %#ok<FNDSB>
- end
- end
- QRS_channel = channelEEG(QRSCount_mode_idx);
- EEG = pop_fmrib_qrsdetect(EEG,QRS_channel(1),'QRS','no'); % FMRIB Toolbox QRS Detection
- % disp(find(channelError==1));
- end
- % Save intermediate
- if(saveIntermediates == 1 && isfield(options, 'step2a_qrs'))
- if(options.step2a_qrs == 1)
- pop_saveset(EEG,'filename',[output_fileName,'_preprocess-2aqrs_eeg'],'filepath',outputDir);
- end
- end
- %% STEP 2b: Pulse Artifact Removal
- PAType = 'median'; % Template for pulse artifact (Default: median)
- EEG = pop_fmrib_pas(EEG,'QRS',PAType); % Pulse Artifact removal
- % Save intermediate
- if(saveIntermediates == 1 && isfield(options, 'step2b_pulse'))
- if(options.step2b_pulse == 1)
- pop_saveset(EEG,'filename',[output_fileName,'_preprocess-2bpulse_eeg'],'filepath',outputDir);
- end
- end
- %% STEP 3: Downsample EEG data to 250Hz
- resample_freq = 250;
- EEG = pop_resample(EEG,resample_freq);
- % Save intermediate
- if(saveIntermediates == 1 && isfield(options, 'step3_downsample'))
- if(options.step3_downsample == 1)
- pop_saveset(EEG,'filename',[output_fileName,'_preprocess-3downsample_eeg'],'filepath',outputDir);
- end
- end
- %% STEP 4: Remove non-EEG channels (i.e., EOG and ECG)
- EEG = pop_select(EEG,'nochannel',electrodeExclude);
- % Save intermediate
- if(saveIntermediates == 1 && isfield(options, 'step4_nonEEG'))
- if(options.step4_nonEEG == 1)
- pop_saveset(EEG,'filename',[output_fileName,'_preprocess-4nonEEG_eeg'],'filepath',outputDir);
- end
- end
- %% STEP 5: Bandpass filter data
- freq_lo = 0.3;
- freq_hi = 50;
- EEG = pop_eegfiltnew(EEG,'locutoff',freq_lo,'hicutoff',freq_hi);
- % Save intermediate
- if(saveIntermediates == 1 && isfield(options, 'step5_bandpass'))
- if(options.step5_bandpass == 1)
- pop_saveset(EEG,'filename',[output_fileName,'_preprocess-5bandpass_eeg'],'filepath',outputDir);
- end
- end
- %% STEP 6: Remove bad channels
- EEG = pop_clean_rawdata(EEG,'FlatlineCriterion',5,...
- 'ChannelCriterion',0.8,...
- 'LineNoiseCriterion',4,...
- 'Highpass',[0.75 1.25],...
- 'BurstCriterion','off',...
- 'WindowCriterion','off',...
- 'BurstRejection','off',...
- 'Distance','Euclidian',...
- 'WindowCriterionTolerances','off');
- % Save intermediate
- if(saveIntermediates == 1 && isfield(options, 'step6_bad'))
- if(options.step6_bad == 1)
- pop_saveset(EEG,'filename',[output_fileName,'_preprocess-6bad_eeg'],'filepath',outputDir);
- end
- end
- %% STEP 7: Clear data using ASR
- EEG = pop_clean_rawdata(EEG,'FlatlineCriterion','off',...
- 'ChannelCriterion','off',...
- 'LineNoiseCriterion','off', ...
- 'Highpass','off', ...
- 'BurstCriterion',20,...
- 'WindowCriterion',0.25, ...
- 'BurstRejection','on', ...
- 'Distance','Euclidian',...
- 'WindowCriterionTolerances',[-inf 7]);
- % Save intermediate
- if(saveIntermediates == 1 && isfield(options, 'step7_asr'))
- if(options.step7_asr == 1)
- pop_saveset(EEG,'filename',[output_fileName,'_preprocess-7asr_eeg'],'filepath',outputDir);
- end
- end
- %% STEP 8: Rereference data using average reference
- EEG = pop_reref(EEG,[]);
- % Save intermediate
- if(saveIntermediates == 1 && isfield(options, 'step8_reference'))
- if(options.step8_reference == 1)
- pop_saveset(EEG,'filename',[output_fileName,'_preprocess-8reference_eeg'],'filepath',outputDir);
- end
- end
- %% STEP 9: Compute ICA, flat IC using ICLabel, and remove ICs highly correlated with muscle and eye artifacts
- EEG = pop_runica(EEG,'icatype','runica','concatcond','on','options',{'pca',-1});
- EEG = pop_iclabel(EEG,'default');
- EEG = pop_icflag(EEG,[NaN NaN; 0.8 1; 0.8 1; NaN NaN; NaN NaN; NaN NaN; NaN NaN]);
- EEG = pop_subcomp(EEG,[]);
- % Save intermediate
- if(saveIntermediates == 1 && isfield(options, 'step9_ica'))
- if(options.step9_ica == 1)
- pop_saveset(EEG,'filename',[output_fileName,'_preprocess-9ica_eeg'],'filepath',outputDir);
- end
- end
- %% STEP 10: Save preprocessing data into output directory
- if(isempty(saveIntermediates) || options.final == 1)
- pop_saveset(EEG,'filename',[output_fileName,'_preprocess_eeg'],'filepath',outputDir);
- end
- end
- %% Subfunction: Extract Event Latency
- function [eventLatency,event_idx] = extract_eventLatency(EEG,eventType)
- X = zeros(length(EEG.event),1);
- eventLatency = zeros(length(EEG.event),1);
- for ii = 1:length(EEG.event)
- if(strcmp(EEG.event(ii).type,eventType))
- X(ii) = 1;
- eventLatency(ii) = EEG.event(ii).latency;
- end
- end
- eventLatency(X==0) = [];
- event_idx = find(X==1);
- end
natview_eeg_preprocess_pipeline.m at commit a7ac63d, under CC-BY-SA-4.0 · at the source
Overview
- Center for Neuroscience Imaging Research, Institute for Basic Science (IBS), Suwon, 16419 Republic of Korea
- Sungkyunkwan University, Suwon, 16419 Republic of Korea
- Research institute of Slowave Inc., Seoul, 06160 Republic of Korea
- Center for Bio-imaging and Translational Research, Korea Basic Science Institute, Ochang, 28119 Republic of Korea
- Department of Metabiohealth, Sungkyunkwan University, Suwon, 16419 Republic of Korea
- Department of Psychology and Neuroscience, Boston College, Chestnut Hill, Massachusetts 02467 USA
- Department of Physics, Sungkyunkwan University, Suwon, 16419 Republic of Korea
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.
Repositories
Its files are read in the Code ↔ Paper reader above, with 15 matches between paragraphs and lines of code.
nathanklineinstitute/natview_eegfmri
a7ac63d526e13817e1031e8a910cc58b46a18ae7, 18 July 2025Availability: 1 check, the latest on 30 September 2026: the link answers
- 30 September 2026: the link answers
20 files
- eeg/
natview_eeg_preprocess_p , MATLAB, 303 lines, 4 matchesipeline.m - eye/
natview_edf2bids.m , MATLAB, 503 lines - eye/
natview_eye_data_qc.m , MATLAB, 214 lines - eye/
natview_eye_preprocess_b , MATLAB, 212 lineslinks.m - fmri/
ccs_preproc_bids_docker. , Shell, 153 lines, 1 matchsh - fmri/
preprocessing/ , Shell, 159 linesccs_bids_01_anatpreproc. sh - fmri/
preprocessing/ , Shell, 141 linesccs_bids_01_anatsurfreco n.sh - fmri/
preprocessing/ , Shell, 193 linesccs_bids_01_funcpreproc. sh - fmri/
preprocessing/ , Shell, 133 linesccs_bids_02_anatregister .sh - fmri/
preprocessing/ , Shell, 263 linesccs_bids_02_funcregister _func2anat.sh - fmri/
preprocessing/ , Shell, 110 linesccs_bids_02_funcregister _func2std.sh - fmri/
preprocessing/ , Shell, 131 linesccs_bids_03_funcsegment. sh - fmri/
preprocessing/ , Shell, 179 lines, 2 matchesccs_bids_04_funcnuisance .sh - fmri/
preprocessing/ , Shell, 218 linesccs_bids_05_funcpreproc_ vol.sh - fmri/
preprocessing/ , Python, 40 linesccs_prep_bids_json2txt.p y - natview_cleaning_pipelin
e.m , MATLAB, 160 lines - stimulus/
natview_stimuli_checkerb , MATLAB, 735 linesoard.m - stimulus/
natview_stimuli_video.m , MATLAB, 828 lines - LICENSE, License, 3 lines
- README.md, Text, 43 lines
MoonBrainLab/GradCPT-Simultaneous-EEG-fMRI-DTI-Data
1f751e0d1a0154bf64a5951156a49a78453028d6, 16 October 2025Availability: 1 check, the latest on 30 September 2026: the link answers
- 30 September 2026: the link answers
10 files
- experiement_code folder/ CPT_withinSubject1_v2.m, MATLAB, 970 lines, 2 matches
- scripts/
dwi/ , Shell, 110 lines, 2 matchesMRtrix_DWI_Preproc.sh - scripts/
dwi/ , Shell, 154 lines, 2 matchesStructural_Connectivity. sh - scripts/
dwi/ , MATLAB, 93 lines, 2 matchesconnectome_csv.m - scripts/
dwi/ , MATLAB, 15 linesextractROIs.m - scripts/
dwi/ , MATLAB, 21 linesplotSeedConnResults.m - scripts/
dwi/ , MATLAB, 37 linessaveniidat.m - scripts/
eeg/ , MATLAB, 145 linesfMRIb_preprocessing_EEG_ fMRI_data_insert_TR.m - scripts/
fmri/ , Shell, 26 linesrun_fmriprep.sh - README.md, Text, 52 lines
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: MoonBrainLab/
GradCPT-Simultaneous-EEG -fMRI-DTI-Data
Read it in the paper: doi.org/10.1038/s41597-026-06616-6.
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:
- 2 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
- 27 scripts, each with its path and the digest of its content;
- 15 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
- doi:10.18112/
openneuro.ds006040.v1.0. , at OpenNeuro; found in “Data availability”1
Data availability statement
The paper has a data 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 a dataset: OpenNeuro 10.18112/
openneuro.ds006040.v1.0. 1
Read it in the paper: doi.org/10.1038/s41597-026-06616-6.
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, 30 September 2026: the first record
Recorded: type, language, journal, volume, issue, pages, dates, 10 authors, 2 keywords, 7 MeSH terms, 1 funder, 35 references.
Cite
This paper
Cha, Y., Lee, Y., Ji, E., Han, S., Min, S., Kim, H., Cho, M., Lee, H. S., Park, Y., & Moon, J.-Y. (2026). Sustained Attention Task (gradCPT) Dataset using simultaneous EEG-fMRI and DTI. Scientific data, 13(1), 573. https://
BibTeX
@article{cha2026sustaine
author = {Cha, Younghwa and Lee, Yeji and Ji, Eunhee and Han, SoHyun and Min, Sunhyun and Kim, Hyoungkyu and Cho, Minseo and Lee, Hae Seong and Park, Youngjai and Moon, Joon-Young},
title = {{Sustained Attention Task (gradCPT) Dataset using simultaneous EEG-fMRI and DTI}},
journal = {Scientific data},
year = {2026},
month = mar,
volume = {13},
number = {1},
pages = {573},
publisher = {Nature Publishing Group},
issn = {2052-4463},
doi = {10.1038/
url = {https://
pmid = {41771931},
pmcid = {PMC13066628}
}
RIS
TY - JOUR
AU - Cha, Younghwa
AU - Lee, Yeji
AU - Ji, Eunhee
AU - Han, SoHyun
AU - Min, Sunhyun
AU - Kim, Hyoungkyu
AU - Cho, Minseo
AU - Lee, Hae Seong
AU - Park, Youngjai
AU - Moon, Joon-Young
TI - Sustained Attention Task (gradCPT) Dataset using simultaneous EEG-fMRI and DTI
T2 - Scientific data
J2 - Sci Data
PY - 2026
DA - 2026/
VL - 13
IS - 1
SP - 573
SN - 2052-4463
PB - Nature Publishing Group
DO - 10.1038/
UR - https://
LA - en
ER -
CSL-JSON
{
"id": "10.1038/
"type": "article-journal",
"title": "Sustained Attention Task (gradCPT) Dataset using simultaneous EEG-fMRI and DTI",
"container-title": "Scientific data",
"author": [
{
"family": "Cha",
"given": "Younghwa"
},
{
"family": "Lee",
"given": "Yeji"
},
{
"family": "Ji",
"given": "Eunhee"
},
{
"family": "Han",
"given": "SoHyun"
},
{
"family": "Min",
"given": "Sunhyun"
},
{
"family": "Kim",
"given": "Hyoungkyu"
},
{
"family": "Cho",
"given": "Minseo"
},
{
"family": "Lee",
"given": "Hae Seong"
},
{
"family": "Park",
"given": "Youngjai"
},
{
"family": "Moon",
"given": "Joon-Young"
}
],
"container-title-short":
"volume": "13",
"issue": "1",
"page": "573",
"DOI": "10.1038/
"PMID": "41771931",
"PMCID": "PMC13066628",
"ISSN": "2052-4463",
"publisher": "Nature Publishing Group",
"URL": "https://
"language": "en",
"issued": {
"date-parts": [
[
2026,
3,
3
]
]
}
}
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