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Copy pathpop_importbids.m
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pop_importbids.m
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% POP_IMPORTBIDS - Import BIDS format folder structure into an EEGLAB
% study.
% Usage:
% >> [STUDY ALLEEG] = pop_importbids(bidsfolder);
% >> [STUDY ALLEEG] = pop_importbids(bidsfolder, 'key', value);
%
% Inputs:
% bidsfolder - a loaded epoched EEG dataset structure.
% options are 'bidsevent', 'bidschanloc' of be turned 'on' (default) or 'off'
% 'outputdir' default is bidsfolder/derivatives/eeglab
% 'studyName' default is eeg
%
% Optional inputs:
% 'studyName' - [string] name of the STUDY
% 'subjects' - [cell array] indices or names of subjects to import
% 'sessions' - [cell array] session numbers or names to import
% 'runs' - [cell array] run numbers or names to import
% 'bidsevent' - ['on'|'off'] import events from BIDS .tsv file and
% ignore events in raw binary EEG files.
% 'bidschanloc' - ['on'|'off'] import channel location from BIDS .tsv file
% and ignore locations (if any) in raw binary EEG files.
% 'outputdir' - [string] output folder (default is to use the BIDS
% folders).
% 'eventtype' - [string] BIDS event column to use for EEGLAB event types.
% common choices are usually 'trial_type' or 'value'.
% Default is 'value'.
% 'bidstask' - [string] value of a key task- allowing to analyze some
% tasks only
% 'metadata' - ['on'|'off'] only import metadata. Default 'off'.
% 'ctffunc' - ['fileio'|'ctfimport'] function to use to import CTF data
% Default 'fileio'.
%
% Outputs:
% STUDY - EEGLAB STUDY structure
% ALLEEG - EEGLAB ALLEEG structure
% bids - BIDS structure (same as ALLEEG(i).BIDS
% stats - BIDS metadata statistics structure
%
% Authors: Arnaud Delorme, SCCN, INC, UCSD, January, 2019
% Cyril Pernet, University of Edinburgh
%
% Example:
% pop_importbids('/data/matlab/bids_matlab/rishikesh_study/BIDS_EEG_meditation_experiment');
% Copyright (C) Arnaud Delorme, 2018
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
function [STUDY, ALLEEG, bids, stats, commands] = pop_importbids(bidsFolder, varargin)
STUDY = [];
ALLEEG = [];
bids = [];
stats = [];
commands = '';
if nargin < 1
bidsFolder = uigetdir('Pick a BIDS folder');
if isequal(bidsFolder,0), return; end
cb_select = [ 'tmpfolder = uigetdir;' ...
'if ~isequal(tmpfolder, 0)' ...
' set(findobj(gcbf, ''tag'', ''folder''), ''string'', tmpfolder);' ...
'end;' ...
'clear tmpfolder;' ];
type_fields = { 'value' 'trial_type' 'event_kind' 'event_type' };
disp('Scanning folders...');
% scan if multiple tasks are present
[tasklist,sessions,runs] = bids_getinfofromfolder(bidsFolder);
% scan for event fields
type_fields = bids_geteventfieldsfromfolder(bidsFolder);
indVal = strmatch('value', type_fields);
if ~isempty(indVal)
type_fields(indVal) = [];
type_fields = {'value' type_fields{:} };
end
bids_event_toggle = ~isempty(type_fields);
if isempty(type_fields) type_fields = { 'n/a' }; end
if isempty(tasklist) tasklist = { 'n/a' }; end
cb_event = 'set(findobj(gcbf, ''userdata'', ''bidstype''), ''enable'', fastif(get(gcbo, ''value''), ''on'', ''off''));';
cb_task = 'set(findobj(gcbf, ''userdata'', ''task'' ), ''enable'', fastif(get(gcbo, ''value''), ''on'', ''off''));';
cb_sess = 'set(findobj(gcbf, ''userdata'', ''sessions''), ''enable'', fastif(get(gcbo, ''value''), ''on'', ''off''));';
cb_run = 'set(findobj(gcbf, ''userdata'', ''runs'' ), ''enable'', fastif(get(gcbo, ''value''), ''on'', ''off''));';
cb_subjects = 'set(findobj(gcbf, ''userdata'', ''subjects''), ''enable'', fastif(get(gcbo, ''value''), ''on'', ''off''));';
promptstr = { ...
{ 'style' 'text' 'string' 'Enter study name (default is BIDS folder name)' } ...
{ 'style' 'edit' 'string' '' 'tag' 'studyName' } ...
{} ...
{ 'style' 'checkbox' 'string' 'Use BIDS electrode.tsv files (when present) for channel locations; off: look up locations using channel labels' 'tag' 'chanlocs' 'value' 1 } ...
{ 'style' 'checkbox' 'string' 'Use BIDS event.tsv files for events and use the following BIDS field for event type' 'tag' 'events' 'value' bids_event_toggle 'callback' cb_event } ...
{ 'style' 'popupmenu' 'string' type_fields 'tag' 'typefield' 'value' 1 'userdata' 'bidstype' 'enable' fastif(bids_event_toggle, 'on', 'off') } ...
{ 'style' 'checkbox' 'string' 'Import only the following BIDS tasks' 'tag' 'bidstask' 'value' 0 'callback' cb_task } ...
{ 'style' 'popupmenu' 'string' tasklist 'tag' 'bidstaskstr' 'value' 1 'userdata' 'task' 'enable' 'off' } {} ...
{ 'style' 'checkbox' 'string' 'Import only the following sessions' 'tag' 'bidssessions' 'value' 0 'callback' cb_sess } ...
{ 'style' 'listbox' 'string' sessions 'tag' 'bidsessionstr' 'max' 2 'value' [] 'userdata' 'sessions' 'enable' 'off' } {} ...
{ 'style' 'checkbox' 'string' 'Import only the following runs' 'tag' 'bidsruns' 'value' 0 'callback' cb_run } ...
{ 'style' 'listbox' 'string' runs 'tag' 'bidsrunsstr' 'max' 2 'value' [] 'userdata' 'runs' 'enable' 'off' } {} ...
{ 'style' 'checkbox' 'string' 'Import only the following participant indices' 'tag' 'bidssubjects' 'value' 0 'callback' cb_subjects } ...
{ 'style' 'edit' 'string' '' 'tag' 'bidssubjectsstr' 'userdata' 'subjects' 'enable' 'off' } {} ...
{} ...
{ 'style' 'text' 'string' 'Study output folder' } ...
{ 'style' 'edit' 'string' fullfile(bidsFolder, 'derivatives', 'eeglab') 'tag' 'folder' 'HorizontalAlignment' 'left' } ...
{ 'style' 'pushbutton' 'string' '...' 'callback' cb_select } ...
};
geometry = {[2 1.5], 1, 1,[1 0.35],[0.6 0.35 0.5],[0.6 0.35 0.5],[0.6 0.35 0.5],[0.6 0.35 0.5],1,[1 2 0.5]};
geomvert = [1 0.5, 1 1 1 1.5 1.5 1 0.5 1];
if isempty(runs)
promptstr(13:15) = [];
geometry(7) = [];
geomvert(7) = [];
end
if isempty(sessions)
promptstr(10:12) = [];
geometry(6) = [];
geomvert(6) = [];
end
[~,~,~,res] = inputgui( 'geometry', geometry, 'geomvert', geomvert, 'uilist', promptstr, 'helpcom', 'pophelp(''pop_importbids'')', 'title', 'Import BIDS data -- pop_importbids()');
if isempty(res), return; end
if ~isempty(type_fields) && ~strcmpi(type_fields{res.typefield}, 'n/a'), options = { 'eventtype' type_fields{res.typefield} }; else options = {}; end
if res.events, options = { options{:} 'bidsevent' 'on' }; else options = { options{:} 'bidsevent' 'off' }; end
if res.chanlocs, options = { options{:} 'bidschanloc' 'on' }; else options = { options{:} 'bidschanloc' 'off' }; end
if ~isempty(res.folder), options = { options{:} 'outputdir' res.folder }; end
if ~isempty(res.studyName), options = { options{:} 'studyName' res.studyName }; end
if res.bidstask && ~strcmpi(tasklist{res.bidstaskstr}, 'n/a'), options = { options{:} 'bidstask' tasklist{res.bidstaskstr} }; end
if isfield(res, 'bidssessions')
if res.bidssessions && ~isempty(res.bidsessionstr), options = { options{:} 'sessions' sessions(res.bidsessionstr) }; end
end
if isfield(res, 'bidsruns')
if res.bidsruns && ~isempty(res.bidsruns), options = { options{:} 'runs' str2double(runs(res.bidsrunsstr)) }; end
end
if isfield(res, 'bidssubjects')
if res.bidsruns && ~isempty(res.bidsruns), options = { options{:} 'subjects' str2double(res.bidssubjectsstr) }; end
end
else
options = varargin;
end
[~,defaultStudyName] = fileparts(bidsFolder);
opt = finputcheck(options, { ...
'bidsevent' 'string' { 'on' 'off' } 'on'; ...
'bidschanloc' 'string' { 'on' 'off' } 'on'; ...
'bidscoord' 'string' { 'on' 'off' } 'on'; ...
'bidstask' {'string' 'cell'} {'',{}} ''; ...
'subjects' {'cell' 'integer'} {{},[]} []; ...
'sessions' 'cell' {} {}; ...
'runs' {'cell' 'integer'} {{},[]} []; ...
'metadata' 'string' { 'on' 'off' } 'off'; ...
'ctffunc' 'string' { 'fileio' 'ctfimport' } 'fileio'; ...
'eventtype' 'string' { } 'value'; ...
'outputdir' 'string' { } fullfile(bidsFolder, 'derivatives', 'eeglab'); ...
'studyName' 'string' { } defaultStudyName ...
}, 'pop_importbids');
if isstr(opt), error(opt); end
if ~exist('jsondecode.m','file')
addpath([fileparts(which('pop_importbids.m')) filesep 'JSONio'])
end
% Options:
% - copy folder
% - use channel location and event
% load change file
changesFile = fullfile(bidsFolder, 'CHANGES');
bids.CHANGES = '';
if exist(changesFile,'File')
bids.CHANGES = bids_loadfile( changesFile, [], true );
end
% load Readme file
readmeFile = fullfile(bidsFolder, 'README');
bids.README = '';
if exist(readmeFile,'File')
bids.README = bids_loadfile( readmeFile, [], true );
end
% load dataset description file
dataset_descriptionFile = fullfile(bidsFolder, 'dataset_description.json');
bids.dataset_description = '';
if exist(dataset_descriptionFile,'File')
bids.dataset_description = bids_loadfile( dataset_descriptionFile );
end
% load participant file
participantsFile = fullfile(bidsFolder, 'participants.tsv');
bids.participants = '';
pInd = 1;
if exist(participantsFile,'File')
bids.participants = bids_loadfile( participantsFile );
if ~isempty(bids.participants) && ~isequal(bids.participants{1}, 'participant_id')
pInd = find(cellfun(@(x)contains(x, 'participant_id'), bids.participants(1,:))); % sometime special chars
if isempty(pInd)
error('Cannot find participant_id column')
end
end
end
% if no participants.tsv, use subjects folder names as their IDs
if isempty(bids.participants)
participantFolders = dir(fullfile(bidsFolder, 'sub-*'));
bids.participants = {'participant_id' participantFolders.name }';
end
bids.participants(strcmp(bids.participants, 'sub-emptyroom'),:) = [];
% load participant sidecar file
participantsJSONFile = fullfile(bidsFolder, 'participants.json');
bids.participantsJSON = '';
if exist(participantsJSONFile,'File')
bids.participantsJSON = bids_loadfile( participantsJSONFile );
end
% scan participants
count = 1;
commands = {};
task = [ 'task-' bidsFolder ];
bids.data = [];
bids.eventInfo = [];
bids.data.eventdesc = [];
bids.data.eventinfo = [];
inconsistentChannels = 0;
inconsistentEvents = 0;
faileddatasets = [];
if isempty(opt.subjects)
opt.subjects = 2:size(bids.participants,1); % indices into the participants.tsv file, ignoring first header row
else
if iscell(opt.subjects) % match ID to particpiants and return index
for sub = length(opt.subjects):-1:1
if contains(opt.subjects{sub},'sub-')
ID = extractAfter(opt.subjects{sub},'sub-');
else
ID = opt.subjects{sub};
end
test = find(cellfun(@(x) strcmp(ID,extractAfter(x,'sub-')), bids.participants(2:end,1))); % starts at 2
if isempty(test)
warning('sub-%s not found',ID)
else
sub_index(sub) = test;
end
end
opt.subjects = sub_index+1;
else % takes integers in
opt.subjects = opt.subjects+1;
end
end
for iSubject = opt.subjects
parentSubjectFolder = fullfile(bidsFolder , bids.participants{iSubject,pInd});
outputSubjectFolder = fullfile(opt.outputdir, bids.participants{iSubject,pInd});
iteration = 0;
while ~exist(parentSubjectFolder, 'dir') && iteration < 3
fprintf(2, 'Folder %s does not exist\n', parentSubjectFolder);
dashpos = find(bids.participants{iSubject,1} == '-');
if ~isempty(dashpos)
bids.participants{iSubject,1} = [ bids.participants{iSubject,1}(1:dashpos) '0' bids.participants{iSubject,1}(dashpos+1:end) ];
parentSubjectFolder = fullfile(bidsFolder , bids.participants{iSubject,pInd});
outputSubjectFolder = fullfile(opt.outputdir, bids.participants{iSubject,pInd});
end
iteration = iteration + 1;
end
% find folder containing eeg
subFolders = dir(fullfile(parentSubjectFolder, 'ses*'));
if ~isempty(subFolders)
subFolders = { subFolders.name };
else
subFolders = {''};
end
subjectFolder = {};
subjectFolderOut = {};
if ~isempty(opt.sessions)
subFolders = intersect(subFolders, opt.sessions);
end
for iFold = 1:length(subFolders)
subjectFolder{ iFold} = fullfile(parentSubjectFolder, subFolders{iFold}, 'eeg');
subjectFolderOut{iFold} = fullfile(outputSubjectFolder, subFolders{iFold}, 'eeg');
if ~exist(subjectFolder{iFold},'dir')
subjectFolder{ iFold} = fullfile(parentSubjectFolder, subFolders{iFold}, 'meg');
subjectFolderOut{iFold} = fullfile(outputSubjectFolder, subFolders{iFold}, 'meg');
if ~exist(subjectFolder{iFold},'dir')
subjectFolder{ iFold} = fullfile(parentSubjectFolder, subFolders{iFold}, 'ieeg');
subjectFolderOut{iFold} = fullfile(outputSubjectFolder, subFolders{iFold}, 'ieeg');
end
end
end
% import data
for iFold = 1:length(subjectFolder) % scan sessions
if ~exist(subjectFolder{iFold},'dir')
fprintf(2, 'No EEG data folder for subject %s session %s\n', bids.participants{iSubject,pInd}, subFolders{iFold});
else
% scans.tsv for time synch information
%-------------------------------------
try
try
scansFile = searchparent(fileparts(subjectFolder{iFold}), '*_scans.tsv');
catch
% for some reason parent search not working - a quick workaround
scansFile = searchparent(fileparts(fileparts(subjectFolder{iFold})), '*_scans.tsv');
end
catch
end
if exist('scansFile', 'var') && ~isempty(scansFile)
useScans = true;
scans = bids_loadfile( scansFile.name, scansFile);
bids.data = setallfields(bids.data, [iSubject-1,iFold,1], struct('scans', {scans}));
else
useScans = false;
end
% MEG, EEG, iEEG, Motion, Physio, or BEH
% which raw data - with folder inheritance
eegFile = searchparent(subjectFolder{iFold}, '*eeg.*');
if isempty(eegFile)
eegFile = searchparent(subjectFolder{iFold}, '*_meg.*');
end
if isempty(eegFile)
eegFile = searchparent(subjectFolder{iFold}, '*_ieeg.*');
end
infoFile = searchparent(subjectFolder{iFold}, '*_eeg.json');
channelFile = searchparent(subjectFolder{iFold}, '*_channels.tsv');
elecFile = searchparent(subjectFolder{iFold}, '*_electrodes.tsv');
eventFile = searchparent(subjectFolder{iFold}, '*_events.tsv');
eventDescFile = searchparent(subjectFolder{iFold}, '*_events.json');
coordFile = searchparent(subjectFolder{iFold}, '*_coordsystem.json');
behFile = searchparent(fullfile(subjectFolder{iFold}, '..', 'beh'), '*_beh.tsv');
motionFile = searchparent(fullfile(subjectFolder{iFold}, '..', 'motion'), '*_motion.tsv');
physioFile = searchparent(fullfile(subjectFolder{iFold}, '..', 'physio'), '*_physio.tsv');
% remove BEH files which have runs (treated separately)
if ~isempty(behFile) && (contains(behFile(1).name, 'run') || contains(behFile(1).name, 'task'))
behFile = {};
end
% check the task
if ~isempty(opt.bidstask)
eegFile = filterFiles(eegFile , opt.bidstask);
infoFile = filterFiles(infoFile , opt.bidstask);
channelFile = filterFiles(channelFile , opt.bidstask);
elecFile = filterFiles(elecFile , opt.bidstask);
eventFile = filterFiles(eventFile , opt.bidstask);
eventDescFile = filterFiles(eventDescFile, opt.bidstask);
coordFile = filterFiles(coordFile , opt.bidstask);
behFile = filterFiles(behFile , opt.bidstask);
end
% check the task
if ~isempty(opt.runs)
eegFile = filterFilesRun(eegFile , opt.runs);
infoFile = filterFilesRun(infoFile , opt.runs);
channelFile = filterFilesRun(channelFile , opt.runs);
elecFile = filterFilesRun(elecFile , opt.runs);
eventFile = filterFilesRun(eventFile , opt.runs);
eventDescFile = filterFilesRun(eventDescFile, opt.runs);
% no runs for BEH or coordsystem
end
% raw data
allFiles = { eegFile.name };
ind = strmatch( 'json', cellfun(@(x)x(end-3:end), allFiles, 'uniformoutput', false) );
if ~isempty(ind)
eegFileJSON = allFiles(ind);
allFiles(ind) = [];
end
ind = strmatch( '.set', cellfun(@(x)x(end-3:end), allFiles, 'uniformoutput', false) ); % EEGLAB
if ~isempty(ind)
eegFileRawAll = allFiles(ind);
elseif length(allFiles) == 1
eegFileRawAll = allFiles;
else
ind = strmatch( '.eeg', cellfun(@(x)x(end-3:end), allFiles, 'uniformoutput', false) ); % BVA
if isempty(ind)
ind = strmatch( '.edf', cellfun(@(x)x(end-3:end), allFiles, 'uniformoutput', false) ); % EDF
if isempty(ind)
ind = strmatch( '.bdf', cellfun(@(x)x(end-3:end), allFiles, 'uniformoutput', false) ); % BDF
if isempty(ind)
ind = strmatch( '.fif', cellfun(@(x)x(end-3:end), allFiles, 'uniformoutput', false) ); % FIF
if isempty(ind)
ind = strmatch( '.gz', cellfun(@(x)x(end-2:end), allFiles, 'uniformoutput', false) ); % FIF
if isempty(ind) && ~isempty(allFiles)
ind = strmatch( '.ds', cellfun(@(x)x(end-2:end), allFiles, 'uniformoutput', false) ); % DS
if isempty(ind) && ~isempty(allFiles)
ind = strmatch( '.mefd', cellfun(@(x)x(end-4:end), allFiles, 'uniformoutput', false) ); % MEFD
if isempty(ind) && ~isempty(allFiles)
fprintf(2, 'No EEG/MEG file found for subject %s\n', bids.participants{iSubject,pInd});
end
end
end
end
ind2 = cellfun(@(x)~isempty(strfind(x, 'acq-crosstalk')), allFiles(ind));
ind(ind2) = [];
end
end
end
eegFileRawAll = allFiles(ind);
end
% identify non-EEG data files
%--------------------------------------------------------------
if ~isempty(behFile) % should be a single file
if length(behFile) > 1
fprintf(2, 'More than 1 BEH file for a given subject, do not know what to do with it\n');
end
behData = readtable(fullfile(behFile(1).folder, behFile(1).name),'FileType','text');
end
otherModality = {};
motionData = {}; % can be multiple files (tracksys, runs)
if ~isempty(motionFile)
for iMotion = 1:numel(motionFile)
motionData{iMotion} = readtable(fullfile(motionFile(iMotion).folder, motionFile(iMotion).name),'FileType','text');
motionFile(iMotion).tracksys = extractBetween(motionFile(iMotion).name,'tracksys-','_');
motionFile(iMotion).run = extractBetween(motionFile(iMotion).name,'run-','_');
end
otherModality{end+1} = 'motion';
end
physioData = {}; % can be multiple files (runs)
if ~isempty(physioFile)
for iPhys = 1:numel(physioFile)
physioData{iPhys} = readtable(fullfile(physioFile(iPhys).folder, physioFile(iPhys).name),'FileType','text');
physioFile(iPhys).run = extractBetween(physioFile(iPhys).name,'run-','_');
end
otherModality{end+1} = 'physio';
end
% skip most import if set file with no need for modication
for iFile = 1:length(eegFileRawAll)
try
eegFileName = eegFileRawAll{iFile};
[~,tmpFileName,fileExt] = fileparts(eegFileName);
eegFileRaw = fullfile(subjectFolder{ iFold}, eegFileName);
eegFileNameOut = fullfile(subjectFolderOut{iFold}, [ tmpFileName '.set' ]);
% what is the run
iRun = 1;
ind = strfind(eegFileRaw, '_run-');
if ~isempty(ind)
tmpEegFileRaw = eegFileRaw(ind(1)+5:end);
indUnder = find(tmpEegFileRaw == '_');
iRun = str2double(tmpEegFileRaw(1:indUnder(1)-1));
if isnan(iRun)
iRun = str2double(tmpEegFileRaw(1:indUnder(1)-2)); % rare case run 5H in ds003190/sub-01/ses-01/eeg/sub-01_ses-01_task-ctos_run-5H_eeg.eeg
if isnan(iRun)
error('Problem converting run information');
end
end
% check for BEH file
filePathTmp = fileparts(eegFileRaw);
behFileTmp = fullfile(filePathTmp,'..', 'beh', [eegFileRaw(1:ind(1)-1) '_beh.tsv' ]);
if exist(behFileTmp, 'file')
behData = readtable(behFileTmp,'FileType','text');
else
behData = [];
end
else
% check for BEH file
[filePathTmp, fileBaseTmp ] = fileparts(eegFileRaw);
behFileTmp = fullfile(filePathTmp, '..', 'beh', [fileBaseTmp(1:end-4) '_beh.tsv' ]);
if exist(behFileTmp, 'file')
try
behData = readtable(behFileTmp,'FileType','text');
catch
disp('Warning: could not load BEH file');
end
else
behData = [];
end
end
% extract task name and modality
underScores = find(tmpFileName == '_');
if ~strcmpi(tmpFileName(underScores(end)+1:end), 'ieeg')
if ~strcmpi(tmpFileName(underScores(end)+1:end), 'eeg')
if ~strcmpi(tmpFileName(underScores(end)+1:end), 'meg.fif')
if ~strcmpi(tmpFileName(underScores(end)+1:end), 'meg')
error('Data file name does not contain eeg, ieeg, or meg'); % theoretically impossible
else
modality = 'meg';
end
else
modality = 'meg';
end
else
modality = 'eeg';
end
else
modality = 'ieeg';
end
% JSON information file
infoData = bids_importjson([ eegFileRaw(1:end-8) '_' modality '.json' ], ['_' modality '.json']); % bids_loadfile([ eegFileRaw(1:end-8) '_eeg.json' ], infoFile);
bids.data = setallfields(bids.data, [iSubject-1,iFold,iFile], infoData);
if contains(tmpFileName,'task')
tStart = strfind(tmpFileName,'_task')+1;
tEnd = underScores - tStart;
tEnd = min(tEnd(tEnd>0)) + tStart - 1;
task = tmpFileName(tStart:tEnd);
end
if ~strcmpi(fileExt, '.set') || strcmpi(opt.bidsevent, 'on') || strcmpi(opt.bidschanloc, 'on') || ~strcmpi(opt.outputdir, bidsFolder)
fprintf('Importing file: %s\n', eegFileRaw);
switch lower(fileExt)
case '.set' % do nothing
if strcmpi(opt.metadata, 'on')
EEG = pop_loadset( 'filename', eegFileRaw, 'loadmode', 'info' );
else
EEG = pop_loadset( 'filename', eegFileName, 'filepath', subjectFolder{iFold});
end
case {'.bdf','.edf'}
EEG = pop_biosig( eegFileRaw ); % no way to read meta data only (because events in channel)
case '.eeg'
[tmpPath,tmpFileName,~] = fileparts(eegFileRaw);
if exist(fullfile(tmpPath, [tmpFileName '.vhdr']), 'file')
ext = '.vhdr';
elseif exist(fullfile(tmpPath, [tmpFileName '.VHDR']), 'file'),
ext = '.VHDR';
else
fprintf(2, 'Warning: eeg file found without BVA header file\n');
break;
end
if strcmpi(opt.metadata, 'on')
EEG = pop_loadbv( tmpPath, [tmpFileName ext], [], [], true );
else
EEG = pop_loadbv( tmpPath, [tmpFileName ext] );
end
case '.fif'
EEG = pop_fileio(eegFileRaw); % fif folder
case '.gz'
gunzip(eegFileRaw);
EEG = pop_fileio(eegFileRaw(1:end-3)); % fif folder
case '.ds'
if strcmpi(opt.ctffunc, 'fileio')
EEG = pop_fileio(eegFileRaw);
else
EEG = pop_ctf_read(eegFileRaw);
end
case '.mefd'
if ~exist('pop_MEF3', 'file')
error('MEF plugin not present, please install the MEF3 plugin first')
end
EEG = pop_MEF3(eegFileRaw); % MEF folder
otherwise
error('No EEG data found for subject/session %s', subjectFolder{iFold});
end
EEG = eeg_checkset(EEG);
% check for group information: get from participants
% file if doesn't exist
if isempty(EEG.group) && sum(ismember(lower(bids.participants(1,:)),'group'))
igroup = bids.participants{iSubject,ismember(lower(bids.participants(1,:)),'group')};
if ~isempty(igroup)
EEG.group = igroup;
end
end
EEGnodata = EEG;
EEGnodata.data = [];
bids.data = setallfields(bids.data, [iSubject-1,iFold,iFile], struct('EEG', EEGnodata));
% channel location data
% ---------------------
selected_chanfile = bids_get_file(eegFileRaw(1:end-8), '_channels.tsv', channelFile);
selected_elecfile = bids_get_file(eegFileRaw(1:end-8), '_electrodes.tsv', elecFile);
if strcmpi(opt.bidschanloc, 'on')
[EEG, channelData, elecData] = bids_importchanlocs(EEG, selected_chanfile, selected_elecfile);
if isempty(EEG.chanlocs) || ~isfield(EEG.chanlocs, 'theta') || all(cellfun(@isempty, { EEG.chanlocs.theta }))
EEG = bids_chan_lookup(EEG, infoData);
end
else
channelData = bids_loadfile(selected_chanfile);
elecData = bids_loadfile(selected_elecfile);
if ~isfield(EEG.chanlocs, 'theta') || all(cellfun(@isempty, { EEG.chanlocs.theta }))
EEG = bids_chan_lookup(EEG, infoData);
else
disp('The EEG file has channel locations associated with it, we are keeping them');
end
end
% look up EEG channel type
disp('Looking up/checking channel type from channel labels');
EEG = eeg_getchantype(EEG);
bids.data = setallfields(bids.data, [iSubject-1,iFold,iFile], struct('chaninfo', { channelData }));
bids.data = setallfields(bids.data, [iSubject-1,iFold,iFile], struct('elecinfo', { elecData }));
% event data
% ----------
if strcmpi(opt.bidsevent, 'on')
eventfile = bids_get_file(eegFileRaw(1:end-8), '_events.tsv', eventFile);
selected_eventdescfile = bids_get_file(eegFileRaw(1:end-8), '_events.json', eventDescFile);
if ~isempty(eventfile)
[EEG, bids, eventData, eventDesc] = bids_importeventfile(EEG, eventfile, 'bids', bids, 'eventDescFile', selected_eventdescfile, 'eventtype', opt.eventtype);
if isempty(eventData), error('bidsevent on but events.tsv has no data'); end
bids.data = setallfields(bids.data, [iSubject-1,iFold,iFile], struct('eventinfo', {eventData}));
bids.data = setallfields(bids.data, [iSubject-1,iFold,iFile], struct('eventdesc', {eventDesc}));
end
end
% coordsystem file
% ----------------
if strcmpi(opt.bidscoord, 'on')
coordFile = bids_get_file(eegFileRaw(1:end-8), '_coordsystem.json', coordFile);
[EEG, bids] = bids_importcoordsystemfile(EEG, coordFile, 'bids', bids);
end
% copy information inside dataset
EEG.subject = bids.participants{iSubject,pInd};
EEG.session = iFold;
EEG.run = iRun;
EEG.task = task(6:end); % task is currently of format "task-<Task name>"
% build `EEG.BIDS` from `bids`
BIDS.gInfo = bids.dataset_description;
BIDS.gInfo.README = bids.README;
BIDS.gInfo.CHANGES = bids.CHANGES;
BIDS.pInfo = [bids.participants(1,:); bids.participants(iSubject,:)]; % header -> iSubject info
BIDS.pInfoDesc = bids.participantsJSON;
BIDS.eInfo = bids.eventInfo;
BIDS.eInfoDesc = bids.data.eventdesc;
BIDS.tInfo = infoData;
BIDS.bidsstats = stats;
BIDS.scannedElectrodes = false;
if ~isempty(elecData)
BIDS.scannedElectrodes = true;
end
if ~isempty(behData)
behData = table2struct(behData);
end
BIDS.behavioral = behData;
EEG.BIDS = BIDS;
if strcmpi(opt.metadata, 'off')
if exist(subjectFolderOut{iFold},'dir') ~= 7
mkdir(subjectFolderOut{iFold});
end
EEG = pop_saveset( EEG, eegFileNameOut);
end
end
% building study command
commands = [ commands { 'index' count 'load' eegFileNameOut 'subject' bids.participants{iSubject,pInd} 'session' iFold 'task' task(6:end) 'run' iRun } ];
% custom numerical fields
for iCol = 2:size(bids.participants,2)
commands = [ commands { bids.participants{1,iCol} bids.participants{iSubject,iCol} } ];
end
if isstruct(behData) && ~isempty(behData)
behFields = fieldnames(behData);
if length(behData) > 1
warning('Behavioral data length larger than 1, only retaining the first element');
end
for iFieldBeh = 1:length(behFields)
commands = [ commands { behFields{iFieldBeh} [behData(1).(behFields{iFieldBeh})] } ];
end
end
count = count+1;
% check dataset consistency
bData = bids.data(iSubject-1,iFold,iFile);
if ~isempty(bData.chaninfo)
if size(bData.chaninfo,1)-1 ~= bData.EEG.nbchan
warning('Warning: inconsistency detected, %d channels in BIDS file vs %d in EEG file for %s\n', size(bData.chaninfo,1)-1, bData.EEG.nbchan, [tmpFileName,fileExt]);
inconsistentChannels = inconsistentChannels+1;
end
end
%{
if ~isempty(bData.eventinfo)
if size(bData.eventinfo,1)-1 ~= length(bData.EEG.event)
fprintf(2, 'Warning: inconsistency detected, %d events in BIDS file vs %d in EEG file for %s\n', size(bData.eventinfo,1)-1, length(bData.EEG.event), [tmpFileName,fileExt]);
inconsistentEvents = inconsistentEvents+1;
end
end
%}
catch ME
faileddatasets = [faileddatasets eegFileRaw];
end
end % end for eegFileRawAll
% import data of other tpyes than EEG, MEG, iEEG
for iMod = 1:numel(otherModality)
try
dataType = otherModality{iMod};
dataFile = eval([dataType 'File']);
dataRaw = eval([dataType 'Data']); % cell array containing tables
subjectID = bids.participants{iSubject,pInd};
subjectDataFolder = subjectFolder{iFold}(1:end-3);
subjectDataFolderOut = subjectFolderOut{iFold}(1:end-3);
if isfield(bids.data(iSubject-1,iFold,1), 'scans')
scansRaw = bids.data(iSubject-1,iFold,1).scans;
else
scansRaw = [];
end
for iDat = 1:numel(dataFile)
[DATA, dataFileOut] = import_noneeg(dataType, dataFile(iDat), dataRaw{iDat}, subjectID, scansRaw, iFold, strcmpi(opt.metadata, 'on'), strcmpi(opt.bidschanloc, 'on'), useScans, subjectDataFolder, subjectDataFolderOut);
if strcmpi(opt.metadata, 'off')
if exist([subjectFolderOut{iFold}(1:end-3), dataType],'dir') ~= 7
mkdir(subjectFolderOut{iFold}(1:end-3), dataType);
end
pop_saveset(DATA, dataFileOut);
end
end
catch exception
fprintf('Error importing non i/M/EEG modality %s. Skipped\n', dataType);
fprintf(getReport(exception));
end
end
fclose all;
end
end
end
% update statistics
% -----------------
stats = bids_metadata_stats(bids, inconsistentChannels);
% study name and study creation
% -----------------------------
if strcmpi(opt.metadata, 'off')
if isempty(commands)
error('No dataset were found');
end
studyName = fullfile(opt.outputdir, [opt.studyName '.study']);
if exist('tasklist','var') && length(tasklist)~=1 && isempty(opt.bidstask)
[STUDY, ALLEEG] = std_editset([], [], 'commands', commands, 'filename', studyName, 'task', 'task-mixed');
else
[STUDY, ALLEEG] = std_editset([], [], 'commands', commands, 'filename', studyName, 'task', task);
end
% track failed datasets
STUDY.etc.bidsimportinfo = [];
STUDY.etc.bidsimportinfo.totaldatasetcount = numel(eegFileRawAll);
STUDY.etc.bidsimportinfo.faileddatasets = faileddatasets;
% import HED tags if exists in top level events.json
% -----------------------------
% scan for top level events.json
top_level_eventsjson = dir(fullfile(bidsFolder, '*_events.json'));
if ~isempty(top_level_eventsjson) && numel(top_level_eventsjson) == 1
top_level_eventsjson = fullfile(top_level_eventsjson.folder, top_level_eventsjson.name);
if plugin_status('HEDTools')
try
fMap = fieldMap.createfMapFromJson(top_level_eventsjson);
if fMap.hasAnnotation()
STUDY.etc.tags = fMap.getStruct();
end
catch ME
warning('Found top-level events.json file and tried importing HED tags but failed');
end
end
end
[STUDY, ALLEEG] = std_editset(STUDY, ALLEEG, 'resave', 'on');
if ~isempty(options)
commands = sprintf('[STUDY, ALLEEG] = pop_importbids(''%s'', %s);', bidsFolder, vararg2str(options));
else
commands = sprintf('[STUDY, ALLEEG] = pop_importbids(''%s'');', bidsFolder);
end
end
% search parent folders (outward search) for the file of given fileName
% ---------------------
function outFile = searchparent(folder, fileName)
% search nestedly outward
% only get exact match and filter out hidden file
outFile = '';
parent = folder;
count = 4;
while ~any(arrayfun(@(x) strcmp(lower(x.name),'dataset_description.json'), dir(parent))) && isempty(outFile) && count > 0 % dataset_description indicates root BIDS folder
outFile = filterHiddenFile(folder, dir(fullfile(parent, fileName)));
parent = fileparts(parent);
count = count-1;
end
if isempty(outFile)
outFile = filterHiddenFile(parent, dir(fullfile(parent, fileName)));
end
function fileList = filterHiddenFile(folder, fileList)
isGoodFile = true(1,numel(fileList));
% loop to identify hidden files
for iFile = 1:numel(fileList) %'# loop only non-dirs
% on OSX, hidden files start with a dot
isGoodFile(iFile) = logical(~strcmp(fileList(iFile).name(1),'.'));
if isGoodFile(iFile) && ispc
% check for hidden Windows files - only works on Windows
[~,stats] = fileattrib(fullfile(folder,fileList(iFile).name));
if stats.hidden
isGoodFile(iFile) = false;
end
end
end
% remove bad files
fileList = fileList(isGoodFile);
% Filter files
% ------------
function fileList = filterFiles(fileList, taskList)
keepInd = zeros(1,length(fileList));
for iFile = 1:length(fileList)
if contains(fileList(iFile).name, taskList)
keepInd(iFile) = 1;
elseif contains(fileList(iFile).name, taskList,'IgnoreCase',true)
warning('matching task ignore case')
keepInd(iFile) = 1;
end
end
fileList = fileList(logical(keepInd));
% Filter file runs
% ----------------
function fileList = filterFilesRun(fileList, runs)
if ~iscell(runs)
runs = {runs}; % integer now in a cell
end
keepInd = arrayfun(@(x) contains(extractAfter(x.name,'run-'),runs), fileList);
% keepInd = zeros(1,length(fileList));
% for iFile = 1:length(fileList)
% runInd = strfind(fileList(iFile).name, '_run-');
% if ~isempty(runInd)
% strTmp = fileList(iFile).name(runInd+5:end);
% underScore = find(strTmp == '_');
% if any(runs == str2double(strTmp(1:underScore(1)-1)))
% keepInd(iFile) = 1;
% end
% end
% end
fileList = fileList(logical(keepInd));
% set structure
% -------------
function sdata = setallfields(sdata, indices, newdata)
if isempty(newdata), return; end
if ~isstruct(newdata), error('Can only assign structures'); end
if length(indices) < 3, error('Must have 3 indices'); end
allFields = fieldnames(newdata);
for iField = 1:length(allFields)
sdata(indices(1), indices(2), indices(3)).(allFields{iField}) = newdata.(allFields{iField});
end
% get BIDS file
function filestr = bids_get_file(baseName, ext, alternateFile)
filestr = '';
if exist([ baseName ext ], 'file')
filestr = [ baseName ext ];
else
if ~isempty(alternateFile) && isfield(alternateFile, 'folder') && isfield(alternateFile, 'name')
tmpFile = fullfile(alternateFile(1).folder, alternateFile(1).name);
if exist(tmpFile, 'file')
filestr = tmpFile;
end
end
end
% format other data types than EEG, MEG, iEEG
%--------------------------------------------
function [DATA, dataFileOut] = import_noneeg(dataType, dataFile, dataRaw, subject, scansData, session, onlyMetadata, useChanlocs, useScans, subjectFolder, subjectDataFolderOut)
disp(['Processing ' dataType ' data'])
% replace extension tsv with set
[~,fileName,fileExt] = fileparts(dataFile.name);
dataFileOut = fullfile(subjectDataFolderOut, dataType, [fileName '.set']);
% check for json file that might be applicable to the current file in current directory using rule 2.b and 2.c
% of https://bids-specification.readthedocs.io/en/stable/common-principles.html#the-inheritance-principle
bids_entity = strsplit(fileName, '_');
bids_entity = bids_entity{end};
dataFileJSON = fullfile([subjectFolder, dataType], ['*_' bids_entity '.json']);
% resolve wildcard if applicable
dataFileJSONDir = dir(dataFileJSON);
if ~isempty(dataFileJSONDir)
for u=1:numel(dataFileJSONDir)
dataFileJSONName_parts = strsplit(dataFileJSONDir(u).name, '_');
dataFileJSONName_parts = dataFileJSONName_parts(1:end-1); % only consider the suffices
if all(cellfun(@(x) contains(fileName, x), dataFileJSONName_parts))
dataFileJSON = fullfile(dataFileJSONDir(u).folder, dataFileJSONDir(u).name);
break
end
end
end
infoData = bids_importjson(dataFileJSON);
% check or construct needed channel files according to the data type
switch dataType
case 'motion'
% look for associated *_channels.tsv
% since *_motion.json share the same principle and already
% looked up above, we only change the postfix
channelFileMotion = [dataFileJSON(1:end-numel('motion.json')) 'channels.tsv']; % replace 'motion.json' with 'channels.tsv'
% channelFile = searchparent([subjectFolder, dataType], channelFileMotion);
channelData = bids_loadfile(channelFileMotion); %channelFile(1).name, channelFile);
case 'physio'
% channel file (for physio data, hidden in json file as 'columns')
channelData = {'name', 'type', 'units'};
for Ci = 1:numel(infoData.Columns)
channelData{end + 1,1} = [char(infoData.Columns{Ci})] ;
end
end
switch lower(fileExt)
case '.set' % do nothing
if onlyMetadata
DATA = pop_loadset( 'filename', dataFile.name, 'loadmode', 'info' );
else
DATA = pop_loadset( 'filename', dataFile.name );
end
case '.tsv'
DATA = eeg_emptyset;
DATA.data = table2array(dataRaw)';
if strcmp(dataType,'motion')
if isfield(infoData, 'SamplingFrequencyEffective')
% 'SamplingFrequencyEffective' can be used if nominal
% https://bids-specification.readthedocs.io/en/stable/modality-specific-files/motion.html#motion-specific-fields
DATA.srate = infoData.SamplingFrequencyEffective;
if isfield(infoData, 'SamplingFrequency')
DATA.etc.nominal_srate = infoData.SamplingFrequency;
end
else
DATA.srate = infoData.SamplingFrequency;
end
else
try
DATA.srate = infoData.SamplingFrequencyEffective; % Actual sampling rate used in motion data. Note that the unit of the time must be in second.
catch
DATA.srate = infoData.SamplingFrequency; % Generic physio data
end
end
% find latency channel
headers = dataRaw.Properties.VariableNames;
useLatency = 0;
if strcmp(dataType,'motion')
latencyInd = find(strcmpi(channelData(:,strcmp(channelData(1,:),'type')), 'latency'));
useLatency = ~isempty(latencyInd);
if useLatency
latencyHeader = channelData{latencyInd,strcmp(channelData(1,:),'name')};
latencyRowInData = find(strcmp(headers, latencyHeader));
end
elseif strcmp(dataType,'physio')
% check if the tracking system comes with latency
latencyInd = find(contains(channelData(:,strcmp(channelData(1,:),'name')), 'latency'));
useLatency = ~isempty(latencyInd);
if useLatency
latencyHeader = channelData{latencyInd,strcmp(channelData(1,:),'name')};
latencyRowInData = find(strcmp(headers, latencyHeader));
end
end
% reconstruct time : use scans.tsv for synching
% it computes offset between motion and eeg data
if useScans
for Coli = 1:size(scansData, 2)
if strcmp(scansData{1,Coli}, 'acq_time')
acqTimeColi = Coli;
elseif strcmp(scansData{1,Coli}, 'filename')
fNameColi = Coli;
end
end
for Rowi = 1:size(scansData, 1)
sesString = '';
taskString = '';
runString = '';
trackSysString = '';
if exist('tracksys', 'var') && ~isempty(tracksys)