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bids_export.m
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% bids_export - this function allows converting a collection of datasets to
% BIDS formated folders and files.
%
% Usage:
% bids_export(files, varargin)
%
% Input:
% files - Structure with the fields 'file','session' and 'run'.
% The field 'file' should be a cell array of strings
% with the path to the data files. The fields 'session'
% and 'run' will contain the session index and the run index
% within the session for the corresponding data file in the
% same index. 'notes' can contain notes about the recording.
%
% See example below for a case with 2 subjects with
% 2 sessions and 2 run each:
% subject(1).file = 'subj1.set';
% subject(1).chanlocs = 'subj1.elp'; % optional
% subject(1).notes = 'Good recording'; % optional
% subject(2).file = 'subj2.set';
% subject(2).chanlocs = 'subj2.elp'; % optional
% subject(2).notes = 'Bad recoding'; % optional
%
% See example below for a case with 2 subjects with
% 2 sessions and 2 runs each:
% subject(1).file = {'subj-1_ss-1-run1' 'subj-1_ss-1-run2' 'subj-1_ss-2-run1' 'subj-1_ss-2-run2'};
% subject(1).session = [ 1 1 2 2 ];
% subject(1).run = [ 1 2 1 2 ];
% subject(1).task = { 'go-no task' 'control task' 'go-no task' 'control task' };
% subject(1).instructions = { 'Press button when you see an animal' 'Look passively at the images' 'Press button when you see an animal' 'Look passively at the images' };
% subject(1).chanlocs = {'subj-1_ss-1-run1.elp' 'subj-1_ss-1-run2.elp' 'subj-1_ss-2-run1.elp' 'subj-1_ss-2-run2.elp'};
% subject(2).file = {'subj-2_ss-1-run1' 'subj-2_ss-1-run2' 'subj-2_ss-2-run1' 'subj-2_ss-2-run2'};
% subject(2).session = [ 1 1 2 2 ];
% subject(2).run = [ 1 2 1 2 ];
% subject(2).task = { 'go-no task' 'control task' 'go-no task' 'control task' };
% subject(2).instructions = { 'Press button when you see an animal' 'Look passively at the images' 'Press button when you see an animal' 'Look passively at the images' };
% subject(2).chanlocs = {'subj-2_ss-1-run1.elp' 'subj-2_ss-1-run2.elp' 'subj-2_ss-2-run1.elp' 'subj-2_ss-2-run2.elp'};
%
% Alternate representation that is also functional:
% subject(1).file(1).file = 'subj-1_ss-1-run1';
% subject(1).file(1).session = 1;
% subject(1).file(1).run = 1;
% subject(1).file(1).task = 'go-no task';
% subject(1).file(1).instructions = 'Press button when you see an animal';
% subject(1).file(1).chanlocs = 'subj-1_ss-1-run1.elp';
% subject(1).file(2).file = 'subj-1_ss-1-run2';
% subject(1).file(2).session = 1;
% subject(1).file(2).run = 2;
% subject(1).file(2).task = 'control task';
% subject(1).file(2).instructions = 'Look passively at the images';
% subject(1).file(2).chanlocs = 'subj-1_ss-1-run2.elp';
% ...
%
% Optional inputs:
% 'targetdir' - [string] target directory. Default is 'bidsexport' in the
% current folder.
%
% 'taskName' - [string] name of the task for all datasets. No spaces and
% special characters are allowed. Default is 'Experiment'
% if no tasks are detected, '<taskname>' when single task detected,
% and 'mixed' when multiple tasks detected. Individual file
% task can be specified using files.task
%
% 'README' - [string] content of the README file. If the string points
% to a file that exists on the path, the file is copied.
% Otherwise a new README file is created and the content of
% this variable is copied to the new file.
%
% 'CHANGES' - [string] content of the README file. If the string points
% to a file that exists on the path, the file is copied.
%
% 'codefiles' - [cell] cell array of file names containing code related
% to importing or processing the data.
%
% 'stimuli' - [cell] cell array of EEGLAB event type and corresponding file
% names for the stimulus on your computer.
% For example: { 'sound1' '/Users/xxxx/sounds/sound1.mp3';
% 'img1' '/Users/xxxx/sounds/img1.jpg' }
% (the semicolumn above is optional). Alternatively, after
% exporting to BIDS, create a stimuli folder and place your
% stimuli in that folder with a README file describing them.
%
% 'gInfo' - [struct] general information fields. See BIDS specifications.
% For example.
% info.ReferencesAndLinks = { 'Pubmed 122032020' };
% info.Name = 'This is a custom task';
% info.License = 'Creative commons';
%
% 'tInfo' - [struct] task information fields. See BIDS specifications.
% For example.
% tInfo.InstitutionAddress = '9500 Gilman Drive, CA92093-0559 La Jolla, USA';
% tInfo.InstitutionName = 'Univesity of California, San Diego';
% tInfo.InstitutionalDepartmentName = 'Institute of Neural Computation';
% tInfo.PowerLineFrequency = 50;
% tInfo.SoftwareFilters = struct('NotchFilter', struct('cutof', '50 (Hz)'));
% tInfo.HardwareFilters = struct('HighpassRCFilter',struct('HalfAmplitudeCutoff', '0.0159 Hz', 'RollOff','6dB/Octave'))
% Notice that SoftwareFilters and HardwareFilters take struct.
%
%
% 'pInfo' - [cell] cell array of participant values, with one row
% per participants. The first row contains columns names.
% For example for 2 participants:
% { 'participant_id' 'sex' 'age';
% 'control01' 'male' 20;
% 'control02' 'female' 25 };
% The columns above are optional and an arbitrary number of custom columns may
% also be specified. When 'participant_id' is specified, it will be used for
% naming subject folders (folders names and file prefix will be sub-<label>,
% <label> being the participant ID).
%
% 'pInfoDesc' - [struct] structure describing participant file columns.
% The fields are described in the BIDS format.
% For example
% pInfo.participant_id.LongName = 'Participant ID';
% pInfo.participant_id.Description = 'Event onset';
% pInfo.sex.LongName = 'Gender';
% pInfo.sex.Description = 'Gender';
% pInfo.age.LongName = 'Age';
% pInfo.age.Description = 'Age in years';
%
% 'eInfo' - [cell] additional event information columns and their corresponding
% event fields in the EEGLAB event structure in format
% { '<BIDS field1>' '<EEG field1>';
% '<BIDS field2>' '<EEG field2>'}
% Note that EEGLAB event latency, duration, and type are inserted
% automatically as columns "sample" (latency), "onset" (latency in sec), "duration"
% (duration in sec), and "value" (EEGLAB event type). For example
% { 'sample' 'latency';
% 'value' 'type' }
% See also trial_type parameter.
%
% 'eInfoDesc' - [struct] structure describing additional or/and original
% event fields if you wish to redefine these.
% These are EEGLAB event fields listed above.
% See the BIDS format for more information
% eInfo.onset.LongName = 'Event onset'; % change default value
% eInfo.onset.Description = 'Event onset';
% eInfo.onset.Units = 'seconds';
% eInfo.HED.LongName = 'Hierarchival Event Descriptors';
% eInfo.reaction_time.LongName = 'Reaction time';
% eInfo.reaction_time.Units = 'seconds';
%
% 'cInfo' - [cell] cell array containing the field names for the
% channel file in addition to the channel "name", "type" and
% "unit" which are extracted from the channel location
% structure. For example, to add the reference as an
% additional column:
% {'reference';
% 'ref' }
%
% 'cInfoDesc' - [struct] structure describing additional or/and original
% channel fields if you wish to redefine these.
% cInfo.name.LongName = 'Channel name'; % change default description
% cInfo.name.Description = 'Channel name';
% cInfo.reference.LongName = 'Channel reference';
% cInfo.reference.Description = 'Channel reference montage 10/20';
%
% 'renametype' - [cell] 2 column cell table for renaming type.
% For example { '2' 'standard';
% '4' 'oddball';
% '128' 'response' }
%
% 'trialtype' - [cell] 2 column cell table indicating the type of event
% for each event type. For example { '2' 'stimulus';
% '4' 'stimulus';
% '128' 'response' }
%
% 'chanlocs' - [file] channel location file (must have the same number
% of channel as the data.
%
% 'chanlookup' - [file] look up channel locations based on file. Default
% not to look up channel location.
%
% 'anattype' - [string] type of anatomical MRI image ('T1w', 'T2w', etc...)
% see BIDS specification for more information.
%
% 'defaced' - ['on'|'off'] indicate if the MRI image is defaced or not.
% Default is 'on'.
%
% 'createids' - ['on'|'off'] do not use Participant IDs and create new
% anonymized IDs instead. Default is 'off'.
%
% 'chanlocs' - [struct or file name] channel location structure or file
% name to use when saving channel information. Note that
% this assumes that all the files have the same number of
% channels.
%
% 'copydata' -[0|1] While exporting EEGLAB data to BIDS (.set, .fdt), this flag
% will enable the copy of all the data files [1], or just create the
% BIDS files hierarchy without the large data files [0]. This
% options is aimed to be used to speedup the troubleshooting
% of bids_export execution. Default: [1]
%
% Validation:
% If the BIDS data created with this function fails to pass the BIDS
% validator (npm install -g https://github.com/bids-standard/bids-validator.git
% Usage bids-validator/bin/bids-validator --bep006 bidsfolder), please
% email [email protected]
%
% Example: The following examples will pass the bids validator.
% data(1).file = 'subject1.set'; data(1).run = 1; data(1).session = 1;
% data(2).file = 'subject2.set'; data(2).run = 1; data(2).session = 1;
% bids_export(data);
%
% Note that important information might be missing. For example, line noise
% is set to 0. Use input 'tInfo' to set the line noise as below.
%
% bids_export( data, 'tInfo', struct('PowerLineFrequency', 50 );
%
% In general, you will want to describe your events and include as much
% information as possible. A detailed and comprehensive example is provided
% in bids_export_example.m
%
%
% Authors: Arnaud Delorme, 2019
% Ramon Martinez-Cancino, 2019
% The following are automatically
% populated using channel structure info ('eeg', 'ecg', 'emg', 'eog', 'trigger')
% tInfo.ECGChannelCount = xxx;
% tInfo.EEGChannelCount = xxx;
% tInfo.EMGChannelCount = xxx;
% tInfo.EOGChannelCount = xxx;
% tInfo.MiscChannelCount = xxx;
% tInfo.TriggerChannelCount = xxx;
% tInfo.EEGReference = xxx;
% tInfo.EpochLength = xxx;
% tInfo.RecordingDuration = xxx;
% tInfo.SamplingFrequency = xxx;
% tInfo.TaskName = 'meditation';
% However, they may be overwritten man.
function bids_export(files, varargin)
if nargin < 1
help bids_format_eeglab;
return
end
if ~exist('jsonwrite')
addpath(fullfile(fileparts(which(mfilename)), 'JSONio'));
end
opt = finputcheck(varargin, {
'Name' 'string' {} '';
'License' 'string' {} '';
'Authors' 'cell' {} {''};
'ReferencesAndLinks' 'cell' {} {''};
'targetdir' 'string' {} fullfile(pwd, 'bidsexport');
'taskName' 'string' {} 'Experiment';
'codefiles' 'cell' {} {};
'stimuli' 'cell' {} {};
'pInfo' 'cell' {} {};
'eInfo' 'cell' {} {};
'cInfo' 'cell' {} {};
'gInfo' 'struct' {} struct([]);
'tInfo' 'struct' {} struct([]);
'pInfoDesc' 'struct' {} struct([]);
'eInfoDesc' 'struct' {} struct([]);
'cInfoDesc' 'struct' {} struct([]);
'trialtype' 'cell' {} {};
'renametype' 'cell' {} {};
'checkresponse' 'string' {} '';
'anattype' '' {} 'T1w';
'chanlocs' '' {} '';
'chanlookup' 'string' {} '';
'interactive' 'string' {'on' 'off'} 'off';
'defaced' 'string' {'on' 'off'} 'on';
'createids' 'string' {'on' 'off'} 'on';
'individualEventsJson' 'string' {'on' 'off'} 'off';
'exportext' 'string' { 'edf' 'eeglab' } 'eeglab';
'README' 'string' {} '';
'CHANGES' 'string' {} '' ;
'copydata' 'real' [0 1] 1 }, 'bids_export');
if isstr(opt), error(opt); end
if size(opt.stimuli,1) == 1 || size(opt.stimuli,2) == 1
opt.stimuli = reshape(opt.stimuli, [2 length(opt.stimuli)/2])';
end
% deleting folder
fprintf('Exporting data to %s...\n', opt.targetdir);
if exist(opt.targetdir,'dir')
if strcmpi(opt.interactive, 'on')
uilist = { ...
{ 'Style', 'text', 'string', 'Output directory exists and all current files will be deleted if continue', 'fontweight', 'bold' }, ...
{ 'Style', 'text', 'string', 'Would you want to proceed?'}, ...
};
geometry = { [1] [1]};
geomvert = [1 1 ];
[results,userdata,isOk,restag] = inputgui( 'geometry', geometry, 'geomvert', geomvert, 'uilist', uilist, 'title', 'Warning');
if isempty(isOk)
disp('BIDS export cancelled...')
return
end
end
disp('Folder exist. Deleting folder...')
rmdir(opt.targetdir, 's');
end
disp('Creating sub-directories...')
mkdir( fullfile(opt.targetdir, 'code'));
mkdir( fullfile(opt.targetdir, 'stimuli'));
% write dataset info (dataset_description.json)
% ---------------------------------------------
gInfoFields = { 'ReferencesAndLinks' 'required' 'cell' { 'n/a' };
'Name' 'required' 'char' '';
'License' 'required' 'char' 'CC0';
'BIDSVersion' 'required' 'char' '1.1.1' ;
'Authors' 'optional' 'cell' { 'n/a' };
'Acknowledgements' 'optional' 'char' '';
'HowToAcknowledge' 'optional' 'char' '';
'Funding' 'optional' 'cell' { 'n/a' };
'DatasetDOI' 'optional' 'char' { 'n/a' }};
if ~isfield(opt.gInfo, 'Name'), opt.gInfo(1).Name = opt.Name; end
if ~isfield(opt.gInfo, 'License'), opt.gInfo.License = opt.License; end
if ~isfield(opt.gInfo, 'Authors'), opt.gInfo.Authors = opt.Authors; end
if ~isfield(opt.gInfo, 'ReferencesAndLinks'), opt.gInfo.ReferencesAndLinks = opt.ReferencesAndLinks; end
opt.gInfo = checkfields(opt.gInfo, gInfoFields, 'gInfo');
jsonwrite(fullfile(opt.targetdir, 'dataset_description.json'), opt.gInfo, struct('indent',' '));
% make cell out of file names if necessary
% ----------------------------------------
for iSubj = 1:length(files)
if ~iscell(files(iSubj).file)
if isstruct(files(iSubj).file)
if isfield(files(iSubj).file, 'session')
files(iSubj).session = [ files(iSubj).file.session ];
end
if isfield(files(iSubj).file, 'run')
files(iSubj).run = [ files(iSubj).file.run ];
end
if isfield(files(iSubj).file, 'task')
files(iSubj).task = { files(iSubj).file.task };
end
if isfield(files(iSubj).file, 'instructions')
files(iSubj).task = { files(iSubj).file.instructions };
end
files(iSubj).file = { files(iSubj).file.file };
else
files(iSubj).file = { files(iSubj).file };
end
end
% channel location
if isfield(files(iSubj), 'chanlocs')
if ~iscell(files(iSubj).chanlocs)
files(iSubj).chanlocs = { files(iSubj).chanlocs };
end
if length(files(iSubj).chanlocs) ~= length(files(iSubj).file)
if length(files(iSubj).chanlocs) == 1
files(iSubj).chanlocs(1:length(files(iSubj).file)) = files(iSubj).chanlocs(1);
else
error('Length of channel list must be the same size as the number of file for each participant');
end
end
end
% run and sessions and tasks
if ~isfield(files(iSubj), 'run') || isempty(files(iSubj).run)
files(iSubj).run = ones(1, length(files(iSubj).file));
end
if ~isfield(files(iSubj), 'session') || isempty(files(iSubj).session)
files(iSubj).session = ones(1, length(files(iSubj).file));
end
if ~isfield(files(iSubj), 'task') || isempty(files(iSubj).task)
[files(iSubj).task{1:length(files(iSubj).file)}] = deal(opt.taskName);
end
% notes
if ~isfield(files(iSubj), 'notes') || isempty(files(iSubj).notes)
files(iSubj).notes = cell(1,length(files(iSubj).file));
else
if ischar(files(iSubj).notes)
files(iSubj).notes = { files(iSubj).notes };
end
if length(files(iSubj).notes) == 1
tmpNote = files(iSubj).notes{1};
files(iSubj).notes = cell(1,length(files(iSubj).file));
files(iSubj).notes(:) = { tmpNote };
end
if length(files(iSubj).notes) < length(files(iSubj).file)
files(iSubj).notes{length(files(iSubj).file)} = [];
end
end
% check that no two files have the same session/run and task
if length(files(iSubj).run) ~= length(files(iSubj).session)
error(sprintf('Length of session and run differ for subject %s', iSubj));
else
if ~isfield(files(iSubj), 'task')
uniq = files(iSubj).run*1000 + files(iSubj).session;
if length(uniq) ~= length(unique(uniq))
error(sprintf('Subject %s does not have unique session and runs for each file', iSubj));
end
else
for iVal = 1:length(files(iSubj).task)
strs = strcat(files(iSubj).task, strsplit(num2str(files(iSubj).run)), strsplit(num2str(files(iSubj).session)));
end
if length(strs) ~= length(unique(strs))
error(sprintf('Subject %s does not have unique task, session and runs for each file', iSubj));
end
end
end
end
% write participant information (participants.tsv)
% -----------------------------------------------
if ~isempty(opt.pInfo)
if isfield(files, 'subject')
uniqueSubject = unique( { files.subject } );
if size(opt.pInfo,1)-1 ~= length( uniqueSubject )
error(sprintf('Wrong number of participant (%d) in pInfo structure, should be %d based on the number of files', size(opt.pInfo,1)-1, length( uniqueSubject )));
end
elseif ~isstruct(files(1).file)
if size(opt.pInfo,1)-1 ~= length( files )
error(sprintf('Wrong number of participant (%d) in pInfo structure, should be %d based on the number of files', size(opt.pInfo,1)-1, length( files )));
end
end
participants = { 'participant_id' };
for iSubj=2:size(opt.pInfo)
if strcmp('participant_id', opt.pInfo{1,1})
if length(opt.pInfo{iSubj,1}) > 3 && isequal('sub-', opt.pInfo{iSubj,1}(1:4))
participants{iSubj, 1} = opt.pInfo{iSubj,1};
elseif strcmpi(opt.createids, 'off')
participants{iSubj, 1} = sprintf('sub-%s', opt.pInfo{iSubj,1});
else
participants{iSubj, 1} = sprintf('sub-%3.3d', iSubj-1);
end
else
participants{iSubj, 1} = sprintf('sub-%3.3d', iSubj-1);
end
end
if strcmp('participant_id', opt.pInfo{1,1})
opt.pInfo = opt.pInfo(:,2:end);
end
participants(:,2:2+size(opt.pInfo,2)-1) = opt.pInfo;
writetsv(fullfile(opt.targetdir, 'participants.tsv'), participants);
end
% write participants field description (participants.json)
% --------------------------------------------------------
descFields = { 'LongName' 'optional' 'char' '';
'Levels' 'optional' 'struct' struct([]);
'Description' 'optional' 'char' '';
'Units' 'optional' 'char' '';
'TermURL' 'optional' 'char' '' };
if ~isempty(opt.pInfo)
fields = fieldnames(opt.pInfoDesc);
if ~isempty(setdiff(fields, participants(1,:)))
error('Some field names in the pInfoDec structure do not have a corresponding column name in pInfo');
end
fields = participants(1,:);
for iField = 1:length(fields)
descFields{1,4} = fields{iField};
if ~isfield(opt.pInfoDesc, fields{iField}), opt.pInfoDesc(1).(fields{iField}) = struct([]); end
opt.pInfoDesc.(fields{iField}) = checkfields(opt.pInfoDesc.(fields{iField}), descFields, 'pInfoDesc');
end
jsonwrite(fullfile(opt.targetdir, 'participants.json'), opt.pInfoDesc,struct('indent',' '));
end
% prepare event file information (_events.json)
% ----------------------------
eInfoDescFields = { 'LongName' 'optional' 'char' '';
'Levels' 'optional' 'struct' struct([]);
'Description' 'optional' 'char' '';
'Units' 'optional' 'char' '';
'TermURL' 'optional' 'char' '';
'HED' 'optional' 'struct' struct([])};
fields = fieldnames(opt.eInfoDesc);
for iField = 1:length(fields)
descFields{1,4} = fields{iField};
if ~isfield(opt.eInfoDesc, fields{iField}), opt.eInfoDesc(1).(fields{iField}) = struct([]); end
opt.eInfoDesc.(fields{iField}) = checkfields(opt.eInfoDesc.(fields{iField}), eInfoDescFields, 'eInfoDesc');
end
if strcmpi(opt.individualEventsJson, 'off')
jsonwrite(fullfile(opt.targetdir, ['task-' opt.taskName '_events.json' ]), opt.eInfoDesc,struct('indent',' '));
end
% Write README files (README)
% ---------------------------
if ~isempty(opt.README)
if exist(opt.README) ~= 2
fid = fopen(fullfile(opt.targetdir, 'README'), 'w');
if fid == -1, error('Cannot write README file'); end
fprintf(fid, '%s', opt.README);
fclose(fid);
else
copyfile(opt.README, fullfile(opt.targetdir, 'README'));
end
end
% Write CHANGES files (CHANGES)
% -----------------------------
if ~isempty(opt.CHANGES)
if ~exist(opt.CHANGES)
fid = fopen(fullfile(opt.targetdir, 'CHANGES'), 'w');
if fid == -1, error('Cannot write README file'); end
fprintf(fid, '%s', opt.CHANGES);
fclose(fid);
else
copyfile(opt.CHANGES, fullfile(opt.targetdir, 'CHANGES'));
end
end
% Write code files (code)
% -----------------------
if ~isempty(opt.codefiles)
for iFile = 1:length(opt.codefiles)
[~,fileName,Ext] = fileparts(opt.codefiles{iFile});
if ~isempty(dir(opt.codefiles{iFile}))
copyfile(opt.codefiles{iFile}, fullfile(opt.targetdir, 'code', [ fileName Ext ]));
else
fprintf('Warning: cannot find code file %s\n', opt.codefiles{iFile})
end
end
end
% Write stimulus files
% --------------------
if ~isempty(opt.stimuli)
disp('Copying stimuli...');
for iStim = 1:size(opt.stimuli,1)
[~,fileName,Ext] = fileparts(opt.stimuli{iStim,2});
if ~isempty(dir(opt.stimuli{iStim,2}))
copyfile(opt.stimuli{iStim,2}, fullfile(opt.targetdir, 'stimuli', [ fileName Ext ]));
else
fprintf('Warning: cannot find stimulus file %s\n', opt.stimuli{iStim,2});
end
opt.stimuli{iStim,2} = [ fileName,Ext ];
end
end
% check task info
% ---------------
if length(unique([files(:).task])) == 1
opt.tInfo(1).TaskName = files(1).task{1};
else
opt.tInfo(1).TaskName = 'mixed';
end
% load channel information
% ------------------------
chanlocs = {};
if ~isempty(opt.chanlocs) && isstr(opt.chanlocs)
opt.chanlocs = readlocs(opt.chanlocs);
end
if ~isfield(files(1), 'chanlocs')
for iSubj = 1:length(files)
for iFile = 1:length(files(iSubj).file)
files(iSubj).chanlocs{iFile} = opt.chanlocs;
end
end
end
% Heuristic for identifying multiple/single-run/sessions
%--------------------------------------------------------------------------
for iSubj = 1:length(files)
allsubjnruns(iSubj) = length(unique(files(iSubj).run));
allsubjnsessions(iSubj) = length(unique(files(iSubj).session));
allsubjntasks(iSubj) = length(unique(files(iSubj).task));
end
multsessionflag = 1;
if all(allsubjnsessions == 1)
multsessionflag = 0;
end
multrunflag = 1;
if all(allsubjnruns == 1)
multrunflag = 0;
end
tmpsessrun = [multsessionflag multrunflag];
if all(tmpsessrun == [0 0]) % Single-Session Single-Run
bidscase = 1;
elseif all(tmpsessrun == [0 1]) % Single-Session Mult-Run
bidscase = 2;
elseif all(tmpsessrun == [1 0]) % Mult-Session Single-Run
bidscase = 3;
elseif all(tmpsessrun == [1 1]) % Mult-Session Mult-Run
bidscase = 4;
end
if ~all(allsubjntasks == 1)
if bidscase == 1
bidscase = 5; % Mult Task: Single-Session Single-Run
end
if bidscase == 3
bidscase = 6; % Mult Task: Mult-Session Single-Run
end
end
%--------------------------------------------------------------------------
% copy EEG files
% --------------
disp('Copying EEG files...')
for iSubj = 1:length(files)
if ~isempty(opt.pInfo)
subjectStr = participants{iSubj+1,1}; % first row of participants contains header
else
subjectStr = sprintf('sub-%3.3d', iSubj);
end
% copy anatomical file if any
if isfield(files(iSubj), 'anat') && ~isempty(files(iSubj).anat)
mkdir(fullfile(opt.targetdir, subjectStr, 'anat'));
% Currently supporting Single-Session Single-Run of MRI anat only.
% If interested in other combinations of run/sessions please contact the authors.
fileOut = fullfile(opt.targetdir, subjectStr, 'anat', [ subjectStr '_mod-' opt.anattype ]);
if strcmpi(opt.defaced, 'on')
fileOut = [ fileOut '_defacemask' ];
end
if files(iSubj).anat(end) == 'z'
fileOut = [ fileOut '.nii.gz' ];
else
fileOut = [ fileOut '.nii' ];
end
copyfile(files(iSubj).anat, fileOut);
end
switch bidscase
case 1 % Single-Session Single-Run
[~,~,fileExt] = fileparts(files(iSubj).file{1});
fileOut = fullfile(opt.targetdir, subjectStr, 'eeg', [ subjectStr '_task-' char(files(iSubj).task) '_eeg' fileExt]);
% copy_data_bids( files(iSubj).file{1}, fileOut, opt.eInfo, opt.tInfo, opt.trialtype, chanlocs{iSubj}, opt.copydata);
copy_data_bids( files(iSubj).file{1}, fileOut, files(iSubj).notes{1}, opt, files(iSubj).chanlocs{1}, opt.copydata, opt.exportext);
case 2 % Single-Session Mult-Run
for iRun = 1:length(files(iSubj).run)
[~,~,fileExt] = fileparts(files(iSubj).file{iRun});
fileOut = fullfile(opt.targetdir, subjectStr, 'eeg', [ subjectStr '_task-' char(files(iSubj).task(iRun)) '_run-' num2str(files(iSubj).run(iRun)) '_eeg' fileExt ]);
copy_data_bids( files(iSubj).file{iRun}, fileOut, files(iSubj).notes{iRun}, opt, files(iSubj).chanlocs{iRun}, opt.copydata, opt.exportext);
end
case 3 % Mult-Session Single-Run
for iSess = 1:length(unique(files(iSubj).session))
[~,~,fileExt] = fileparts(files(iSubj).file{iSess});
fileOut = fullfile(opt.targetdir, subjectStr, sprintf('ses-%2.2d', iSess), 'eeg', [ subjectStr sprintf('_ses-%2.2d', iSess) '_task-' char(files(iSubj).task{iSess}) '_eeg' fileExt]);
copy_data_bids( files(iSubj).file{iSess}, fileOut, files(iSubj).notes{iSess}, opt, files(iSubj).chanlocs{iSess}, opt.copydata, opt.exportext);
end
case 4 % Mult-Session Mult-Run
for iSess = 1:length(unique(files(iSubj).session))
runindx = find(files(iSubj).session == iSess);
for iSet = runindx
iRun = files(iSubj).run(iSet);
[~,~,fileExt] = fileparts(files(iSubj).file{iSet});
fileOut = fullfile(opt.targetdir, subjectStr, sprintf('ses-%2.2d', iSess), 'eeg', [ subjectStr sprintf('_ses-%2.2d', iSess) '_task-' char(files(iSubj).task(iRun)) '_run-' num2str(files(iSubj).run(iRun)) '_eeg' fileExt]);
copy_data_bids(files(iSubj).file{iSet}, fileOut, files(iSubj).notes{iSet}, opt, files(iSubj).chanlocs{iSet}, opt.copydata, opt.exportext);
end
end
case 5 % Mult Task: Single-Session Single-Run
for iTask = 1:length(files(iSubj).task)
[~,~,fileExt] = fileparts(files(iSubj).file{iTask});
fileOut = fullfile(opt.targetdir, subjectStr, 'eeg', [ subjectStr '_task-' char(files(iSubj).task(iTask)) '_eeg' fileExt ]);
copy_data_bids( files(iSubj).file{iTask}, fileOut, files(iSubj).notes{iTask}, opt, files(iSubj).chanlocs{iTask}, opt.copydata, opt.exportext);
end
case 6 % Mult Task: Mult-Session Single-Run
for iSess = 1:length(unique(files(iSubj).session))
runindx = find(files(iSubj).session == iSess);
for iSet = runindx
[~,~,fileExt] = fileparts(files(iSubj).file{iSet});
fileOut = fullfile(opt.targetdir, subjectStr, sprintf('ses-%2.2d', iSess), 'eeg', [ subjectStr sprintf('_ses-%2.2d', iSess) '_task-' char(files(iSubj).task(iSet)) '_eeg' fileExt]);
copy_data_bids(files(iSubj).file{iSet}, fileOut, files(iSubj).notes{iSet}, opt, files(iSubj).chanlocs{iSet}, opt.copydata, opt.exportext);
end
end
end
end
%--------------------------------------------------------------------------
%--------------------------------------------------------------------------
%function copy_data_bids(fileIn, fileOut, eInfo, tInfo, trialtype, chanlocs, copydata)
function copy_data_bids(fileIn, fileOut, notes, opt, chanlocs, copydata, exportExt)
folderOut = fileparts(fileOut);
if ~exist(folderOut)
mkdir(folderOut);
end
if ~exist(fileOut)
end
% if BDF file anonymize records
tInfo = opt.tInfo;
[~,~,ext] = fileparts(fileOut);
if strcmpi(ext, '.bdf')
fileIDIn = fopen(fileIn,'rb','ieee-le'); % see sopen
fileIDOut = fopen(fileOut,'wb','ieee-le'); % see sopen
data = fread(fileIDIn, Inf);
data(9:9+160-1) = ' '; % remove potential identity
fwrite(fileIDOut, data);
fclose(fileIDIn);
fclose(fileIDOut);
tInfo.EEGReference = 'CMS/DRL';
tInfo.Manufacturer = 'BIOSEMI';
EEG = pop_biosig(fileOut);
elseif strcmpi(ext, '.vhdr')
rename_brainvision_files(fileIn, fileOut, 'rmf', 'off');
[fpathin, fname, ext] = fileparts(fileIn);
EEG = pop_loadbv(fpathin, [fname ext]);
elseif strcmpi(ext, '.set')
[outfilepath, outfilename,outfileext] = fileparts(fileOut);
if copydata
EEGin = pop_loadset(fileIn);
if strcmp(exportExt,'edf')
pop_writeeeg(EEG, [outfilepath filesep outfilename '.edf'], 'TYPE','EDF');
else
EEG = pop_saveset(EEGin, 'filename',[outfilename outfileext], 'filepath', outfilepath);
end
else
copyfile(fileIn, fileOut);
EEG = pop_loadset([outfilename outfileext],outfilepath, 'loadmode', 'info');
end
elseif strcmpi(ext, '.cnt')
EEG = pop_loadcnt(fileIn, 'dataformat', 'auto');
datFile = [fileIn(1:end-4) '.dat'];
if exist(datFile,'file')
EEG = pop_importevent(EEG, 'indices',1:length(EEG.event), 'append','no', 'event', datFile,...
'fields',{'DatTrial','DatResp','DatType','DatCorrect','DatLatency'},'skipline',20,'timeunit',NaN,'align',0);
end
pop_saveset(EEG, 'filename', fileOut);
elseif strcmpi(ext, '.mff')
EEG = pop_mffimport(fileIn,{'code'});
pop_saveset(EEG, 'filename', fileOut);
elseif strcmpi(ext, '.raw')
EEG = pop_readegi(fileIn);
pop_saveset(EEG, 'filename', fileOut);
elseif strcmpi(ext, '.eeg')
[tmpPath,tmpFileName,~] = fileparts(fileIn);
if exist(fullfile(tmpPath, [tmpFileName '.vhdr']), 'file')
EEG = pop_loadbv( tmpPath, [tmpFileName '.vhdr'] );
pop_saveset(EEG, 'filename', fileOut);
else
error('.eeg files not from BrainVision are currently not supported')
end
else
error('Data format not supported');
end
% Getting events latency
insertEpoch = false;
if EEG.trials > 1
% get TLE events
insertEpoch = true;
eventlat = abs(eeg_point2lat( [ EEG.event.latency ], [ EEG.event.epoch ], EEG.srate, [EEG.xmin EEG.xmax]));
indtle = find(eventlat == 0);
if length(indtle) < EEG.trials
indtle = find(eventlat < 0.02);
end
if length(indtle) ~= EEG.trials
insertEpoch = false;
end
end
% write event file information
% --- _events.json
[folderOut,fileOut,~] = fileparts(fileOut);
fileOut = fullfile(folderOut,fileOut);
if ~isempty(EEG.event)
if strcmpi(opt.individualEventsJson,'on')
jsonwrite([ fileOut(1:end-3) 'events.json' ], opt.eInfoDesc,struct('indent',' '));
end
% --- _events.tsv
fid = fopen( [ fileOut(1:end-3) 'events.tsv' ], 'w');
% -- parse eInfo
if isempty(opt.eInfo)
if isfield(EEG.event, 'onset') opt.eInfo(end+1,:) = { 'onset' 'onset' };
else opt.eInfo(end+1,:) = { 'onset' 'latency' }; end
opt.eInfo(end+1,:) = { 'sample' 'latency' };
if isfield(EEG.event, 'trial_type') opt.eInfo(end+1,:) = { 'trial_type' 'trial_type' };
elseif ~isempty(opt.trialtype) opt.eInfo(end+1,:) = { 'trial_type' 'xxxx' }; end % to be filled with event type based on opt.trialtype mapping
if isfield(EEG.event, 'duration') opt.eInfo(end+1,:) = { 'duration' 'duration' }; end
if isfield(EEG.event, 'value') opt.eInfo(end+1,:) = { 'value' 'value' };
else opt.eInfo(end+1,:) = { 'value' 'type' }; end
if isfield(EEG.event, 'response_time'), opt.eInfo(end+1,:) = { 'response_time' 'response_time' }; end
if isfield(EEG.event, 'stim_file'), opt.eInfo(end+1,:) = { 'stim_file' 'stim_file' }; end
if isfield(EEG.event, 'HED'), opt.eInfo(end+1,:) = { 'HED' 'HED' }; end
else
bids_fields = opt.eInfo(:,1);
if ~any(strcmp(bids_fields,'onset'))
if isfield(EEG.event, 'onset')
opt.eInfo(end+1,:) = { 'onset' 'onset' };
else
opt.eInfo(end+1,:) = { 'onset' 'latency' };
end
end
if ~any(strcmp(bids_fields,'sample')) && isfield(EEG.event, 'latency'), opt.eInfo(end+1,:) = { 'sample' 'latency' }; end
if ~any(strcmp(bids_fields,'value'))
if isfield(EEG.event, 'value')
opt.eInfo(end+1,:) = { 'value' 'value' };
else
opt.eInfo(end+1,:) = { 'value' 'type' };
end
end
if ~any(strcmp(bids_fields,'duration')) && isfield(EEG.event, 'duration'), opt.eInfo(end+1,:) = { 'duration' 'duration' }; end
if ~isempty(opt.trialtype), opt.eInfo(end+1,:) = { 'trial_type' 'xxxx' }; end
end
if ~isempty(opt.stimuli)
opt.eInfo(end+1,:) = { 'stim_file' '' };
end
% reorder fields so it matches BIDS
fieldOrder = { 'onset' 'duration' 'sample' 'trial_type' 'response_time' 'stim_file' 'value'}; % 'HED' }; % remove HED from default column in events.tsv as HED tags should be put in events.json instead
newOrder = [];
for iField = 1:length(fieldOrder)
ind = strmatch(fieldOrder{iField}, opt.eInfo(:,1)', 'exact');
if isempty(ind) % add unfound field to opt.eInfo, skipping HED
if ~strcmpi(fieldOrder{iField}, 'HED') % skip HED (create problem with validator)
opt.eInfo(end+1,1:2) = { fieldOrder{iField} 'n/a' }; % indicating that there's no column in eInfo matching fieldOrder{iField}
ind = size(opt.eInfo,1);
else
ind = [];
end
end
newOrder = [ newOrder ind ];
end
remainingInd = setdiff([1:size(opt.eInfo,1)], newOrder);
newOrder = [ newOrder remainingInd];
opt.eInfo = opt.eInfo(newOrder,:);
fprintf(fid,'onset%s\n', sprintf('\t%s', opt.eInfo{2:end,1}));
% scan events
for iEvent = 1:length(EEG.event)
str = {};
for iField = 1:size(opt.eInfo,1)
tmpField = opt.eInfo{iField,2};
if strcmpi(tmpField, 'n/a')
str{end+1} = tmpField;
else
switch opt.eInfo{iField,1}
case 'onset'
onset = (EEG.event(iEvent).(tmpField)-1)/EEG.srate;
str{end+1} = sprintf('%1.10f', onset);
case 'duration'
if isfield(EEG.event, tmpField) && ~isempty(EEG.event(iEvent).(tmpField))
duration = num2str(EEG.event(iEvent).(tmpField), '%1.10f');
else
duration = 'n/a';
end
if isempty(duration) || strcmpi(duration, 'NaN')
duration = 'n/a';
end
str{end+1} = duration;
case 'sample'
if isfield(EEG.event, tmpField)
sample = num2str(EEG.event(iEvent).(tmpField)-1);
else
sample = 'n/a';
end
if isempty(sample) || strcmpi(sample, 'NaN')
sample = 'n/a';
end
str{end+1} = sample;
case 'trial_type'
% trial type (which is the experimental condition - not the same as EEGLAB)
if isfield(EEG.event(iEvent), tmpField) && ~isempty(EEG.event(iEvent).(tmpField))
trialType = EEG.event(iEvent).(tmpField);
else
trialType = 'STATUS';
eventVal = EEG.event(iEvent).type;
if ~isempty(opt.trialtype)
% mapping on event value
if ~isempty(eventVal)
indTrial = strmatch(num2str(eventVal), opt.trialtype(:,1), 'exact');
if ~isempty(indTrial)
trialType = opt.trialtype{indTrial,2};
end
end
end
if insertEpoch
if any(indtle == iEvent)
trialType = 'Epoch';
end
end
end
if isnumeric(trialType)
trialType = num2str(trialType);
end
str{end+1} = trialType;
case 'response_time'
if isfield(EEG.event, tmpField)
response_time = num2str(EEG.event(iEvent).(tmpField));
else
response_time = 'n/a';
end
if isempty(response_time) || strcmpi(response_time, 'NaN')
response_time = 'n/a';
end
str{end+1} = response_time;
case 'stim_file'
if isempty(tmpField)
indStim = strmatch(EEG.event(iEvent).type, opt.stimuli(:,1));
if ~isempty(indStim)
stim_file = opt.stimuli{indStim, 2};
else
stim_file = 'n/a';
end
elseif isfield(EEG.event, tmpField)
if ~isempty(opt.stimuli)
error('Cannot use "stim_file" as a BIDS event field and use the "stimuli" option')
end
stim_file = num2str(EEG.event(iEvent).(tmpField));
else
stim_file = 'n/a';
end
if isempty(stim_file) || strcmpi(stim_file, 'NaN')
stim_file = 'n/a';
end
str{end+1} = stim_file;
case 'value'
if isfield(EEG.event, tmpField) && ~isempty(EEG.event(iEvent).(tmpField))
if isempty(opt.renametype)
eventValue = num2str(EEG.event(iEvent).(tmpField));
else
posType = strmatch(num2str(EEG.event(iEvent).(tmpField)), opt.renametype(:,1), 'exact');
if ~isempty(posType)
eventValue = opt.renametype{posType,2};
else
eventValue = num2str(EEG.event(iEvent).(tmpField));
end
end
if ~isempty(opt.checkresponse)
if iEvent+1 <= length(EEG.event) && strcmpi(EEG.event(iEvent+1).type, opt.checkresponse) && ~strcmpi(EEG.event(iEvent).type, opt.checkresponse)
eventValue = [ eventValue '_with_reponse' ];
response_time = (EEG.event(iEvent+1).latency - EEG.event(iEvent).latency)/EEG.srate;
str{end-1} = num2str(response_time*1000,'%1.0f');
end
end
else
eventValue = 'n/a';
end
if isequal(eventValue, 'NaN') || isempty(eventValue)
eventValue = 'n/a';
end
str{end+1} = eventValue;
% case 'HED'
% hed = 'n/a';
% if isfield(EEG.event, tmpField) && ~isempty(EEG.event(iEvent).(tmpField))
% hed = EEG.event(iEvent).(tmpField);
% else
% if isfield(EEG.event, 'HED') && ~isempty(EEG.event(iEvent).usertags)
% hed = EEG.event(iEvent).usertags;
% if isfield(EEG.event, 'hedtags') && ~isempty(EEG.event(iEvent).hedtags)
% hed = [hed ',' EEG.event(iEvent).hedtags];
% end
% elseif isfield(EEG.event, 'hedtags') && ~isempty(EEG.event(iEvent).hedtags)
% hed = EEG.event(iEvent).hedtags;
% end
% end
% str{end+1} = hed;
otherwise
if isfield(EEG.event, opt.eInfo{iField,2})
tmpVal = num2str(EEG.event(iEvent).(opt.eInfo{iField,2}));
if isequal(tmpVal, 'NaN')
tmpVal = 'n/a';
end
else
tmpVal = 'n/a';
end
str{end+1} = tmpVal;
end % switch
end
end
strConcat = sprintf('%s\t', str{:});
fprintf(fid, '%s\n', strConcat(1:end-1));
end
fclose(fid);
end
% Write channel file information (channels.tsv)
% Note: Consider using here electrodes_to_tsv.m
fid = fopen( [ fileOut(1:end-3) 'channels.tsv' ], 'w');
miscChannels = 0;
if ~isempty(chanlocs)
EEG.chanlocs = chanlocs;
if ischar(EEG.chanlocs)
EEG.chanlocs = readlocs(EEG.chanlocs);