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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.
% The optional 'eventtype', 'eventindex' 'timeoffset' allow
% selecting portions of files. For example 'timeoffset' of
% [0 1800] selects the first 30 minutes of a file. Default
% 'timeoffset' is 0. Add 'eventype' equals to { 'beg' 'end' }
% and 'eventindex' of [1 1] and the portion of data between the
% first 'beg' event and 1800 seconds after the first 'end' event
% is selected. If 'eventtype' is not specified, then events of
% all types are considered.
%
% 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).eventtype = { {'beg' 'end'} {'beg' 'end'} {'beg' 'end'} {'beg' 'end'} };
% subject(1).eventindex = { [1 1] [1 1] [1 1] [1 1] };
% subject(1).timeoffset = { [0 1000] [0 1000] [0 1000] [0 1000] };
% subject(1).session = [ 1 1 2 2 ];
% subject(1).run = [ 1 2 1 2 ];
% subject(1).task = { 'go-nogo' 'control' 'go-nogo' 'control' };
% 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).eventtype = { {'beg' 'end'} {'beg' 'end'} {'beg' 'end'} {'beg' 'end'} };
% subject(2).eventrange = { [1 1] [1 1] [1 1] [1 1] };
% subject(2).timerange = { [0 1000] [0 1000] [0 1000] [0 1000] };
% subject(2).session = [ 1 1 2 2 ];
% subject(2).run = [ 1 2 1 2 ];
% subject(2).task = { 'go-nogo' 'control' 'go-nogo' 'control' };
% 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-nogo';
% 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';
% 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';
% info.GeneratedBy.Name = {'bids-matlab-tools'};
% info.SourceDatasets.DOI = 'xxx';
%
% '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.
%
% 'tInfoeye' - [struct] task information fields for eye tracking. See BIDS specifications.
% For example.
%
% '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' }
%
% 'elecexport' - ['on'|'off'|'auto'] export electrode file. Default is
% 'auto'.
%
% 'eventexport' - ['on'|'off'|'auto'] export event file. Default is 'auto'.
%
% 'eventfieldignore' - ['on'|'off'] ignore event field defined in eInfo if
% it not present in the dataset. Setting to 'off' fills a
% column with 'n/a' for that field. Default is 'on'.
%
% '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'.
%
% 'noevents' - ['on'|'off'] do not save event files. Default is 'off'.
%
% 'forcesession' - ['on'|'off'] force to export sessions even if there is
% only one. Default is 'off'.
%
% 'forcerun' - ['on'|'off'] force to export runs even if there is
% only one. Default is 'off'.
%
% 'rmtempfiles' - ['on'|'off'] remove temporary EEGLAB set files created by
% pop_studywizard. Default 'on'.
%
% '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.
%
% 'importfunc' - [function handle or string] function to import raw data to
% EEG format. Default: auto.
%
% 'exportformat' - ['same'|'eeglab'|'edf'|'bdf'] export files in the 'same' format
% as given as input or export in 'eeglab' .set, 'edf', or 'bdf' format.
% Default is 'eeglab'. If you use 'eventtype', 'eventindex' or 'timeoffset'
% and the export format is set to 'same', files will be automatically
% exported in the 'eeglab' format.
%
% 'modality' - ['eeg'|'ieeg'|'meg'|'auto'] type of data. 'auto' means the
% format is determined from the file extension. Default is
% 'auto'.
%
% 'ctffunc' - ['fileio'|'ctfimport'] function to use to import CTF data
% Default 'fileio'.
%
% 'deleteExportDir' - ['on'|'off'] remove the target BIDS directory if previously
% present. This should be almost always 'on'. The
% exception is having multi-task sessions in which each
% task has specific eInfo and/or tInfo inputs. Default is 'on'.
%
% 'writePInfoOnly' - ['on'|'off'] bids_export ends after exporting
% participants.tsv file. This should be almost always
% 'off'. Use case is when 'deleteExportDir' is 'off',
% the participants.tsv will be potentially incomplete,
% as it was overwritten. The solution is to regenerate
% the file, but without touching the other contents of
% the directory. Default is 'off'.
% 'GeneratedBy' - [struct] structure indicating how the data was generated. same as gInfo.GeneratedBy.
% For example:
% GeneratedBy.Name = 'NEMAR-pipeline';
% GeneratedBy.Description = 'A validated EEG pipeline';
% GeneratedBy.Version = '0.1';
% GeneratedBy.CodeURL = 'https://github.com/sccn/NEMAR-pipeline/blob/main/eeg_nemar_preprocess.m';
% descriptionTag = 'filtered'; % optional description for the desc- entity
%
% 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 eeglab@sccn.ucsd.edu
%
% 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, 2019-2020
% Dung Truong 2021
% 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' {} '';
'codefiles' 'cell' {} {};
'stimuli' 'cell' {} {};
'pInfo' 'cell' {} {};
'eInfo' 'cell' {} {};
'cInfo' 'cell' {} {};
'gInfo' 'struct' {} struct([]);
'tInfo' 'struct' {} struct([]);
'tInfoeye' 'struct' {} struct([]);
'pInfoDesc' 'struct' {} struct([]);
'eInfoDesc' 'struct' {} struct([]);
'cInfoDesc' 'struct' {} struct([]);
'behInfo' 'struct' {} struct([]);
'generatedBy' 'struct' {} struct([]);
'GeneratedBy' 'struct' {} struct([]);
'sourceDatasets' 'struct' {} struct([]);
'SourceDatasets' 'struct' {} struct([]);
'trialtype' 'cell' {} {};
'renametype' 'cell' {} {};
'checkresponse' 'string' {} '';
'anattype' '' {} 'T1w';
'chanlocs' '' {} '';
'chanlookup' 'string' {} '';
'elecexport' 'string' {'on' 'off' 'auto'} 'auto';
'eventexport' 'string' {'on' 'off' 'auto'} 'auto';
'eventfieldignore' 'string' {'on' 'off'} 'on';
'interactive' 'string' {'on' 'off'} 'off';
'defaced' 'string' {'on' 'off'} 'on';
'createids' 'string' {'on' 'off'} 'off';
'noevents' 'string' {'on' 'off'} 'off';
'forcesession' 'string' {'on' 'off'} 'off';
'forcerun' 'string' {'on' 'off'} 'off';
'rmtempfiles' 'string' {'on' 'off'} 'on';
'exportformat' 'string' {'same' 'eeglab' 'edf' 'bdf'} 'eeglab';
'individualEventsJson' 'string' {'on' 'off'} 'off';
'modality' 'string' {'ieeg' 'meg' 'eeg' 'auto'} 'auto';
'README' 'string' {} '';
'CHANGES' 'string' {} '' ;
'copydata' 'integer' {} [0 1]; % legacy, does nothing now
'ctffunc' 'string' { 'fileio' 'ctfimport' } 'fileio'; ...
'importfunc' '' {} '';
'deleteExportDir' 'string' {'on' 'off'} 'on' ;
'writePInfoOnly' 'string' {'on' 'off'} 'off' ;
'descriptionTag' 'string' {} ''}, 'bids_export');
if isstr(opt), error(opt); end
if ~isempty(opt.taskName)
fprintf(2, 'Task name input is deprecated and not used, use tInfo.TaskName instead\n');
opt.tInfo(1).TaskName = opt.taskName;
end
if size(opt.stimuli,1) == 1 || size(opt.stimuli,2) == 1
opt.stimuli = reshape(opt.stimuli, [2 length(opt.stimuli)/2])';
end
if ~isempty(opt.generatedBy)
opt.GeneratedBy = opt.generatedBy;
end
if ~isempty(opt.sourceDatasets)
opt.SourceDatasets = opt.sourceDatasets;
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
if strcmpi(opt.deleteExportDir, 'on')
disp('Folder exists. Deleting folder...')
rmdir(opt.targetdir, 's');
else
warning('Folder exists. You chose not to delete the folder. Results may not be satisfactory.')
end
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' '1.8.0' ;
'HEDVersion' 'required' 'char' '8.1.0' ;
'DatasetType' 'optional' 'char' { 'derivative' 'raw' };
'Authors' 'optional' 'cell' { 'n/a' };
'Acknowledgements' 'optional' 'char' '';
'HowToAcknowledge' 'optional' 'char' '';
'SourceDatasets' 'optional' 'struct' struct([]);
'Funding' 'optional' 'cell' { 'n/a' };
'GeneratedBy' 'required' 'struct' struct('Name', 'bids-matlab-tools', 'Version', bids_matlab_tools_ver);
'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
if ~isfield(opt.gInfo, 'GeneratedBy') && ~isempty(opt.GeneratedBy), opt.gInfo.GeneratedBy = opt.GeneratedBy; end
if ~isfield(opt.gInfo, 'SourceDatasets') && ~isempty(opt.SourceDatasets), opt.gInfo.SourceDatasets = opt.SourceDatasets; end
% write dataset_description.json removing double lists
opt.gInfo = bids_checkfields(opt.gInfo, gInfoFields, 'gInfo');
datasetDescriptionFile = fullfile(opt.targetdir, 'dataset_description.json');
gInfo = opt.gInfo;
if isfield(gInfo, 'GeneratedBy')
gInfo.GeneratedBy = { gInfo.GeneratedBy };
end
if isfield(gInfo, 'SourceDatasets')
gInfo.SourceDatasets = { gInfo.SourceDatasets };
end
try
jsonStr = jsonencode(gInfo,'PrettyPrint', true);
catch
jsonStr = jsonwrite(opt.gInfo, struct('indent',' '));
indDoubleList = strfind(jsonStr, '[['); jsonStr(indDoubleList) = [];
indDoubleList = strfind(jsonStr, '[ ['); jsonStr(indDoubleList) = [];
indDoubleList = strfind(jsonStr, ']]'); jsonStr(indDoubleList) = [];
end
fid = fopen(datasetDescriptionFile, 'w');
fprintf(fid, jsonStr);
fclose(fid);
% make cell out of file names if necessary
% ----------------------------------------
for iSubj = 1:length(files)
if ~isfield(files, 'file')
if isfield(files, 'eyefile')
files(iSubj).file = cell(1,length(files(iSubj).eyefile));
files(iSubj).file(:) = {''};
else
error('A field named "file" or "eyefile" must be present in the data structure')
end
end
if isfield(files, 'file') && ~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
% behavioral data
if isfield(files(iSubj), 'beh')
if ~iscell(files(iSubj).beh)
files(iSubj).beh = { files(iSubj).beh };
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)
if isfield(opt.tInfo, 'TaskName')
[files(iSubj).task{1:length(files(iSubj).file)}] = deal(opt.tInfo.TaskName);
else
error('''TaskName'' is a required field for tInfo input; alternatively you can assign a task to each input dataset');
end
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
% event and time range extraction
if ~isfield(files(iSubj), 'timeoffset') || isempty(files(iSubj).timeoffset)
files(iSubj).timeoffset = cell(1,length(files(iSubj).file));
end
if ~isfield(files(iSubj), 'eventtype') || isempty(files(iSubj).eventtype)
files(iSubj).eventtype = cell(1,length(files(iSubj).file));
end
if ~isfield(files(iSubj), 'eventindex') || isempty(files(iSubj).eventindex)
files(iSubj).eventindex = cell(1,length(files(iSubj).file));
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 length(files(iSubj).task) ~= length(files(iSubj).session)
error(sprintf('Length of session and task differ for subject %s', iSubj));
end
if length(files(iSubj).notes) ~= length(files(iSubj).session)
error(sprintf('Length of session and notes differ for subject %s', iSubj));
end
% convert all runs and session to cell array of string
if ~iscell(files(iSubj).run) files(iSubj).run = mattocell(files(iSubj).run); end
if ~iscell(files(iSubj).session) files(iSubj).session = mattocell(files(iSubj).session); end
strs = {};
for iVal = 1:length(files(iSubj).task)
files(iSubj).run{ iVal} = num2str(files(iSubj).run{ iVal});
files(iSubj).session{iVal} = num2str(files(iSubj).session{iVal});
strs{iVal} = strcat(files(iSubj).task{iVal}, files(iSubj).run{iVal}, files(iSubj).session{iVal});
end
if length(strs) ~= length(unique(strs))
error(sprintf('Subject %d does not have unique task, session and runs for each file', iSubj));
end
end
end
% write participant information (participants.tsv)
% -----------------------------------------------
if isempty(opt.pInfo)
opt.pInfo{1} = 'participant_id';
if isfield(files, 'subject')
opt.pInfo = [opt.pInfo; { files.subject }' ];
else
for iFile = 1:length(files)
opt.pInfo{iFile+1,1} = sprintf('%3.3d', iFile);
end
end
end
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,1)
if strcmp('participant_id', opt.pInfo{1,1})
opt.pInfo{iSubj,1} = removeInvalidChar(opt.pInfo{iSubj,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 size(opt.pInfo,1) > 1
if strcmp('participant_id', opt.pInfo{1,1})
participants(:,2:size(opt.pInfo,2)) = opt.pInfo(:,2:end);
else
participants(:,2:size(opt.pInfo,2)+1) = opt.pInfo;
end
end
% remove empty columns
for iInfo = size(participants,2):-1:1
if all(cellfun(@isempty, participants(2:end,iInfo)))
if isfield(opt.pInfoDesc, participants{1,iInfo})
opt.pInfoDesc = rmfield(opt.pInfoDesc, participants{1,iInfo});
end
participants(:,iInfo) = [];
end
end
writetsv(fullfile(opt.targetdir, 'participants.tsv'), participants);
% 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}) = bids_checkfields(opt.pInfoDesc.(fields{iField}), descFields, 'pInfoDesc');
end
% remove empty fields for BIDS compliance
for iField = 1:length(fields)
if isempty(opt.pInfoDesc.(fields{iField}))
opt.pInfoDesc = rmfield(opt.pInfoDesc, fields{iField});
end
end
if ~isempty(fieldnames(opt.pInfoDesc))
jsonwrite(fullfile(opt.targetdir, 'participants.json'), opt.pInfoDesc, struct('indent',' '));
end
end
if strcmpi(opt.writePInfoOnly, 'on'), return; end % for a rare case that the particiapnts.tsv table needs to be re-created.
% 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}) = bids_checkfields(opt.eInfoDesc.(fields{iField}), eInfoDescFields, 'eInfoDesc');
end
% Write README files (README)
% ---------------------------
if isempty(opt.README)
opt.README = bids_template_README();
end
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
% set beh info (behavioral)
% ------------
if ~isfield(files(1), 'beh')
for iSubj = 1:length(files)
files(iSubj).beh = cell(1,length(files(iSubj).file));
end
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) && ~strcmpi(opt.forcesession, 'on')
multSessionFlag = 0;
end
multRunFlag = 1;
if all(allsubjnruns == 1) && ~strcmpi(opt.forcerun, 'on')
multRunFlag = 0;
end
hasTaskFlag = 0;
if all(allsubjntasks >= 1)
hasTaskFlag = 1;
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 bidscase == 5
% bidscase = 1; % Mult Task: Single-Session Single-Run
% end
% if bidscase == 6
% bidscase = 3; % Mult Task: Mult-Session Single-Run
% 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
for iItem = 1:length(files(iSubj).file) % scan files for subject
structOut = getElement(files(iSubj), iItem);
sessFolder = '';
fileStr = subjectStr;
if multSessionFlag
fileStr = [ fileStr '_ses-' files(iSubj).session{iItem} ];
sessFolder = [ 'ses-' files(iSubj).session{iItem} ];
end
if hasTaskFlag
fileStr = [ fileStr '_task-' char(files(iSubj).task(iItem)) ];
opt.tInfo(1).TaskName = char(files(iSubj).task(iItem)); % will be written below
end
if strcmpi(opt.individualEventsJson, 'off') % top level file overwriten every iteration but that's OK
jsonwrite(fullfile(opt.targetdir, ['task-' opt.tInfo.TaskName '_events.json' ]), opt.eInfoDesc, struct('indent',' '));
end
if multRunFlag
if ~strcmp(files(iSubj).run{iItem}, 'NaN')
fileStr = [ fileStr '_run-' files(iSubj).run{iItem} ];
end
end
fileOutBeh = fullfile(opt.targetdir, subjectStr, sessFolder, 'beh', [fileStr '_beh.tsv' ]);
copy_data_bids_eeg( structOut, subjectStr, sessFolder, fileStr, opt);
bids_writebehfile(files(iSubj).beh{iItem}, opt.behInfo, fileOutBeh);
end
end
%--------------------------------------------------------------------------
%--------------------------------------------------------------------------
function copy_data_bids_eeg(sIn, subjectStr, sess, fileStr, opt)
fileIn = sIn.file;
notes = sIn.notes;
chanlocs = sIn.chanlocs;
timeoffset = sIn.timeoffset;
eventtype = sIn.eventtype;
eventindex = sIn.eventindex;
if isempty(fileIn)
return
end
% force EEGLAB export if anything is done on the file
if ~isempty(eventtype) || ~isempty(eventindex) || ~isempty(timeoffset)
fprintf('File will be exported in EEGLAB formet because of segment selection\n')
opt.exportformat = 'eeglab';
end
% import data
tInfo = opt.tInfo;
[pathIn,fileInNoExt,ext] = fileparts(fileIn);
fprintf('Processing file %s\n', fileIn);
[EEG,opt.modality] = eeg_import(fileIn, 'modality', opt.modality, 'noevents', opt.noevents, 'importfunc', opt.importfunc);
if contains(fileIn, '_bids_tmp_') && strcmpi(opt.rmtempfiles, 'on')
fprintf('Deleting temporary file %s\n', fileIn);
delete(fileIn);
end
% Add description tag if any to the files
if isfield(opt, 'descriptionTag') && ~isempty(opt.descriptionTag)
fileStr = [fileStr '_desc-' opt.descriptionTag];
end
% output folder creation
fileBase = fullfile(opt.targetdir, subjectStr, sess, opt.modality, fileStr);
folderOut = fileparts(fileBase);
if ~exist(folderOut)
mkdir(folderOut);
end
fileOut = [fileBase '_' opt.modality ext];
% select data subset
EEG = eeg_selectsegment(EEG, 'eventtype', eventtype, 'eventindex', eventindex, 'timeoffset', timeoffset );
if ~isequal(opt.exportformat, 'same') || isequal(ext, '.set')
% export data if necessary
[filePathTmp,fileOutNoExt,~] = fileparts(fileOut);
if isequal(opt.exportformat, 'eeglab')
pop_saveset(EEG, 'filename', [ fileOutNoExt '.set' ], 'filepath', filePathTmp);
else
pop_writeeeg(EEG, fullfile(filePathTmp, [ fileOutNoExt '.' opt.exportformat]), 'TYPE',upper(opt.exportformat));
end
else
% copy the file
if ~strcmpi(ext, { '.bdf', '.edf', '.set', '.vhdr', '.ds', '.fiff', '.mefd', '.nwb', '.gz' })
error('''exportformat'' set to copy the file to the BIDS output folder but the file is not BIDS compliant')
else
if isequal(ext, '.bdf') || isequal(ext, '.edf')
% anonymize file
fprintf('EDF or BDF file detected, anonymizing the file...\n');
fileIDIn = fopen(fileIn,'rb','ieee-le'); % see sopen
fileIDOut = fopen(fileOut,'wb','ieee-le'); % see sopen
if fileIDIn == -1, error('Cannot read file %s', fileIn); end
if fileIDOut == -1, error('Cannot write file %s', fileOut); end
data = fread(fileIDIn, Inf);
data(9:9+160-1) = ' '; % remove potential identity
fwrite(fileIDOut, data);
fclose(fileIDIn);
fclose(fileIDOut);
if strcmpi(ext, '.bdf')
tInfo.EEGReference = 'CMS/DRL';
tInfo.Manufacturer = 'BIOSEMI';
end
elseif isequal(ext, '.vhdr') || isequal(ext, '.eeg')
rename_brainvision_files(fileIn, fileOut, 'rmf', 'off');
else
copyfile(fileIn, fileOut);
end
end
end
% export eye-tracking data
eyeWritenStatus = save_bids_eye_tracking(sIn, fileBase, EEG, opt);
% write events
indExt = find(fileOut == '_');
fileOutRed = fileOut(1:indExt(end)-1);
if ~strcmpi(opt.eventexport, 'off')
if strcmpi(opt.eventexport, 'on') || ~isempty(EEG.event)
bids_writeeventfile(EEG, fileOutRed, 'eInfo', opt.eInfo, 'eInfoDesc', opt.eInfoDesc, 'individualEventsJson', opt.individualEventsJson, ...
'ignoreemptyfields', opt.eventfieldignore, 'renametype', opt.renametype, 'stimuli', opt.stimuli, 'checkresponse', opt.checkresponse, 'omitsample', fastif(eyeWritenStatus, 'on', 'off'));
end
end
% Write channel file information (channels.tsv)
% Note: Consider using here electrodes_to_tsv.m
% fid = fopen( [ fileOutRed 'channels.tsv' ], 'w');
% miscChannels = 0;
if ~isempty(chanlocs)
EEG.chanlocs = chanlocs;
if ischar(EEG.chanlocs)
EEG.chanlocs = readlocs(EEG.chanlocs);
end
EEG = eeg_checkchanlocs(EEG);
if length(EEG.chanlocs) == EEG.nbchan+1
for iChan = 1:length(EEG.chanlocs)
EEG.chanlocs(iChan).ref = EEG.chanlocs(end).labels;
end
elseif length(EEG.chanlocs) ~= EEG.nbchan
error(sprintf('Number of channels in channel location inconsistent with data for file %s', fileIn));
end
end
if ischar(opt.chanlookup) && ~isempty(opt.chanlookup)
EEG=pop_chanedit(EEG, 'lookup', opt.chanlookup);
end
% Write electrode file information (electrodes.tsv and coordsystem.json)
bids_writechanfile(EEG, fileOutRed);
bids_writeelectrodefile(EEG, fileOutRed, 'export', opt.elecexport);
if strcmpi(opt.modality, 'eeg')
bids_writetinfofile(EEG, tInfo, notes, fileOutRed);
EEG.etc.datatype = 'eeg';
elseif strcmpi(opt.modality, 'ieeg')
bids_writeieegtinfofile(EEG, tInfo, notes, fileOutRed);
EEG.etc.datatype = 'ieeg';
elseif strcmpi(opt.modality, 'meg')
bids_writemegtinfofile(EEG, tInfo, notes, fileOutRed);
EEG.etc.datatype = 'meg';
end
% write channel information
% cInfo.name.LongName = 'Channel name';
% cInfo.name.Description = 'Channel name';
% cInfo.type.LongName = 'Channel type';
% cInfo.type.Description = 'Channel type';
% cInfo.units.LongName = 'Channel unit';
% cInfo.units.Description = 'Channel unit';
% jsonStr = jsonencode(cInfo);
% fid = fopen( [fileOut(1:end-3) 'channels.json' ], 'w');
% fprintf(fid, '%s', jsonStr);
% fclose(fid);
%--------------------------------------------------------------------------
%--------------------------------------------------------------------------
function eyeWritenStatus = save_bids_eye_tracking(sIn, fileBase, EEG, opt)
eyeWritenStatus = false;