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update example and add EDF export
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@arnodelorme
arnodelorme committed Oct 6, 2021
1 parent f71295f commit 2f4edc6
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Showing 2 changed files with 95 additions and 74 deletions.
25 changes: 15 additions & 10 deletions bids_export.m
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Original file line number Diff line number Diff line change
Expand Up @@ -265,6 +265,7 @@ function bids_export(files, varargin)
'chanlookup' 'string' {} '';
'defaced' 'string' {'on' 'off'} 'on';
'createids' 'string' {'on' 'off'} 'on';
'exportext' 'string' { 'edf' 'eeglab' } 'eeglab';
'README' 'string' {} '';
'CHANGES' 'string' {} '' ;
'copydata' 'real' [0 1] 1 }, 'bids_export');
Expand Down Expand Up @@ -601,22 +602,22 @@ function bids_export(files, varargin)
[~,~,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);
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);
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) '_eeg' ffileExt]);
copy_data_bids( files(iSubj).file{iSess}, fileOut, files(iSubj).notes{iSess}, opt, files(iSubj).chanlocs{iSess}, opt.copydata);
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
Expand All @@ -627,15 +628,15 @@ function bids_export(files, varargin)
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);
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);
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
Expand All @@ -644,7 +645,7 @@ function bids_export(files, varargin)
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);
copy_data_bids(files(iSubj).file{iSet}, fileOut, files(iSubj).notes{iSet}, opt, files(iSubj).chanlocs{iSet}, opt.copydata, opt.exportext);
end
end
end
Expand All @@ -653,7 +654,7 @@ function bids_export(files, varargin)
%--------------------------------------------------------------------------
%--------------------------------------------------------------------------
%function copy_data_bids(fileIn, fileOut, eInfo, tInfo, trialtype, chanlocs, copydata)
function copy_data_bids(fileIn, fileOut, notes, opt, chanlocs, copydata)
function copy_data_bids(fileIn, fileOut, notes, opt, chanlocs, copydata, exportExt)
folderOut = fileparts(fileOut);
if ~exist(folderOut)
mkdir(folderOut);
Expand Down Expand Up @@ -683,7 +684,11 @@ function copy_data_bids(fileIn, fileOut, notes, opt, chanlocs, copydata)
[outfilepath, outfilename,outfileext] = fileparts(fileOut);
if copydata
EEGin = pop_loadset(fileIn);
EEG = pop_saveset(EEGin, 'filename',[outfilename outfileext], 'filepath', outfilepath);
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');
Expand Down Expand Up @@ -1105,7 +1110,7 @@ function copy_data_bids(fileIn, fileOut, notes, opt, chanlocs, copydata)
'EEGGround' 'RECOMMENDED ' 'char' '';
'HeadCircumference' 'OPTIONAL ' '' 0;
'MiscChannelCount' ' OPTIONAL' '' '';
'TriggerChannelCount' 'RECOMMENDED' 'char' '';
'TriggerChannelCount' 'RECOMMENDED' 'char' ''; % double in Bucanl's fork
'EEGPlacementScheme' 'RECOMMENDED' 'char' '';
'Manufacturer' 'RECOMMENDED' 'char' '';
'ManufacturersModelName' 'OPTIONAL' 'char' '';
Expand Down
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