adding files from Cyril

channelloc_to_tsv.m

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+function channelloc_to_tsv(EEG)
+
+% From an EEG variable (i.e. EEG=pop_loadset(*.set), export the channel
+% location as tsv file following the BIDS specification
+%
+% FORMAT channelloc_to_tvs(EEG)
+%
+% Author: Cyril Pernet - LIMO Team, University of Edinurgh
+
+% list of labels for which we know it's not an EEG channel
+known_labels = {'EXG','TRIG','ECG','EOG','VEOG','HEOG','EMG','MISC'};
+
+% channel.tsv
+for electrode = 1:size(EEG.chanlocs,2)
+    ename{electrode}     = EEG.chanlocs(electrode).labels; 
+    if contains(EEG.chanlocs(electrode).labels,known_labels)
+        type{electrode} = EEG.chanlocs(electrode).labels;
+        if contains(EEG.chanlocs(electrode).labels,'EOG')
+            unit{electrode} = [num2str(char(181)) 'V'];
+        elseif contains(EEG.chanlocs(electrode).labels,'ECG')
+            unit{electrode} = 'mV';
+        else
+            unit{electrode} = ' ';
+        end
+    else
+        type{electrode} = 'EEG';
+        unit{electrode} = [num2str(char(181)) 'V']; % char(181) is mu in ASCII
+    end
+    sampling_frequency(electrode)  = EEG.srate;
+    reference{electrode} = EEG.ref;
+end
+
+t = table(ename',type',unit',sampling_frequency',reference','VariableNames',{'name','type','units','sampling_reference','reference'});
+channels_tsv_name = [EEG.filepath filesep EEG.filename(1:end-4) '_channels.tsv'];
+writetable(t,channels_tsv_name,'FileType','text','Delimiter','\t');
+

electrodes_to_tsv.m

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+function electrodes_to_tsv(EEG)
+
+% From an EEG variable (i.e. EEG=pop_loadset(*.set), export the EEG.channel
+% locations as tsv file and initiate the json file following the BIDS 
+% specification
+%
+% FORMAT electrodes_to_tsv(EEG)
+%
+% Author: Cyril Pernet - LIMO Team, University of Edinurgh
+
+% electrode.tsv
+for electrode = 1:size(EEG.chanlocs,2)
+    ename{electrode} = EEG.chanlocs(electrode).labels; 
+    x(electrode)     = EEG.chanlocs(electrode).X;
+    y(electrode)     = EEG.chanlocs(electrode).Y;
+    z(electrode)     = EEG.chanlocs(electrode).Z;
+    type{electrode}  = EEG.chanlocs(electrode).type;
+end
+
+t = table(ename',x',y',z',type','VariableNames',{'name','x','y','z','type'});
+electrodes_tsv_name = [EEG.filepath filesep EEG.filename(1:strfind(EEG.filename,'run-')-1) 'electrodes.tsv'];
+writetable(t,electrodes_tsv_name,'FileType','text','Delimiter','\t');
+
+% coordsystem.json
+EEGCoordinateSystem = 'RAS';
+EEGCoordinateUnits  = 'mm';
+json = struct('EEGCoordinateSystem','RAS', ...
+        'EEGCoordinateUnits','mm');
+jsonwrite([EEG.filepath filesep EEG.filename(1:strfind(EEG.filename,'run-')-1) 'electrodes.json'],json,struct('indent','  '))
+
+

events_to_tsv.m

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+function events_to_tsv(EEG)
+
+% From an EEG variable (i.e. EEG=pop_loadset(*.set), export the EEG.event
+% as tsv file 
+%
+% FORMAT electrodes_to_tsv(EEG)
+%
+% Author: Cyril Pernet - LIMO Team, University of Edinurgh
+
+for event=1:size(EEG.event,2)
+    onset(event)        = EEG.event(event).latency;
+    trial_type{event}   = EEG.event(event).urevent;
+    if ~isfield(EEG.event(event),'duration')
+        duration(event) = 0;
+    else
+        duration(event) = EEG.event(event).duration;
+    end        
+end
+
+t = table(onset',duration',trial_type','VariableNames',{'onset','duration','trial_type'});
+events_tsv_name = [EEG.filepath filesep EEG.filename(1:end-4) '_events.tsv'];
+writetable(t,events_tsv_name,'FileType','text','Delimiter','\t');
+
+

rename_brainvision_files.m

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+function rename_brainvision_files(varargin)
+
+% RENAME_BRAINVISION_FILES renames a BrainVision EEG dataset, which consists of a vhdr header
+% file, vmrk marker file and a data file that usually has the extension dat, eeg or seg.
+%
+% Use as
+%   rename_brainvision_files(oldname, newname, 'rmf', 'on')
+% where both the old and the new filename should be strings corresponding to the
+% header file, i.e. including the vhdr extension.
+% 'rmf' option indicates to remove old files and can be turned 'on' of 'off' (default)
+%
+% See also http://www.fieldtriptoolbox.org/ and https://sccn.ucsd.edu/wiki/EEGLAB for
+% open source software to process BrainVision EEG data.
+%
+% Robert Oostenveld https://gist.github.com/robertoostenveld/e31637a777c514bf1e86272e1092316e
+% Cyril Pernet - fixed few bugs here and there https://gist.github.com/CPernet/e037df46e064ca83a49fb4c595d4566a
+
+%% deal with inputs
+
+rmf = 'off'; % by default do not delete files
+if nargin >= 3
+    if strcmpi(varargin{3},'rmf')
+        if nargin == 3
+            disp('no value associated to the remove file option, assumning off')
+        else
+            rmf = varargin{4};
+        end
+    else
+        error(['unrecognized option argument ''' varargin{3} ''''])
+    end
+end
+
+oldheaderfile = varargin{1};
+newheaderfile = varargin{2};
+clear varargin
+
+% determine whether the file extensions should be in lower or upper case
+if ~isempty(regexp(newheaderfile, 'VHDR$', 'once'))
+  switchcase = @upper;
+else
+  switchcase = @lower;
+end
+
+% determine the filename without extension
+[~, f, ~] = fileparts(newheaderfile);
+
+%% do the renaming
+
+% deal with the header file
+assert(exist(oldheaderfile, 'file')~=0, 'the file %s does not exists', oldheaderfile);
+assert(exist(newheaderfile, 'file')==0, 'the file %s already exists', newheaderfile);
+fid1 = fopen(oldheaderfile, 'r'); % read old
+fid2 = fopen(newheaderfile, 'w'); % write new
+
+while ~feof(fid1)
+  line = fgetl(fid1);
+  if ~isempty(regexp(line, '^MarkerFile', 'once'))
+    [~, rem] = strtok(line, '=');
+    oldmarkerfile = rem(2:end);
+    [~, ~, x] = fileparts(oldmarkerfile);
+    newmarkerfile = [f switchcase(x)];
+    line = sprintf('MarkerFile=%s', newmarkerfile);
+  elseif ~isempty(regexp(line, '^DataFile', 'once'))
+    [~, rem] = strtok(line, '=');
+    olddatafile = rem(2:end);
+    [~, ~, x] = fileparts(olddatafile);
+    newdatafile = [f switchcase(x)];
+    line = sprintf('DataFile=%s', newdatafile);
+  end
+  fprintf(fid2, '%s\r\n', line);
+end
+fclose(fid1);
+fclose(fid2);
+
+% deal with the marker file
+if exist(oldmarkerfile, 'file') == 0
+    [~,~,ext] = fileparts(oldmarkerfile);
+    [~, ff, ~] = fileparts(oldheaderfile); % re-reading as sometimes weird names comes up
+    if exist([ff ext], 'file')
+        oldmarkerfile = [ff ext];
+    else
+        error('the file %s does not exists', oldmarkerfile);
+    end
+end
+assert(exist(newmarkerfile, 'file')==0, 'the file %s already exists', newmarkerfile);
+fid1 = fopen(oldmarkerfile, 'r');
+fid2 = fopen(newmarkerfile, 'w');
+
+while ~feof(fid1)
+  line = fgetl(fid1);
+  if ~isempty(regexp(line, '^HeaderFile', 'once'))
+    [~, rem] = strtok(line, '=');
+    oldheaderfile = rem(2:end);
+    [~, ~, x] = fileparts(oldheaderfile);
+    newheaderfile = [f switchcase(x)];
+    line = sprintf('HeaderFile=%s', newheaderfile);
+  elseif ~isempty(regexp(line, '^DataFile', 'once'))
+    [~, rem] = strtok(line, '=');
+    olddatafile = rem(2:end);
+    [~, ~, x] = fileparts(olddatafile);
+    newdatafile = [f switchcase(x)];
+    line = sprintf('DataFile=%s', newdatafile);
+  end
+  fprintf(fid2, '%s\r\n', line);
+end
+fclose(fid1);
+fclose(fid2);
+
+% deal with the data file
+if exist(olddatafile, 'file') == 0
+    [~,~,ext] = fileparts(olddatafile);
+    [~, ff, ~] = fileparts(oldheaderfile); % re-reading as sometimes weird names comes up
+    if exist([ff ext], 'file')
+        olddatafile = [ff ext];
+    else
+        error('the file %s does not exists', oldmarkerfile);
+    end
+end
+assert(exist(newdatafile, 'file')==0, 'the file %s already exists', newdatafile);
+status = copyfile(olddatafile, newdatafile);
+if ~status
+  error('failed to copy data from %s to %s', olddatafile, newdatafile);
+end
+
+%% delete old files *try* in case of user restriction
+if strcmpi(rmf,'on')
+    try delete(oldheaderfile); end
+    try delete(oldmarkerfile); end
+    try delete(olddatafile); end
+end