Tags: example video eeg nirs plotting

Making a synchronous movie of EEG or NIRS combined with video recordings

Inspecting your data is important to get a better understanding of it. You might have video recordings of your participant or the experimental setting. Playing the video recordings synchronously with the EEG or NIRS data can provide a lot of insight, for example to detect possible motion artifacts or to detect clear effects of the experimental stimuli.

This example script shows how to make a movie of your data with the help of ft_databrowser and MATLAB’s Videowriter function. Subsequently, you synchronize this movie with your actual video data with video editing software like Adobe Premiere Pro or using annotation software like ELAN.

EEG and fNIRS are often used in freely moving subjects and in motion research. The following is a movie of fNIRS signals and artifacts during walking, turning, frowning, head movements and jumping. The example video shown here below was edited with Premiere Pro.

MATLAB script

% read the continuous data in memory, this results in one long segment (trial)
cfg = [];
cfg.dataset = 'motioncapture.snirf';
data_continuous = ft_preprocessing(cfg);

% we also want to plot the events (if present)
event = ft_read_event('motioncapture.snirf');

%%

begtime = 0;
endtime = 60 - 1/data_continuous.fsample; % 60 seconds minus one sample
increment = 1; % stepwise in seconds

% make a figure with the desired size, see https://en.wikipedia.org/wiki/Display_resolution
close all
figh = figure;

set(figh, 'position', [10 10 1280 720]);
% set(figh, 'WindowState', 'maximized');

% prepare the video file
vidObj = VideoWriter('databrowser', 'MPEG-4');
vidObj.FrameRate = 1/increment;
vidObj.Quality = 100;
open(vidObj);

% prevent too much feedback info to be printed on screen
ft_debug off
ft_info off
ft_notice off

%%

while (endtime < data_continuous.time{1}(end)) && ishandle(figh)
  
  % cut a short piece of data from the continuous recording
  cfg = [];
  cfg.toilim = [begtime endtime];
  cfg.trackcallinfo = 'no';
  cfg.showcallinfo = 'no';
  data_piece = ft_redefinetrial(cfg, data_continuous);
  
  cfg = [];
  cfg.figure = figh;            % IMPORTANT: reuse the existing figure
  cfg.trackcallinfo = 'no';     % prevent too much feedback info to be printed on screen
  cfg.showcallinfo = 'no';      % prevent too much feedback info to be printed on screen
  cfg.viewmode = 'vertical';
  cfg.event = event;
  cfg.ploteventlabels = 'value';
  cfg.plotlabels = 'yes';
  cfg.fontsize = 5;
  cfg.continuous = 'yes';
  cfg.blocksize = round(endtime-begtime);
  cfg.nirsscale = 15;
  cfg.preproc.demean = 'yes';
  cfg.linecolor = [0.9290 0.6940 0.1250;0.8500 0.3250 0.0980; 0.6350 0.0780 0.1840; 0.4660 0.6740 0.1880; 0 0 0];
  cfg.colorgroups = [ones(1,4), 5*ones(1,2), ones(1,4), 5*ones(1,2), 2*ones(1,8), 5*ones(1,2), 2*ones(1,2), 5*ones(1,2),...
    ones(1,4), 5*ones(1,2), ones(1,4), 5*ones(1,2), 2*ones(1,8), 5*ones(1,2), 2*ones(1,2), 5*ones(1,2),...
    3*ones(1,4), 5*ones(1,2), 3*ones(1,4), 5*ones(1,2), 4*ones(1,2), 5*ones(1,2), 4*ones(1,4), 5*ones(1,2),...
    3*ones(1,4), 5*ones(1,2), 3*ones(1,4), 5*ones(1,2), 4*ones(1,2), 5*ones(1,2), 4*ones(1,4), 5*ones(1,2)];

  ft_databrowser(cfg, data_piece);
  
  set(gca, 'XGrid', 'on');
  currFrame = getframe(gcf);
  writeVideo(vidObj,currFrame);

  % go to the next segment of data
  begtime = begtime + increment;
  endtime = endtime + increment;
end

%%

% close the file
close(vidObj);

See also

Tags: example video eeg nirs plotting