MATLAB: Create events/annotations on EEGLAB

.seizures fileannotation;eeglabevents

Can I manually create events/annotations in .set EEG files on EEGLAB without previously importing epoch info or event info? The EEGs which I want to analyze with EEGLAB have files with respective event annotations, but those files are in .edf.seizures format, which I can't figure out how to open on EEGLAB.

Best Answer

Hello Maanasi,

I understand that you want to import ‘ .edf.seizures ’ files into MATLAB for processing by EEGLAB. Please refer to the EEGLAB documentation for more information:

https://sccn.ucsd.edu/wiki/A01:_Importing_Continuous_and_Epoched_Data#Importing_a_Matlab_array

Since ‘ .edf.seizures ’ seems to be a non-standard file format, it is possible to write your own MATLAB function to import event annotations from these files. The following MATLAB Answers page provides more information about this:

http://www.mathworks.com/matlabcentral/answers/225716-how-i-can-read-chb01_03-edf-seizures-file-from-chb-mit-database-in-matlab-as-i-am-using-this-file-f

Building on the above answer, assuming that you want to read more than one seizure event, you can use the following MATLAB function:

function [ number_of_seizures, seizure_start_time_offsets, seizure_lengths ] = get_seizure_periods( annotation_file_location )
      file_descriptor = fopen(annotation_file_location);
      byte_array = fread(file_descriptor);
      number_of_seizures = (sum(byte_array == hex2dec('ec')) - 1) / 2;
      for i=1:number_of_seizures
         seizure_start_time_offsets(i) = bin2dec(strcat(dec2bin(byte_array(23 + (i*16))),dec2bin(byte_array(26 + (i*16)))));
         seizure_lengths(i) = byte_array(34 + (i*16));
      end
end

The above function provides the number of seizure events, the seizure start time offsets (from the previous event), and the duration of the seizures. In the above function, I have assumed that the seizure data stays at the same byte positions in each ‘ .edf.seizures ’ file. I also used the publicly-available ‘ .edf.seizures ’ data from the CHB-MIT Scalp EEG Database to test the above function:

https://www.physionet.org/pn6/chbmit/

If you are getting your ‘ .edf.seizures ’ files from a different source, you may want to write your own data import function. Also, since EEGLAB may want the data in the form of a matrix, you may want to reshape the above arrays into a matrix before importing it into EEGLAB.

In order to import this data from the MATLAB workspace into EEGLAB, you might want to use the “Import Epoch Info” feature of EEGLAB. Please refer to the EEGLAB documentation for more information about importing epoch information:

https://sccn.ucsd.edu/wiki/A02:_Importing_Event_Epoch_Info#Importing_events_from_a_Matlab_array_or_text_file

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This question is not really related to MATLAB; instead it is about the confusion in the definition of terms used in EEGLAB. Therefore, this question is best directed to developers of EEGLAB. You are more likely to find answers from them as compared to this website. Also, I suggest reading their documentation: https://sccn.ucsd.edu/wiki/EEGLAB. Especially read this page: https://sccn.ucsd.edu/wiki/I.1:_Loading_Data_in_EEGLAB It discusses loading the data in EEGLAB.

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I would go for a solution close to what you implemented, but splitting the file content first into blocks of data. For example:

 buffer = fileread('chb01-summary.txt') ;
 blocks = regexp(buffer, 'File Name', 'split') ;
 if length(blocks) < 2,  error('No content found in file.') ;  end
 blocks  = blocks(2:end) ;                           % 1st block is header.
 nBlocks = length(blocks) ;
 results = cell(nBlocks, 1) ;
 for bId = 1 : nBlocks  
    results{bId}.fileName = regexp(blocks{bId}, '\S+(?=\.edf)', 'match') ;
    results{bId}.fileStartTime = regexp(blocks{bId}, ...
        '(?<=File Start Time:\s*)\S+', 'match') ;
    results{bId}.fileEndTime = regexp(blocks{bId}, ...
        '(?<=File End Time:\s*)\S+', 'match') ;
    results{bId}.nSeizures = str2double( regexp(blocks{bId}, ...
        '(?<=in File:\s*)\d+', 'match') ) ;
    if results{bId}.nSeizures > 0
        results{bId}.seizures = regexp(blocks{bId}, ...
            'Seizure Start Time: (?<startTime>\d+).+?Seizure End Time: (?<endTime>\d+)', 'names') ;
    end
 end

With that, you get:

 >> results
 results = 
    [1x1 struct]
    [1x1 struct]
 >> results{1}
 ans = 
         fileName: {'chb01_02'}
    fileStartTime: {'12:42:57'}
      fileEndTime: {'13:42:57'}
        nSeizures: 0
 >> results{2}
 ans = 
         fileName: {'chb01_03'}
    fileStartTime: {'13:43:04'}
      fileEndTime: {'14:43:04'}
        nSeizures: 1
         seizures: [1x1 struct]
 >> results{2}.seizures
 ans = 
    startTime: '2996'
      endTime: '3036'

and what is left is probably a few conversions to numeric for relevant times.

Note that results{k}.seizures is a struct array, so if the 2nd entry in your file had been

 File Name: chb01_03.edf
 File Start Time: 13:43:04
 File End Time: 14:43:04
 Number of Seizures in File: 2
 Seizure Start Time: 2996 seconds
 Seizure End Time: 3036 seconds
 Seizure Start Time: 2997 seconds
 Seizure End Time: 3037 seconds

seizures times would be accessible through:

 >> results{2}.seizures
 ans = 
 1x2 struct array with fields:
    startTime
    endTime
 >> results{2}.seizures(1)
 ans = 
    startTime: '2996'
      endTime: '3036'
 >> results{2}.seizures(2)
 ans = 
    startTime: '2997'
      endTime: '3037'
 >> results{2}.seizures(2).startTime
 ans =
 2997

EDIT: note that the regexp inside the IF statement in the FOR loop is extracting data using named tokens. I did that for the example, but you could also go for a more common approach, e.g.

 if results{bId}.nSeizures > 0
     startTimes = regexp(blocks{bId}, '(?<=Seizure Start Time:\s*)\d+', 'match') ;
     endTimes = regexp(blocks{bId}, '(?<=Seizure End Time:\s*)\d+', 'match') ;
     results{bId}.seizures = str2double([startTimes; endTimes].') ;
 end

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