Unable to load an EEG in .e format

Fran · May 1, 2018, 1:45am

Hello, everybody!

I have been not able to load an EEG file in .e format (from Nicolet) using MATLAB 2017b and excelent values of CPU usage and physical memory.

After creating a new protocol with ‘Yes, use protocol’s default anatomy’ and 'No, use one channel file per acquisition run (MEG/EEG)', creating a new subject, and clicking on ‘Review raw file’ (I also tried 'Import MEG/EEG', an error message appeared.

I have tried the file with the Nicolet EEG Viewer (from Viasys Healthcare, Inc.) and it's all right.

Once I manage to load the file, I would also like to export it in .edf format since it is easier to manage (my EEG software doesn't allow to do it).

Thanks in advance for your help!

Francois · May 1, 2018, 7:46am

Hello,

This wrapper for Brainstorm around the Nicolet reader was developed without any documentation, based on the reverse engineering of a few example files. I am not surprised it is not capable of handling all the .e recordings.

Would it be possible for you to share with me an example file? A short .e file that you cannot read in Brainstorm and that doesn’t contain any sensitive patient information?
Zip it, upload it somewhere (dropbox, google drive, one drive…) and send me the link a private message using this forum.

Otherwise, you’d have to debug it yourself: place a breakpoint a line 92 and try to understand what are the issues in the code I wrote:

github.com

brainstorm-tools/brainstorm3/blob/master/toolbox/io/in_fopen_nicolet.m#L92


sFile.prop.nAvg    = 1;




%% ===== CREATE EMPTY CHANNEL FILE =====
ChannelMat = db_template('channelmat');
ChannelMat.Comment = [sFile.device ' channels'];
ChannelMat.Channel = repmat(db_template('channeldesc'), [1, hdr.numchan]);
% For each channel
for i = hdr.selchan
ChannelMat.Channel(i).Type    = 'EEG';
ChannelMat.Channel(i).Name    = strrep(str_clean(hdr.obj.segments(1).chName{hdr.selchan(i)}), ' ', '');
ChannelMat.Channel(i).Name = strrep(ChannelMat.Channel(i).Name, '-Ref', '');
ChannelMat.Channel(i).Name = strrep(ChannelMat.Channel(i).Name, '-ref', '');
ChannelMat.Channel(i).Name = strrep(ChannelMat.Channel(i).Name, '-REF', '');
strRef = str_clean(hdr.obj.segments(1).refName{hdr.selchan(i)});
if ~isempty(strRef)
    ChannelMat.Channel(i).Comment = ['Reference: ', strRef];
end
end

Cheers,
Francois

Fran · May 2, 2018, 3:12pm

Thanks a lot for your quick answer.

I’ll send to you an .e file as soon as possible (with no sensitive information).

Francois · June 7, 2018, 4:26pm

Thank you for the example file.
There was indeed a bug in the Brainstorm reader.
The channels with lower sampling rates are currently ignored because Brainstorm cannot handle signals with multiple sampling frequency at the moment, but this was not done correctly. I think I fixed the issue.

Please update Brainstorm and try again.

Fran · June 7, 2018, 5:15pm

Thank you very much, indeed! I am going to update the software and try again.