[FieldTrip] importing large edf data

Sat May 7 08:21:21 CEST 2016

Leila,

I don’t know much about the EDF format, but perhaps you should consider that the ‘hdr’ should probably stay consistent with the data. That is, some data formats have a header that specifies the number of data samples. If you create ‘new’ data with an extra number of samples, it could be that the header needs to be updated as well.

Best,
Jan-Mathijs

On 05 May 2016, at 16:34, Leila Ayoubian <leilayou_54 at yahoo.com<mailto:leilayou_54 at yahoo.com>> wrote:

 Hi,
I am trying to concatenate two EDF files in Matlab and convert it back to EDF. (basically sticking the original data to on piece)
Here is my code. It does create the 'a' file but it does not open as EDF.
Any suggestion?

clc;
clear all;
close all;
%%
[fileName1, pathName1] = uigetfile({'*.edf;*.e', 'Nicolete files (*.edf;*.e)'; '*.*', 'All files (*.*)'}, 'Select edf file');
file1 = fullfile(pathName1, fileName1);
cfg1 = [];
%cfg.trl = [1 1000 0];%45min*60=2700 sec % 2700sec*1000=2700000 ms
cfg1.trialdef.triallength = 5;
cfg1.dataset =file1; %'For leila.edf';
cfg1= ft_definetrial( cfg1 );
cfg1.continuous = 'yes';
datastr1 = ft_preprocessing(cfg1);
data1=datastr1.trial{1,1};

Fs=datastr1.fsample;

hdr=datastr1.hdr;
%%

[fileName2, pathName2] = uigetfile({'*.edf;*.e', 'Nicolete files (*.edf;*.e)'; '*.*', 'All files (*.*)'}, 'Select edf file');
file2 = fullfile(pathName2, fileName2);
cfg2 = [];
%cfg.trl = [1 1000 0];%45min*60=2700 sec % 2700sec*1000=2700000 ms
cfg2.trialdef.triallength = 5;
cfg2.dataset =file2; %'For leila.edf';
cfg2= ft_definetrial( cfg2 );
cfg2.continuous = 'yes';
datastr2 = ft_preprocessing(cfg2);

data2=datastr2.trial{1,1};

Fs2=datastr2.fsample;

% EEG=cat(2,data1,data2)
% EEG=EEG';
% HDR=hdr1
% out=EDFCreator(EEG);

dat = cat(2,data1,data2);
%%
% write_edf('a', hdr, dat);

ft_write_data('a', dat, 'header', hdr,'dataformat','edf' )

__________________________________________________
Leila Ayoubian, PhD.
Institute of Psychiatry, Psychology and Neuroscience
King's College London

________________________________
From: Arjen Stolk <a.stolk8 at gmail.com<mailto:a.stolk8 at gmail.com>>
To: FieldTrip discussion list <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>>
Sent: Tuesday, February 9, 2016 3:32 PM
Subject: Re: [FieldTrip] importing large edf data

Hi both,
There might be information on the date and time of recording in the orig field of the header, if that's what you're looking for. Don't know the name of the subfield from the top of my head.
Arjen

On Feb 9, 2016, at 3:19 AM, Stephen Politzer-Ahles <stephen.politzer-ahles at ling-phil.ox.ac.uk<mailto:stephen.politzer-ahles at ling-phil.ox.ac.uk>> wrote:

Hi Leila,

I'm sorry but I'm afraid I have not quite understood your issue. Can you give some more detail about what the problem is?

In general, the fieldtrip structure output by ft_preprocessing() should have a .time field (indicating what timepoint during the epoch each sample corresponds to) and an .fsample field indicating the sampling rate (which you would also be able to use to figure out the time of each sample).

Best,
Steve

---
Stephen Politzer-Ahles
University of Oxford
Language and Brain Lab
Faculty of Linguistics, Phonetics & Philology
http://users.ox.ac.uk/~cpgl0080/

Message: 1
Date: Mon, 8 Feb 2016 11:51:05 +0000 (UTC)
From: Leila Ayoubian <leilayou_54 at yahoo.com<mailto:leilayou_54 at yahoo.com>>
To: FieldTrip discussion list <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>>
Subject: Re: [FieldTrip] importing large edf data
Message-ID:
        <1195829915.655104.1454932265573.JavaMail.yahoo at mail.yahoo.com<mailto:1195829915.655104.1454932265573.JavaMail.yahoo at mail.yahoo.com>>
Content-Type: text/plain; charset="utf-8"

Hi Stephen:I just happen to realize that when I load the data as you mentioned below, I can not get hold of the real time of the EEG file. (e.g.18:32:43 ).Could you please point out as how I could retrieve the real time of the EEG file after loading.
Thanks a lot.Kind regards
__________________________________________________ Leila Ayoubian, PhD.
Institute of Psychiatry, Psychology and Neuroscience
King's College London

      From: Stephen Politzer-Ahles <stephen.politzer-ahles at ling-phil.ox.ac.uk<mailto:stephen.politzer-ahles at ling-phil.ox.ac.uk>>
 To: fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>
 Sent: Friday, December 18, 2015 12:37 PM
 Subject: Re: [FieldTrip] importing large edf data

Hello Leila,

I think there are a few possible options for you. If you're not interested in analyzing high frequencies, then you could import the data one sample at a time, downsampling each channel, and then concatenate the channels into one structure, as described in http://www.fieldtriptoolbox.org/faq/how_can_i_preprocess_a_dataset_that_is_too_large_to_fit_into_memory. I don't know what your sampling rate was, but if your sampling rate was extremely high then this can save you a lot of space. For example, if you're only interested in frequencies up to high gamma (around 90-100 Hz), then your data only need to be sampled at around 250 Hz (per the Nyquist theorem, plus a little extra wiggle room), so if you sampled at e.g. 2500 Hz (which our EDF system does by default) or 5000 Hz then you have way more samples than necessary; downsampling like this will greatly reduce your array size.

If that is not an option, then you can read in a segment of data as a 'trial'. ft_preprocessing understands trial start and end times from cfg.trl, which minimally is an Nx3 matrix (N is the number of trials to read, and the columns are the start sample for each trial, the end sample for each trial, and the trigger value associated with the trial; you could just put 0 if there's no trigger). So let's say you want to read the first through thousandth sample of the recording, then you would set up your cfg as normal, then add:

cfg.trl = [1 1000 0];

and then use ft_preprocessing.

By way of example, here is code that reads in raw data as a series of 1-second "trials":

cfg = [];
cfg.dataset = 'C:\Users\Steve\Desktop\subj2.vhdr';
cfg.trialdef.triallength = 1; % see documentation for ft_definetrial for an explanation of these parameters
cfg.trialdef.ntrials = Inf;
cfg = ft_definetrial( cfg );

cfg.continuous = 'yes';
data = ft_preprocessing(cfg);

After doing whatever you need to these trials, you could concatenate them back into continuous data (see http://mailman.science.ru.nl/pipermail/fieldtrip/2011-June/003971.html for details).

Best,
Steve

---
Stephen Politzer-Ahles
University of Oxford
Language and Brain Lab
Faculty of Linguistics, Phonetics & Philology
http://users.ox.ac.uk/~cpgl0080/
On Fri, Dec 18, 2015 at 11:00 AM, <fieldtrip-request at science.ru.nl<mailto:fieldtrip-request at science.ru.nl>> wrote:

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Message: 1
Date: Fri, 18 Dec 2015 09:43:43 +0000 (UTC)
From: Leila Ayoubian <leilayou_54 at yahoo.com<mailto:leilayou_54 at yahoo.com>>
To: "fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>" <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>>
Subject: [FieldTrip] importing large edf data
Message-ID:
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Content-Type: text/plain; charset="utf-8"

Hi:Thanks for providing us with this amazing toolbox.
I am new to fieldtrip. I am trying to import EEG data in the format of *.edf for the purpose of seizure detection for epileptic patients. I can't break up the data as you understand the detection has to have continuous data. However I could load section of the data at a time and clear what is already used and reload again.?
So trying to load the data like this:
cfg.dataset= ('mydata.edf');
rawdata=ft_preprocessing(cfg);
This is the error message I get :
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error using zeros
Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a long time
and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.

Error in read_edf (line 403)
? dat = zeros(length(chanindx),nepochs*epochlength);

Error in ft_read_data (line 622)
??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);

Error in ft_preprocessing (line 566)
????? dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary',
????? strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat);

Error in ReadFedfiles (line 8)
rawdata=ft_preprocessing(cfg);%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
I tried the ft_redefinetrial, but since the input to this file is the output from ft-PREPROCESSING it gives me the same error.

I also tried to use ft_read_data to choose the samples I want to load :?filename???? = 'mydata.edf'
?hdr?? = ft_read_header(filename);
?sample.start=1
?sample.end=100
dat = ft_read_data(filename,'sample.start','1','sample.end','100')
and here is again the error message:
Error using zeros
Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a
long time and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.

Error in read_edf (line 403)
? dat = zeros(length(chanindx),nepochs*epochlength);

Error in ft_read_data (line 622)
??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);

Error in ReadFedfiles (line 31)
dat = ft_read_data(filename,'sample.start','1','sample.end','100')
?
>>

Could you please direct me as to which functions and in which order I should be using the functions to load data in smaller samples.Some examples would be useful.
Thanks again for your support and assistance.
We appreciate your effort.
Kind regards

___________________________________________________ Dr. Leila Ayoubian
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