[FieldTrip] importing large edf data

Fri Dec 18 13:37:52 CET 2015

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> wrote:

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>    1. importing large edf data (Leila Ayoubian)
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> ----------------------------------------------------------------------
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> Message: 1
> Date: Fri, 18 Dec 2015 09:43:43 +0000 (UTC)
> From: Leila Ayoubian <leilayou_54 at yahoo.com>
> To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
> Subject: [FieldTrip] importing large edf data
> Message-ID:
>         <807603762.476165.1450431823359.JavaMail.yahoo at mail.yahoo.com>
> 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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