[FieldTrip] ITC

[Jaishree Jalewa]

Dear Julian,

Many thanks for getting back to me.

Sorry to bother you again but can I humbly request you to please have a look at the script below as I am unable to run this script. The script that is provided on the link defines 'data' as a simulation I believe, but I am trying out with one preprocessed real rat EEG data file (x.set) (I have little knowledge of programming), not sure how to define data and trials (can it take the number of trials from the file or do I need to mention):
cfg        = [];

load data = 'x.set';

filename = 'x.set';

%cfg.numtrl = 100

%data       = ft_freqsimulation(cfg.data); % simulate some data

dat = ft_read_data(filename, ...);



cfg        = [];

cfg.method = 'wavelet';

cfg.toi    = [-0.1 0.3];

cfg.foi    = [1 100];

cfg.output = 'fourier';

freq       = ft_freqanalysis(cfg, data);



% make a new FieldTrip-style data structure containing the ITC

% copy the descriptive fields over from the frequency decomposition



itc           = [];

itc.label     = freq.label;

itc.freq      = freq.freq;

itc.time      = freq.time;

itc.dimord    = 'chan_freq_time';





F = freq.fourierspctrm;   % copy the Fourier spectrum

N = size(F,1);           % number of trials



% compute inter-trial phase coherence (itpc)

itc.itpc      = F./abs(F);         % divide by amplitude

itc.itpc      = sum(itc.itpc,1);   % sum angles

itc.itpc      = abs(itc.itpc)/N;   % take the absolute value and normalize

itc.itpc      = squeeze(itc.itpc); % remove the first singleton dimension



% compute inter-trial linear coherence (itlc)

itc.itlc      = sum(F) ./ (sqrt(N*sum(abs(F).^2)));

itc.itlc      = abs(itc.itlc);     % take the absolute value, i.e. ignore phase

itc.itlc      = squeeze(itc.itlc); % remove the first singleton dimension



figure

subplot(2, 1, 1);

imagesc(itc.time, itc.freq, squeeze(itc.itpc(1,:,:)));

axis xy

title('inter-trial phase coherence');

subplot(2, 1, 2);

imagesc(itc.time, itc.freq, squeeze(itc.itlc(1,:,:)));

axis xy

title('inter-trial linear coherence');

Once again sorry to bother you,

Thanks,
Jaishree
________________________________
From: fieldtrip <fieldtrip-bounces at science.ru.nl> on behalf of Julian Keil <julian.keil at gmail.com>
Sent: Wednesday, 12 August 2020 5:28 PM
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] ITC

Dear Jaishree,

you can find information on how to compute ITC in FieldTrip here: http://www.fieldtriptoolbox.org/faq/itc/<http://www.fieldtriptoolbox.org/faq/itc/>
You should be able to read in the .set files using ft_read_data: http://www.fieldtriptoolbox.org/faq/dataformat/<http://www.fieldtriptoolbox.org/faq/dataformat/>

Hope this helps,

Julian

________________
Prof. Dr. Julian Keil

Biological Psychology
Olshausenstrasse 62 - R. 306
24118 Kiel, Germany

+49 - 0431 - 880 - 4872
http://www.biopsych.uni-kiel.de/en<http://www.biopsych.uni-kiel.de/en>

Am 12.08.2020 um 04:56 schrieb Jaishree Jalewa <Jaishree.Jalewa at uon.edu.au<mailto:Jaishree.Jalewa at uon.edu.au>>:

Hi, Can I please request some help with performing ITC using Fieldtrip as I have no experience with it.
I am willing to use preprocessed rat EEG data with multiple groups and conditions involved.  Can anyone please let me know how to load the .set files in order to run the Fieldtrip script.

Any help will be much appreciated.
Thanks,
Jaishree
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