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Dear Julian,</div>
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Thank you very much for all your help.</div>
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Regards,<br>
Jaishree</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> fieldtrip <fieldtrip-bounces@science.ru.nl> on behalf of Julian Keil <julian.keil@gmail.com><br>
<b>Sent:</b> Wednesday, 12 August 2020 7:20 PM<br>
<b>To:</b> FieldTrip discussion list <fieldtrip@science.ru.nl><br>
<b>Subject:</b> Re: [FieldTrip] ITC</font>
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<div class="" style="word-wrap:break-word; line-break:after-white-space">Dear Jaishree,
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</div>
<div class="">as your question regarding how to get your own data into FieldTrip is concerned with the basics of the logic behind the FieldTrip data structure, I suggest taking a look at the tutorials provided on the website. This will allow you to get a feel
for the meaning behind the structures described in your code.</div>
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<div class=""><a href="http://www.fieldtriptoolbox.org/video/" class="">http://www.fieldtriptoolbox.org/video/</a></div>
<div class=""><a href="http://www.fieldtriptoolbox.org/walkthrough/" class="">http://www.fieldtriptoolbox.org/walkthrough/</a></div>
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<div class="">If you have problems reading in the .set-data (I assumed it’s coming from EEGLab, which uses .set-files), you can also take a look at this reference page.</div>
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</div>
<div class=""><a href="http://www.fieldtriptoolbox.org/reading_data/" class="">http://www.fieldtriptoolbox.org/reading_data/</a></div>
<div class=""><a href="http://www.fieldtriptoolbox.org/example/getting_started_with_reading_raw_eeg_or_meg_data/" class="">http://www.fieldtriptoolbox.org/example/getting_started_with_reading_raw_eeg_or_meg_data/</a></div>
<div class=""><br class="">
<div>Hope this helps,</div>
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</div>
<div>Julian</div>
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<blockquote type="cite" class="">
<div class="">Am 12.08.2020 um 10:41 schrieb Jaishree Jalewa <<a href="mailto:Jaishree.Jalewa@uon.edu.au" class="">Jaishree.Jalewa@uon.edu.au</a>>:</div>
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Dear Julian,</div>
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Many thanks for getting back to me.</div>
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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):</div>
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<span class="" style="font-family:Helvetica; font-size:10px; background-color:rgb(255,255,255); display:inline!important">cfg</span><span class="x_Apple-converted-space" style="margin:0px; font-family:Helvetica; font-size:10px"> <span class="x_Apple-converted-space"> </span></span><span class="" style="font-family:Helvetica; font-size:10px; background-color:rgb(255,255,255); display:inline!important">=
[];</span><br class="">
</div>
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<span class="" style="">load<span class="x_Apple-converted-space"> </span></span>data<span class="" style=""><span class="x_Apple-converted-space"> </span></span>=<span class="" style=""><span class="x_Apple-converted-space"> </span></span>'x.set'<span class="" style="">;</span></div>
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<span class="" style="">filename =<span class="x_Apple-converted-space"> </span></span>'x.set'<span class="" style="">;</span></div>
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%cfg.numtrl = 100</div>
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%data<span class="x_Apple-converted-space"> </span><span class="x_Apple-converted-space"> <span class="x_Apple-converted-space"> </span></span>= ft_freqsimulation(cfg.data); % simulate some data</div>
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dat = ft_read_data(filename,<span class="x_Apple-converted-space"> </span><span class="" style="color:rgb(0,0,255)">...</span><span class="" style="color:rgb(60,118,61)">);</span></div>
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cfg<span class="x_Apple-converted-space"> <span class="x_Apple-converted-space"> </span></span>= [];</div>
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cfg.method =<span class="x_Apple-converted-space"> </span><span class="" style="color:rgb(160,32,240)">'wavelet'</span>;</div>
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cfg.toi<span class="x_Apple-converted-space"> <span class="x_Apple-converted-space"> </span></span>= [-0.1 0.3];</div>
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cfg.foi<span class="x_Apple-converted-space"> <span class="x_Apple-converted-space"> </span></span>= [1 100];</div>
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cfg.output =<span class="x_Apple-converted-space"> </span><span class="" style="color:rgb(160,32,240)">'fourier'</span>;</div>
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freq<span class="x_Apple-converted-space"> </span><span class="x_Apple-converted-space"> <span class="x_Apple-converted-space"> </span></span>= ft_freqanalysis(cfg, data);</div>
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% make a new FieldTrip-style data structure containing the ITC</div>
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% copy the descriptive fields over from the frequency decomposition</div>
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itc<span class="x_Apple-converted-space"> </span><span class="x_Apple-converted-space"> <span class="x_Apple-converted-space"> </span></span>= [];</div>
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itc.label<span class="x_Apple-converted-space"> </span><span class="x_Apple-converted-space"> <span class="x_Apple-converted-space"> </span></span>= freq.label;</div>
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itc.freq<span class="x_Apple-converted-space"> <span class="x_Apple-converted-space"> </span></span>= freq.freq;</div>
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itc.time<span class="x_Apple-converted-space"> <span class="x_Apple-converted-space"> </span></span>= freq.time;</div>
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itc.dimord<span class="x_Apple-converted-space"> <span class="x_Apple-converted-space"> </span></span>=<span class="x_Apple-converted-space"> </span><span class="" style="color:rgb(160,32,240)">'chan_freq_time'</span>;</div>
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<span class="" style="">F = freq.fourierspctrm;<span class="x_Apple-converted-space"> </span><span class="x_Apple-converted-space"> <span class="x_Apple-converted-space"> </span></span></span>% copy the Fourier spectrum</div>
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N = size(F,1);<span class="x_Apple-converted-space"> </span><span class="x_Apple-converted-space"> <span class="x_Apple-converted-space"> </span></span><span class="" style="color:rgb(60,118,61)">% number of trials</span></div>
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% compute inter-trial phase coherence (itpc)</div>
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itc.itpc<span class="x_Apple-converted-space"> <span class="x_Apple-converted-space"> </span></span>= F./abs(F);<span class="x_Apple-converted-space"> </span><span class="x_Apple-converted-space"> <span class="x_Apple-converted-space"> </span></span><span class="" style="color:rgb(60,118,61)">%
divide by amplitude</span></div>
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itc.itpc<span class="x_Apple-converted-space"> <span class="x_Apple-converted-space"> </span></span>= sum(itc.itpc,1);<span class="x_Apple-converted-space"> </span><span class="x_Apple-converted-space"> <span class="x_Apple-converted-space"> </span></span><span class="" style="color:rgb(60,118,61)">%
sum angles</span></div>
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<span class="" style="">itc.itpc<span class="x_Apple-converted-space"> <span class="x_Apple-converted-space"> </span></span>= abs(itc.itpc)/N;<span class="x_Apple-converted-space"> </span><span class="x_Apple-converted-space"> <span class="x_Apple-converted-space"> </span></span></span>%
take the absolute value and normalize</div>
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<span class="" style="">itc.itpc<span class="x_Apple-converted-space"> <span class="x_Apple-converted-space"> </span></span>= squeeze(itc.itpc);<span class="x_Apple-converted-space"> </span></span>% remove the first singleton dimension</div>
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% compute inter-trial linear coherence (itlc)</div>
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itc.itlc<span class="x_Apple-converted-space"> <span class="x_Apple-converted-space"> </span></span>= sum(F) ./ (sqrt(N*sum(abs(F).^2)));</div>
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<span class="" style="">itc.itlc<span class="x_Apple-converted-space"> <span class="x_Apple-converted-space"> </span></span>= abs(itc.itlc);<span class="x_Apple-converted-space"> </span><span class="x_Apple-converted-space"> <span class="x_Apple-converted-space"> </span></span></span>%
take the absolute value, i.e. ignore phase</div>
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<span class="" style="">itc.itlc<span class="x_Apple-converted-space"> <span class="x_Apple-converted-space"> </span></span>= squeeze(itc.itlc);<span class="x_Apple-converted-space"> </span></span>% remove the first singleton dimension</div>
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figure</div>
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subplot(2, 1, 1);</div>
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imagesc(itc.time, itc.freq, squeeze(itc.itpc(1,:,:)));</div>
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axis<span class="x_Apple-converted-space"> </span><span class="" style="color:rgb(160,32,240)">xy</span></div>
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<span class="" style="">title(</span>'inter-trial phase coherence'<span class="" style="">);</span></div>
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subplot(2, 1, 2);</div>
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imagesc(itc.time, itc.freq, squeeze(itc.itlc(1,:,:)));</div>
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axis<span class="x_Apple-converted-space"> </span><span class="" style="color:rgb(160,32,240)">xy</span></div>
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<span class="" style="">title(</span>'inter-trial linear coherence'<span class="" style="">);</span></div>
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Once again sorry to bother you,</div>
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Thanks,</div>
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Jaishree</div>
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<font face="Calibri, sans-serif" class="" style="font-size:11pt"><b class="">From:</b><span class="x_Apple-converted-space"> </span>fieldtrip <<a href="mailto:fieldtrip-bounces@science.ru.nl" class="">fieldtrip-bounces@science.ru.nl</a>> on behalf of Julian
Keil <<a href="mailto:julian.keil@gmail.com" class="">julian.keil@gmail.com</a>><br class="">
<b class="">Sent:</b><span class="x_Apple-converted-space"> </span>Wednesday, 12 August 2020 5:28 PM<br class="">
<b class="">To:</b><span class="x_Apple-converted-space"> </span>FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl" class="">fieldtrip@science.ru.nl</a>><br class="">
<b class="">Subject:</b><span class="x_Apple-converted-space"> </span>Re: [FieldTrip] ITC</font>
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Dear Jaishree,
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<div class="">you can find information on how to compute ITC in FieldTrip here: <a href="http://www.fieldtriptoolbox.org/faq/itc/" class="">http://www.fieldtriptoolbox.org/faq/itc/</a></div>
<div class="">You should be able to read in the .set files using ft_read_data: <a href="http://www.fieldtriptoolbox.org/faq/dataformat/" class="">http://www.fieldtriptoolbox.org/faq/dataformat/</a></div>
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<div class="">Hope this helps,</div>
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<div class="">Julian</div>
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________________<br class="">
Prof. Dr. Julian Keil<br class="">
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Biological Psychology<br class="">
Olshausenstrasse 62 - R. 306<br class="">
24118 Kiel, Germany<br class="">
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+49 - 0431 - 880 - 4872<br class="">
<a href="http://www.biopsych.uni-kiel.de/en" class="">http://www.biopsych.uni-kiel.de/en</a><br class="">
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<div class="">Am 12.08.2020 um 04:56 schrieb Jaishree Jalewa <<a href="mailto:Jaishree.Jalewa@uon.edu.au" class="">Jaishree.Jalewa@uon.edu.au</a>>:</div>
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Hi, Can I please request some help with performing ITC using Fieldtrip as I have no experience with it.<span class="x_x_Apple-converted-space"> </span><br class="">
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.<br class="">
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Any help will be much appreciated.<br class="">
Thanks,<br class="">
Jaishree<br class="">
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<span class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; float:none; display:inline!important">_______________________________________________</span><br class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none">
<span class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; float:none; display:inline!important">fieldtrip
mailing list</span><br class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none">
<a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none">
<a href="https://doi.org/10.1371/journal.pcbi.1002202" class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px">https://doi.org/10.1371/journal.pcbi.1002202</a></div>
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<span class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; float:none; display:inline!important">_______________________________________________</span><br class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none">
<span class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; float:none; display:inline!important">fieldtrip
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<a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none">
<a href="https://doi.org/10.1371/journal.pcbi.1002202" class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px">https://doi.org/10.1371/journal.pcbi.1002202</a></div>
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