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Hello Xavier, <br>
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Thank you for your response. I have tried ft_appendata and here is the result:<br>
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>> cfg = [];
<div class="ContentPasted0">cfg.keepsampleinfo = 'no';</div>
<div class="ContentPasted0">data_all_sbj2 = ft_appenddata(cfg, allData{2,1}, allData{2,2}, allData{2,3});</div>
<div class="ContentPasted0">Error using ft_appenddata</div>
cannot append this data</div>
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<br>
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Do you think a possible reason for this could be that the input datasets do not have the same number of trials or channels?
<br>
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<br>
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Block 1: allData{2, 1} has 39 channels and 44 trials</div>
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Block 2: allData{2, 2} has 47 channels and 49 trials<br>
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Block 3: allData{2, 3} has 45 channels and 57 trials</div>
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<br>
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Is there any other way of doing this other than using the ft_appendata?<br>
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Any help is very much appreciated <span id="🙂">🙂</span><br>
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Vera<br>
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<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" class="elementToProof" face="Calibri, sans-serif" color="#000000"><b>From:</b> fieldtrip <fieldtrip-bounces@science.ru.nl> on behalf of fieldtrip-request@science.ru.nl <fieldtrip-request@science.ru.nl><br>
<b>Sent:</b> Friday, November 11, 2022 1:00 PM<br>
<b>To:</b> fieldtrip@science.ru.nl <fieldtrip@science.ru.nl><br>
<b>Subject:</b> fieldtrip Digest, Vol 144, Issue 5</font>
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<div class="PlainText elementToProof">Send fieldtrip mailing list submissions to<br>
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Today's Topics:<br>
<br>
1. some general questions about gamma-related analyses<br>
(Ivaylo Iotchev)<br>
2. Within/Between Cluster Analysis (Erica Flaten)<br>
3. group blocks with preprocessed data (Barbara Tsogli)<br>
4. Re: group blocks with preprocessed data (Xavier Vrijdag)<br>
5. Re: some general questions about gamma-related analyses<br>
(Tzvetan Popov)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Thu, 10 Nov 2022 12:05:34 +0100<br>
From: Ivaylo Iotchev <ivaylo.iotchev@gmail.com><br>
To: FieldTrip discussion list <fieldtrip@science.ru.nl><br>
Subject: [FieldTrip] some general questions about gamma-related<br>
analyses<br>
Message-ID:<br>
<CAO-ud34t1SzLgrGLyjJTH9TBrSW+Ln1xdPB--ZS-j0zB7HKMzQ@mail.gmail.com><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear all,<br>
<br>
I am fairly new to frequency-band analyses and have dealt mostly with<br>
transients (sleep spindles) so far. Thus forgive the maybe stupid<br>
questions, however, one on-point professional answer could spare me<br>
scavanging for parts across many unrelated papers.<br>
<br>
The whole of the gamma range expands well beyond 30 Hz, the noise<br>
threshold, and thus the first question is whether low-pass filtering below<br>
30 Hz is at all applied when looking for gamma coherence, power etc. ...<br>
One reason I kept the classical filter settings at first is to be<br>
consistent across the many different analyses I apply to the same data<br>
sets, not all of which have to do with gamma, but it dawned on me that<br>
filtering out frequencies above 30 is probably not a good idea(?) for<br>
gamma-related questions?<br>
<br>
Moreover, is it acceptable to look for the point of maximum coherence<br>
within that range, rather than average within the range? The data suggests<br>
that the point of maximum coherence shifts across time to higher and higher<br>
frequencies, thus I decided for the time being to report the maximum<br>
coherence (across electrodes) value within the gamma range.<br>
<br>
Let me know if there is any additional information I can provide to help<br>
you help me, best wishes and regards,<br>
<br>
Ivaylo Iotchev, PhD<br>
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Message: 2<br>
Date: Thu, 10 Nov 2022 15:38:04 +0000<br>
From: Erica Flaten <flatene@mcmaster.ca><br>
To: "fieldtrip@science.ru.nl" <fieldtrip@science.ru.nl><br>
Subject: [FieldTrip] Within/Between Cluster Analysis<br>
Message-ID:<br>
<YT2PR01MB82325F6A437A7189D87858B9B5019@YT2PR01MB8232.CANPRD01.PROD.OUTLOOK.COM><br>
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------------------------------<br>
<br>
Message: 3<br>
Date: Thu, 10 Nov 2022 19:51:04 +0000<br>
From: Barbara Tsogli <Barbara.Tsogli@uib.no><br>
To: "fieldtrip@science.ru.nl" <fieldtrip@science.ru.nl><br>
Subject: [FieldTrip] group blocks with preprocessed data<br>
Message-ID:<br>
<PAXPR01MB9219EA0EFE6FD14B0E1BBC9DEE019@PAXPR01MB9219.eurprd01.prod.exchangelabs.com><br>
<br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Dear FieltTripers, <br>
<br>
I was given some preprocessed EEG data in order to perform a Time-Frequency analysis. The experiment has 3 blocks (or sessions); therefore, for each subject, there are 3 different .mat files (Subj1_Block1.mat, Subj1_Block2.mat, Subj1_Block3.mat). Given that
we are not interested to consider the block as a factor in our statistical analysis, is there a way to group the 3 .mat files that represent the 3 blocks? in other words, is there a way to create a mat file that contains the information of the 3 blocks (i.e.:
Subj1_Block1to3.mat)?<br>
<br>
Thank you for your time in advance, <br>
Vera<br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 4<br>
Date: Thu, 10 Nov 2022 20:47:45 +0000<br>
From: Xavier Vrijdag <x.vrijdag@auckland.ac.nz><br>
To: FieldTrip discussion list <fieldtrip@science.ru.nl><br>
Subject: Re: [FieldTrip] group blocks with preprocessed data<br>
Message-ID: <ED515986-3152-4117-8CFF-2120F0F7FFC9@auckland.ac.nz><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hello Vera,<br>
<br>
If the .mat files contain fieldtrip data structures, you can use ft_appenddata to concatenate them into one data structure. You than can save that data structure into a new .mat file.<br>
<br>
Regards,<br>
<br>
Xavier<br>
<br>
Dr Xavier Vrijdag, MSc PhD<br>
<br>
Research fellow<br>
Department of Anaesthesiology │ School of Medicine<br>
Faculty of Medical & Health Sciences │ The University of Auckland<br>
Private Bag 92019 │ Auckland 1142 │ New Zealand<br>
<br>
M +64 21 0230 4558<br>
E x.vrijdag@auckland.ac.nz<mailto:x.vrijdag@auckland.ac.nz><br>
<br>
[FMHS Logo]<br>
<br>
<br>
<br>
<br>
From: fieldtrip <fieldtrip-bounces@science.ru.nl> on behalf of Barbara Tsogli via fieldtrip <fieldtrip@science.ru.nl><br>
Reply to: FieldTrip discussion list <fieldtrip@science.ru.nl><br>
Date: Friday, 11 November 2022 at 8:59 AM<br>
To: "fieldtrip@science.ru.nl" <fieldtrip@science.ru.nl><br>
Cc: Barbara Tsogli <Barbara.Tsogli@uib.no><br>
Subject: [FieldTrip] group blocks with preprocessed data<br>
<br>
Dear FieltTripers,<br>
<br>
I was given some preprocessed EEG data in order to perform a Time-Frequency analysis. The experiment has 3 blocks (or sessions); therefore, for each subject, there are 3 different .mat files (Subj1_Block1.mat, Subj1_Block2.mat, Subj1_Block3.mat). Given that
we are not interested to consider the block as a factor in our statistical analysis, is there a way to group the 3 .mat files that represent the 3 blocks? in other words, is there a way to create a mat file that contains the information of the 3 blocks (i.e.:
Subj1_Block1to3.mat)?<br>
<br>
Thank you for your time in advance,<br>
Vera<br>
<br>
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<a href="https://doi.org/10.1371/journal.pcbi.1002202<https://doi.org/10.1371/journal.pcbi.1002202>" data-auth="NotApplicable">https://doi.org/10.1371/journal.pcbi.1002202<https://doi.org/10.1371/journal.pcbi.1002202></a><br>
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Message: 5<br>
Date: Fri, 11 Nov 2022 09:39:08 +0100<br>
From: Tzvetan Popov <tzvetan.popov@uni-konstanz.de><br>
To: FieldTrip discussion list <fieldtrip@science.ru.nl><br>
Subject: Re: [FieldTrip] some general questions about gamma-related<br>
analyses<br>
Message-ID: <C996C864-719A-49C0-8F7A-43A8F5903DB3@uni-konstanz.de><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear Ivo,<br>
<br>
> The whole of the gamma range expands well beyond 30 Hz, the noise threshold, and thus the first question is whether low-pass filtering below 30 Hz is at all applied when looking for gamma coherence, power etc. ... One reason I kept the classical filter settings
at first is to be consistent across the many different analyses I apply to the same data sets, not all of which have to do with gamma, but it dawned on me that filtering out frequencies above 30 is probably not a good idea(?) for gamma-related questions?<br>
No, do not apply 30Hz LP. You filter out your signal of interest.<br>
> <br>
> Moreover, is it acceptable to look for the point of maximum coherence within that range, rather than average within the range? The data suggests that the point of maximum coherence shifts across time to higher and higher frequencies, thus I decided for the
time being to report the maximum coherence (across electrodes) value within the gamma range.<br>
One typically applies smoothening in the frequency domain when evaluating gamma (power and coherence). I suggest to study this lecture
<a href="https://www.youtube.com/watch?v=dHTuzMsjVJA" data-auth="NotApplicable">https://www.youtube.com/watch?v=dHTuzMsjVJA</a> <<a href="https://www.youtube.com/watch?v=dHTuzMsjVJA" data-auth="NotApplicable">https://www.youtube.com/watch?v=dHTuzMsjVJA</a>>.
In particular, at minute 25:49 the advantage of the freq smoothening is highlighted. Given that example your peak frequency will change depending on your decision how much to smooth.<br>
<br>
Of note, channel level coherence, particularly for gamma is not recommended. A lot of other stuff is added to the mix (e.g. cardiac, neck muscles etc.). Their contribution will change over time in your experiment. At the end you will not be able to interpret
the results and/or you might be fooled.<br>
I suggest you also study this lecture <a href="https://www.youtube.com/watch?v=ZBwh0Vm4fh4" data-auth="NotApplicable">
https://www.youtube.com/watch?v=ZBwh0Vm4fh4</a> <<a href="https://www.youtube.com/watch?v=ZBwh0Vm4fh4" data-auth="NotApplicable">https://www.youtube.com/watch?v=ZBwh0Vm4fh4</a>> and in particular the issues raised from minute 42:49 or so.<br>
<br>
Good luck<br>
Tzvetan<br>
<br>
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End of fieldtrip Digest, Vol 144, Issue 5<br>
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