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Hi Vera,
<div class=""><br class="">
</div>
<div class="">To be honest, the amount of relevant information you have providing us with so far, has been qualitatively a bit inferior, which leaves the readership of this list a bit ‘in the unknown’. We therefore, we can only randomly guess as to what the
best answer to your question would be. </div>
<div class=""><br class="">
</div>
<div class="">As Xavier mentioned in his earlier response in this thread provided “the .mat files contain fieldtrip data structures, you can use ft_appenddata to concatenate them into one data structure”.</div>
<div class="">In short, all of this starts with the valid assumption that the contents of the .mat files (note that the extension .mat just means that it the file most likely is a file that contains binary data that can be read by MATLAB, so nothing specific
to fieldtrip yet) are a valid FieldTrip data structure (<a href="https://www.fieldtriptoolbox.org/faq/how_are_the_various_data_structures_defined/" class="">https://www.fieldtriptoolbox.org/faq/how_are_the_various_data_structures_defined/</a>), more specifically
a data structure according to ft_datatype_raw (the first one in the list). In that sense, Xavier made a lucky guess and pointed you into the right direction. Keep them coming, those answers, Xavier!</div>
<div class="">
<div><br class="">
</div>
<div>Yet, reading the help section of ft_appenddata <a href="https://github.com/fieldtrip/fieldtrip/blob/master/ft_appenddata.m" class="">https://github.com/fieldtrip/fieldtrip/blob/master/ft_appenddata.m</a> it should be clear what can be expected from ft_appenddata.
Indeed, if the input data does not match along at least one of the dimensions of the input (i.e. same collection of trials with identical time axes, but collected with different sets of channels, or a collection of different trials collected with a set of
identical channels), then the function fails, as you report.</div>
<div><br class="">
</div>
<div>If your individual blocks have different channels, then you need to prune the data first such that all data objects contain only the intersection of the channels. If the aim is to combine across trials, it does not make sense to include channels for which
not all trials contain data. Selection of channels can be achieved with the ft_selectdata function.</div>
<div><br class="">
</div>
<div>Apart from this practical tip, I would however first consult the people who gave you the data, to get some understanding of why the data are incompatible across blocks, in order to avoid the risk of comparing apples with oranges. Also, it would be crucial
to understand and know about the processing steps that have been applied to the recorded data in order to create the mat-files on disk.</div>
<div><br class="">
</div>
<div>-Can it be assumed that the channels that have the same label across blocks were collected from the same position on the cap?</div>
<div>-Has any frequency filtering been applied? (not good for time-frequency analysis)</div>
<div>-What is the cause of the missing channels? Were those channels classified as ‘bad’? If so, why?</div>
<div>-Has any spatial filtering been applied? e.g. ICA followed by backprojection of identified components? -> in general not good if done per block</div>
<div>-...</div>
<div><br class="">
</div>
<div>Good luck,</div>
<div><br class="">
</div>
<div>Jan-Mathijs</div>
<div><br class="">
</div>
<div><br class="">
</div>
<div><br class="">
</div>
<div><br class="">
</div>
<div><br class="">
</div>
<div><br class="">
<blockquote type="cite" class="">
<div class="">On 11 Nov 2022, at 20:12, Barbara Tsogli via fieldtrip <<a href="mailto:fieldtrip@science.ru.nl" class="">fieldtrip@science.ru.nl</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
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Hello Xavier,<span class="Apple-converted-space"> </span><br class="">
</div>
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Thank you for your response. I have tried ft_appendata and here is the result:<br class="">
</div>
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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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Do you think a possible reason for this could be that the input datasets do not have the same number of trials or channels?<span class="Apple-converted-space"> </span><br class="">
</div>
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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 class="">
</div>
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Block 3: allData{2, 3} has 45 channels and 57 trials</div>
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<br class="">
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Is there any other way of doing this other than using the ft_appendata?<br class="">
</div>
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<br class="">
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Any help is very much appreciated<span class="Apple-converted-space"> </span><span id="🙂" class="">🙂</span><br class="">
</div>
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Vera<br class="">
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<font class="elementToProof" face="Calibri, sans-serif" style="font-size: 11pt;"><b class="">From:</b><span class="Apple-converted-space"> </span>fieldtrip <<a href="mailto:fieldtrip-bounces@science.ru.nl" class="">fieldtrip-bounces@science.ru.nl</a>> on behalf
of<span class="Apple-converted-space"> </span><a href="mailto:fieldtrip-request@science.ru.nl" class="">fieldtrip-request@science.ru.nl</a><span class="Apple-converted-space"> </span><<a href="mailto:fieldtrip-request@science.ru.nl" class="">fieldtrip-request@science.ru.nl</a>><br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>Friday, November 11, 2022 1:00 PM<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span><a href="mailto:fieldtrip@science.ru.nl" class="">fieldtrip@science.ru.nl</a><span class="Apple-converted-space"> </span><<a href="mailto:fieldtrip@science.ru.nl" class="">fieldtrip@science.ru.nl</a>><br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>fieldtrip Digest, Vol 144, Issue 5</font>
<div class=""> </div>
</div>
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To subscribe or unsubscribe via the World Wide Web, visit<br class="">
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or, via email, send a message with subject or body 'help' to<br class="">
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When replying, please edit your Subject line so it is more specific<br class="">
than "Re: Contents of fieldtrip digest..."<br class="">
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<br class="">
Today's Topics:<br class="">
<br class="">
1. some general questions about gamma-related analyses<br class="">
(Ivaylo Iotchev)<br class="">
2. Within/Between Cluster Analysis (Erica Flaten)<br class="">
3. group blocks with preprocessed data (Barbara Tsogli)<br class="">
4. Re: group blocks with preprocessed data (Xavier Vrijdag)<br class="">
5. Re: some general questions about gamma-related analyses<br class="">
(Tzvetan Popov)<br class="">
<br class="">
<br class="">
----------------------------------------------------------------------<br class="">
<br class="">
Message: 1<br class="">
Date: Thu, 10 Nov 2022 12:05:34 +0100<br class="">
From: Ivaylo Iotchev <<a href="mailto:ivaylo.iotchev@gmail.com" class="">ivaylo.iotchev@gmail.com</a>><br class="">
To: FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl" class="">fieldtrip@science.ru.nl</a>><br class="">
Subject: [FieldTrip] some general questions about gamma-related<br class="">
analyses<br class="">
Message-ID:<br class="">
<<a href="mailto:CAO-ud34t1SzLgrGLyjJTH9TBrSW+Ln1xdPB--ZS-j0zB7HKMzQ@mail.gmail.com" class="">CAO-ud34t1SzLgrGLyjJTH9TBrSW+Ln1xdPB--ZS-j0zB7HKMzQ@mail.gmail.com</a>><br class="">
Content-Type: text/plain; charset="utf-8"<br class="">
<br class="">
Dear all,<br class="">
<br class="">
I am fairly new to frequency-band analyses and have dealt mostly with<br class="">
transients (sleep spindles) so far. Thus forgive the maybe stupid<br class="">
questions, however, one on-point professional answer could spare me<br class="">
scavanging for parts across many unrelated papers.<br class="">
<br class="">
The whole of the gamma range expands well beyond 30 Hz, the noise<br class="">
threshold, and thus the first question is whether low-pass filtering below<br class="">
30 Hz is at all applied when looking for gamma coherence, power etc. ...<br class="">
One reason I kept the classical filter settings at first is to be<br class="">
consistent across the many different analyses I apply to the same data<br class="">
sets, not all of which have to do with gamma, but it dawned on me that<br class="">
filtering out frequencies above 30 is probably not a good idea(?) for<br class="">
gamma-related questions?<br class="">
<br class="">
Moreover, is it acceptable to look for the point of maximum coherence<br class="">
within that range, rather than average within the range? The data suggests<br class="">
that the point of maximum coherence shifts across time to higher and higher<br class="">
frequencies, thus I decided for the time being to report the maximum<br class="">
coherence (across electrodes) value within the gamma range.<br class="">
<br class="">
Let me know if there is any additional information I can provide to help<br class="">
you help me, best wishes and regards,<br class="">
<br class="">
Ivaylo Iotchev, PhD<br class="">
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Message: 2<br class="">
Date: Thu, 10 Nov 2022 15:38:04 +0000<br class="">
From: Erica Flaten <<a href="mailto:flatene@mcmaster.ca" class="">flatene@mcmaster.ca</a>><br class="">
To: "<a href="mailto:fieldtrip@science.ru.nl" class="">fieldtrip@science.ru.nl</a>" <<a href="mailto:fieldtrip@science.ru.nl" class="">fieldtrip@science.ru.nl</a>><br class="">
Subject: [FieldTrip] Within/Between Cluster Analysis<br class="">
Message-ID:<br class="">
<<a href="mailto:YT2PR01MB82325F6A437A7189D87858B9B5019@YT2PR01MB8232.CANPRD01.PROD.OUTLOOK.COM" class="">YT2PR01MB82325F6A437A7189D87858B9B5019@YT2PR01MB8232.CANPRD01.PROD.OUTLOOK.COM</a>><br class="">
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<br class="">
Message: 3<br class="">
Date: Thu, 10 Nov 2022 19:51:04 +0000<br class="">
From: Barbara Tsogli <<a href="mailto:Barbara.Tsogli@uib.no" class="">Barbara.Tsogli@uib.no</a>><br class="">
To: "<a href="mailto:fieldtrip@science.ru.nl" class="">fieldtrip@science.ru.nl</a>" <<a href="mailto:fieldtrip@science.ru.nl" class="">fieldtrip@science.ru.nl</a>><br class="">
Subject: [FieldTrip] group blocks with preprocessed data<br class="">
Message-ID:<br class="">
<<a href="mailto:PAXPR01MB9219EA0EFE6FD14B0E1BBC9DEE019@PAXPR01MB9219.eurprd01.prod.exchangelabs.com" class="">PAXPR01MB9219EA0EFE6FD14B0E1BBC9DEE019@PAXPR01MB9219.eurprd01.prod.exchangelabs.com</a>><br class="">
<span class="Apple-converted-space"> </span><br class="">
Content-Type: text/plain; charset="iso-8859-1"<br class="">
<br class="">
Dear FieltTripers,<span class="Apple-converted-space"> </span><br class="">
<br class="">
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 class="">
<br class="">
Thank you for your time in advance,<span class="Apple-converted-space"> </span><br class="">
Vera<br class="">
<br class="">
<br class="">
<br class="">
------------------------------<br class="">
<br class="">
Message: 4<br class="">
Date: Thu, 10 Nov 2022 20:47:45 +0000<br class="">
From: Xavier Vrijdag <<a href="mailto:x.vrijdag@auckland.ac.nz" class="">x.vrijdag@auckland.ac.nz</a>><br class="">
To: FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl" class="">fieldtrip@science.ru.nl</a>><br class="">
Subject: Re: [FieldTrip] group blocks with preprocessed data<br class="">
Message-ID: <<a href="mailto:ED515986-3152-4117-8CFF-2120F0F7FFC9@auckland.ac.nz" class="">ED515986-3152-4117-8CFF-2120F0F7FFC9@auckland.ac.nz</a>><br class="">
Content-Type: text/plain; charset="utf-8"<br class="">
<br class="">
Hello Vera,<br class="">
<br class="">
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 class="">
<br class="">
Regards,<br class="">
<br class="">
Xavier<br class="">
<br class="">
Dr Xavier Vrijdag, MSc PhD<br class="">
<br class="">
Research fellow<br class="">
Department of Anaesthesiology │ School of Medicine<br class="">
Faculty of Medical & Health Sciences │ The University of Auckland<br class="">
Private Bag 92019 │ Auckland 1142 │ New Zealand<br class="">
<br class="">
M +64 21 0230 4558<br class="">
E<span class="Apple-converted-space"> </span><a href="mailto:x.vrijdag@auckland.ac.nz" class="">x.vrijdag@auckland.ac.nz</a><<a href="mailto:x.vrijdag@auckland.ac.nz" class="">mailto:x.vrijdag@auckland.ac.nz</a>><br class="">
<br class="">
[FMHS Logo]<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
From: fieldtrip <<a href="mailto:fieldtrip-bounces@science.ru.nl" class="">fieldtrip-bounces@science.ru.nl</a>> on behalf of Barbara Tsogli via fieldtrip <<a href="mailto:fieldtrip@science.ru.nl" class="">fieldtrip@science.ru.nl</a>><br class="">
Reply to: FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl" class="">fieldtrip@science.ru.nl</a>><br class="">
Date: Friday, 11 November 2022 at 8:59 AM<br class="">
To: "<a href="mailto:fieldtrip@science.ru.nl" class="">fieldtrip@science.ru.nl</a>" <<a href="mailto:fieldtrip@science.ru.nl" class="">fieldtrip@science.ru.nl</a>><br class="">
Cc: Barbara Tsogli <<a href="mailto:Barbara.Tsogli@uib.no" class="">Barbara.Tsogli@uib.no</a>><br class="">
Subject: [FieldTrip] group blocks with preprocessed data<br class="">
<br class="">
Dear FieltTripers,<br class="">
<br class="">
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 class="">
<br class="">
Thank you for your time in advance,<br class="">
Vera<br class="">
<br class="">
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<a href="https://urldefense.com/v3/__https://doi.org/10.1371/journal.pcbi.1002202*3Chttps:/*doi.org/10.1371/journal.pcbi.1002202*3E__;JS8l!!HJOPV4FYYWzcc1jazlU!6GId_Hulr8-Sb9Hre-1ZSkNuE_E7behI0w_V59XmmbJ-EelRQG8DTFdyJ_j14uzbRU2KvIjv3r41LcaaZaDX6CPEORuXdhQoDMMC3Q$" data-auth="NotApplicable" class="">https://doi.org/10.1371/journal.pcbi.1002202<https://doi.org/10.1371/journal.pcbi.1002202></a><br class="">
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Message: 5<br class="">
Date: Fri, 11 Nov 2022 09:39:08 +0100<br class="">
From: Tzvetan Popov <<a href="mailto:tzvetan.popov@uni-konstanz.de" class="">tzvetan.popov@uni-konstanz.de</a>><br class="">
To: FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl" class="">fieldtrip@science.ru.nl</a>><br class="">
Subject: Re: [FieldTrip] some general questions about gamma-related<br class="">
analyses<br class="">
Message-ID: <<a href="mailto:C996C864-719A-49C0-8F7A-43A8F5903DB3@uni-konstanz.de" class="">C996C864-719A-49C0-8F7A-43A8F5903DB3@uni-konstanz.de</a>><br class="">
Content-Type: text/plain; charset="utf-8"<br class="">
<br class="">
Dear Ivo,<br class="">
<br class="">
> 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 class="">
No, do not apply 30Hz LP. You filter out your signal of interest.<br class="">
><span class="Apple-converted-space"> </span><br class="">
> 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 class="">
One typically applies smoothening in the frequency domain when evaluating gamma (power and coherence). I suggest to study this lecture<span class="Apple-converted-space"> </span><a href="https://urldefense.com/v3/__https://www.youtube.com/watch?v=dHTuzMsjVJA__;!!HJOPV4FYYWzcc1jazlU!6GId_Hulr8-Sb9Hre-1ZSkNuE_E7behI0w_V59XmmbJ-EelRQG8DTFdyJ_j14uzbRU2KvIjv3r41LcaaZaDX6CPEORuXdhRmJKagdA$" data-auth="NotApplicable" class="">https://www.youtube.com/watch?v=dHTuzMsjVJA</a><<a href="https://urldefense.com/v3/__https://www.youtube.com/watch?v=dHTuzMsjVJA__;!!HJOPV4FYYWzcc1jazlU!6GId_Hulr8-Sb9Hre-1ZSkNuE_E7behI0w_V59XmmbJ-EelRQG8DTFdyJ_j14uzbRU2KvIjv3r41LcaaZaDX6CPEORuXdhRmJKagdA$" data-auth="NotApplicable" class="">https://www.youtube.com/watch?v=dHTuzMsjVJA</a>>.
In particular, at minute 25:49 the advantage of the freq smoothening is highlighted. Given that example your peak frequency will change depending on your decision how much to smooth.<br class="">
<br class="">
Of note, channel level coherence, particularly for gamma is not recommended. A lot of other stuff is added to the mix (e.g. cardiac, neck muscles etc.). Their contribution will change over time in your experiment. At the end you will not be able to interpret
the results and/or you might be fooled.<br class="">
I suggest you also study this lecture<span class="Apple-converted-space"> </span><a href="https://urldefense.com/v3/__https://www.youtube.com/watch?v=ZBwh0Vm4fh4__;!!HJOPV4FYYWzcc1jazlU!6GId_Hulr8-Sb9Hre-1ZSkNuE_E7behI0w_V59XmmbJ-EelRQG8DTFdyJ_j14uzbRU2KvIjv3r41LcaaZaDX6CPEORuXdhR10amViA$" data-auth="NotApplicable" class="">https://www.youtube.com/watch?v=ZBwh0Vm4fh4</a><<a href="https://urldefense.com/v3/__https://www.youtube.com/watch?v=ZBwh0Vm4fh4__;!!HJOPV4FYYWzcc1jazlU!6GId_Hulr8-Sb9Hre-1ZSkNuE_E7behI0w_V59XmmbJ-EelRQG8DTFdyJ_j14uzbRU2KvIjv3r41LcaaZaDX6CPEORuXdhR10amViA$" data-auth="NotApplicable" class="">https://www.youtube.com/watch?v=ZBwh0Vm4fh4</a>>
and in particular the issues raised from minute 42:49 or so.<br class="">
<br class="">
Good luck<br class="">
Tzvetan<br class="">
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<a href="https://urldefense.com/v3/__https://doi.org/10.1371/journal.pcbi.1002202__;!!HJOPV4FYYWzcc1jazlU!6GId_Hulr8-Sb9Hre-1ZSkNuE_E7behI0w_V59XmmbJ-EelRQG8DTFdyJ_j14uzbRU2KvIjv3r41LcaaZaDX6CPEORuXdhTCvoxIBQ$" data-auth="NotApplicable" class="">https://doi.org/10.1371/journal.pcbi.1002202</a><br class="">
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End of fieldtrip Digest, Vol 144, Issue 5<br class="">
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