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Hi Peter,
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<div class="">Apologies, I was a bit sloppy in my earlier code snippet. I think it should have read something like this</div>
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<div class="PlainText elementToProof">channellist = {‘channel1’;’channel2’;…’channelN’};</div>
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<div class="PlainText elementToProof">cfg = [];</div>
<div class="PlainText elementToProof">cfg.<someoptionsfor filtering etc><br class="">
for k = 1:numel(channellist)<br class="">
%% NOT THIS: cfg.channel = channellist{k}; % or something equivalent, at least instructing the reading function to grab a channel specific file</div>
<div class="PlainText elementToProof"> cfg.dataset = sprintf(‘%s.ncs’,channellist{k});<br class="">
data{k} = ft_preprocessing(cfg);<br class="">
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<div>If each channel is represented as a single file, ft_preprocessing needs to be instructed in each iteration of the loop with a fresh cfg.dataset</div>
<div>Once you have ‘appended’ the channels through ft_appenddata (note that this requires each of the channels' data structures to have the same number of samples) , you should be able to re-reference.</div>
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<div>I hope that this helps to get you on your way.</div>
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<div>Good luck,</div>
<div>Jan-Mathijs</div>
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<div class="">On 11 Apr 2023, at 22:30, Peter Kaskan via fieldtrip <<a href="mailto:fieldtrip@science.ru.nl" class="">fieldtrip@science.ru.nl</a>> wrote:</div>
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Hello Jan-Mathijs,<span class="Apple-converted-space"> </span><br class="">
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Thanks for the reply; I was traveling and just got back to this...</div>
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In my initial, very rudimentary preprocessing script, cfg.dataset will take a single neuralynx file:</div>
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<i class=""><span class=""> <span class="Apple-converted-space"> </span></span>cfg.dataset = 'CSC4.ncs';</i></div>
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<i class=""> cfg.continuous = 'yes';</i></div>
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<div class="ContentPasted1"><i class=""> highpass, lowlass, demean, detrend etc..</i></div>
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<i class=""> filtContData = ft_preprocessing(cfg);</i></div>
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<span class="ContentPasted2 ContentPasted0" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);">But the question was how to reference one channel with another.<span class="Apple-converted-space"> </span><br class="">
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<span class="ContentPasted2 ContentPasted0" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);">I<span class="Apple-converted-space"> </span></span>have been trying to implement your channellist
and appenddata suggestion as you describe (below) using channellist = {'CSC1.ncs'; 'CSC2.ncs'; 'CSC3.ncs'} and the subsequent data loop.<br class="">
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However, my initial attempt left some errors related to<span class="Apple-converted-space"> </span><br class="">
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<blockquote style="margin-top: 0px; margin-bottom: 0px;" class=""><i class="">Error using ft_checkconfig (line 163)</i>
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<div class="ContentPasted3"><i class="">The field cfg.datafile is required</i></div>
<div class="ContentPasted3"><i class="">The field cfg.headerfile is required</i></div>
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<div class="ContentPasted3"><i class="">Error in ft_preprocessing (line 385)</i></div>
<div class="ContentPasted3"><i class=""><span class=""> </span>cfg = ft_checkconfig(cfg, 'required', {'headerfile', 'datafile'});</i></div>
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After digging a little further in ft_preprocessing lines 446-447<br class="">
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<i class=""><span class="ContentPasted4" style="font-size: 10pt; font-family: Consolas; color: rgb(0, 128, 19);">% translate the channel groups (like 'all' and 'MEG') into real labels</span><span style="font-size: 10pt; font-family: Consolas;" class=""></span></i></div>
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<i class=""><span class="ContentPasted4" style="font-size: 10pt; font-family: Consolas;"> cfg.channel = ft_channelselection(cfg.channel, hdr);</span></i></div>
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<i class=""><span class="ContentPasted4" style="font-size: 10pt; font-family: Consolas;"> assert(~isempty(cfg.channel),<span class="Apple-converted-space"> </span><span class="ContentPasted4" style="color: rgb(167, 9, 245);">'the selection of channels is empty'</span>);</span></i></div>
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<span style="font-family: Calibri, Helvetica, sans-serif;" class="">... we rescued the error by resetting<span class="Apple-converted-space"> </span><br class="">
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<span class="ContentPasted5 ContentPasted4" style="font-size: 10pt; font-family: Consolas;"><i class="">cfg.channel = CSC1.ncs;</i></span></div>
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<span style="font-family: Calibri, Helvetica, sans-serif;" class="">Do you know what is happening? If we use: channellist = {'CSC1.ncs'; 'CSC2.ncs'; 'CSC3.ncs'}</span></div>
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does the cfg.datafile and cfg.headerfile need to be defined some other way?<br class="">
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Thanks, Peter</div>
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<font face="Calibri, sans-serif" style="font-size: 11pt;" class=""><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>Monday, March 27, 2023 6:00 AM<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 148, Issue 24</font>
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Today's Topics:<br class="">
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<div class="PlainText elementToProof">1. Re: re-referencing using neuralynx.csc channels<br class="">
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<div class="PlainText elementToProof"> (Schoffelen, J.M. (Jan Mathijs))<br class="">
<br class="">
Date: Mon, 27 Mar 2023 08:20:40 +0000<br class="">
From: "Schoffelen, J.M. (Jan Mathijs)"<br class="">
<<a href="mailto:janmathijs.schoffelen@donders.ru.nl" class="">janmathijs.schoffelen@donders.ru.nl</a>><br class="">
<br class="">
Hi Peter,<br class="">
<br class="">
ft_read_data is a so-called ‘intermediate’ level fieldtrip function and not typically called directly by the casual user.<br class="">
<br class="">
I think your use case calls for the following strategy:<br class="">
<br class="">
channellist = {‘channel1’;’channel2’;…’channelN’};<br class="">
for k = 1:numel(channellist)<br class="">
cfg.channel = channellist{k}; % or something equivalent, at least instructing the reading function to grab a channel specific file<br class="">
data{k} = ft_preprocessing(cfg);<br class="">
end<br class="">
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alldata = ft_appenddata([], data{:});<br class="">
<br class="">
Once you have the alldata object, you can apply re-referencing. Perhaps indeed this is best done by creating a ‘montage’, and apply it to the data.<br class="">
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Best wishes,<br class="">
<br class="">
Jan-Mathijs<br class="">
<br class="">
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On 23 Mar 2023, at 22:12, Peter Kaskan via fieldtrip <<a href="mailto:fieldtrip@science.ru.nl" class="">fieldtrip@science.ru.nl</a><<a href="mailto:fieldtrip@science.ru.nl" class="">mailto:fieldtrip@science.ru.nl</a>>> wrote:<br class="">
<br class="">
Hello,<br class="">
<br class="">
I am writing a ft_preprocessing script; I can give it channel1.csc and proceed with filtering, defining trials etc.<br class="">
<br class="">
...but, how do I re-reference to another channel?<br class="">
<br class="">
Is there a way to use ft_read_data to create a structure with all channels, and then tell it what channel I want to use as a reference?<br class="">
<br class="">
Or do I need to create a montage, and how do I do that with n #s of separate neuralynx.csc channels?<br class="">
<br class="">
<br class="">
<br class="">
Thanks - Peter<br class="">
<br class="">
<br class="">
Peter M. Kaskan, Ph.D.<br class="">
Assistant Professor<br class="">
Albert Einstein College of Medicine<br class="">
Leo M. Davidoff Department of Neurological Surgery<br class="">
1410 Pelham Parkway South<br class="">
Kennedy Center Room 429B<br class="">
Bronx, NY 10461<br class="">
<br class="">
phone: 718-430-2763<br class="">
_______________________________________________<br class="">
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<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; 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; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">fieldtrip
mailing list</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; 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; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" style="font-family: Helvetica; font-size: 14px; 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; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; 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; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<a href="https://urldefense.com/v3/__https://doi.org/10.1371/journal.pcbi.1002202__;!!HJOPV4FYYWzcc1jazlU!8H-lRU5w5rb--EVlbOiAf99N0XMGrhyk-fsQJ4BQw56I7POkez-dEqFrtQ9SJ4BnZTgBsuTZW_xvbhw4oCE_CdjMrPU0P11VRlXGfw$" style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">https://urldefense.com/v3/__https://doi.org/10.1371/journal.pcbi.1002202__;!!HJOPV4FYYWzcc1jazlU!8H-lRU5w5rb--EVlbOiAf99N0XMGrhyk-fsQJ4BQw56I7POkez-dEqFrtQ9SJ4BnZTgBsuTZW_xvbhw4oCE_CdjMrPU0P11VRlXGfw$</a><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; 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; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class=""></span></div>
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