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Dear Herbert,
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<div class="">I have unsubscribed you. To all, note that you can manage your subscription yourself on the listservers interface, which can be reached through <a href="http://www.fieldtriptoolbox.org/discussion_list" class="">http://www.fieldtriptoolbox.org/discussion_list</a> (following
the first link therein).</div>
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<div class="">Best wishes,</div>
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<div class="">Jan-Mathijs Schoffelen</div>
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<div class="">On 31 Jul 2018, at 15:37, Herbert J Gould (hgould) <<a href="mailto:hgould@memphis.edu" class="">hgould@memphis.edu</a>> wrote:</div>
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Please eliminate me from the mailing list. I have retired. </div>
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Thank you.</div>
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<div style="font-size: 9px; color: rgb(87, 87, 87);" class="">Sent from my Verizon Wireless 4G LTE smartphone</div>
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-------- Original message --------</div>
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From: "Jörn M. Horschig"</div>
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Date:07/31/2018 2:18 AM (GMT-06:00)</div>
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To: 'FieldTrip discussion list'</div>
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Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data</div>
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Hi Sunny,</div>
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Thanks for sending the data. As discussed offline, there are no events in these data. You can also verify this using fieldtrip by running this code:</div>
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<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span style="font-family: 'Courier New';" class="">>> cfg = [];</span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span style="font-family: 'Courier New';" class="">>> cfg.dataset = 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3';</span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span style="font-family: 'Courier New';" class="">>> cfg.trialdef.eventtype = '?';</span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span style="font-family: 'Courier New';" class="">>> ft_definetrial(cfg);</span></div>
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</p>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
The output will be:</div>
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<i class=""><span style="font-family: 'Courier New';" class="">Warning: no trialfun was specified, using ft_trialfun_general</span></i></div>
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<i class=""><span style="font-family: 'Courier New';" class=""> In ft_definetrial at line 138</span></i></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<i class=""><span style="font-family: 'Courier New';" class=""> </span></i></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<i class=""><span style="font-family: 'Courier New';" class="">evaluating trialfunction 'ft_trialfun_general'</span></i></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<i class=""><span style="font-family: 'Courier New';" class="">reading the header from 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3'</span></i></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<i class=""><span style="font-family: 'Courier New';" class="">reading the events from 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3'</span></i></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<i class=""><span style="font-family: 'Courier New';" class="">the following events were found in the datafile</span></i></div>
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<i class=""><span style="font-family: 'Courier New';" class="">event type: 'ADC001'</span></i></div>
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<i class=""><span style="font-family: 'Courier New';" class="">with event values: 1.5</span></i></div>
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<i class=""><span style="font-family: 'Courier New';" class=""> </span></i></div>
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<i class=""><span style="font-family: 'Courier New';" class="">no trials have been defined yet, see FT_DEFINETRIAL for further help</span></i></div>
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<i class=""><span style="font-family: 'Courier New';" class="">found 1 events</span></i></div>
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<i class=""><span style="font-family: 'Courier New';" class="">created 0 trials</span></i></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<i class=""><span style="font-family: 'Courier New';" class="">the call to "ft_definetrial" took 1 seconds</span></i></div>
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The found event corresponds to the individual values of the AD channel, which in this case is the battery level (so not very useful for you right now).</div>
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You can still read in the oxy3-data running this code:</div>
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<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span style="font-size: 10pt; font-family: 'Courier New';" class="">>> cfg = [];</span><span style="font-size: 12pt; font-family: 'Courier New';" class=""></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class="">>> cfg.dataset =<span class="Apple-converted-space"> </span></span><span style="font-size: 10pt; font-family: 'Courier New'; color: rgb(160, 32, 240);" class="">'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3'</span><span style="font-size: 10pt; font-family: 'Courier New';" class="">;</span><span style="font-size: 12pt; font-family: 'Courier New';" class=""></span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span style="font-size: 10pt; font-family: 'Courier New';" class="">>> data = ft_preprocessing(cfg);</span><span style="font-size: 12pt; font-family: 'Courier New';" class=""></span></div>
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</p>
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</p>
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The output will be:</div>
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<i class=""><span style="font-family: 'Courier New';" class="">processing channel { 'Rx1-Tx1 [839nm]' 'Rx1-Tx1 [757nm]' 'Rx1-Tx2 [839nm]' 'Rx1-Tx2 [757nm]' 'Rx1-Tx3 [839nm]' 'Rx1-Tx3 [757nm]' 'Rx1-Tx4 [839nm]' 'Rx1-Tx4 [757nm]' 'Rx2-Tx5 [839nm]' 'Rx2-Tx5 [757nm]'
'Rx2-Tx6 [839nm]' 'Rx2-Tx6 [757nm]' 'Rx2-Tx7 [839nm]' 'Rx2-Tx7 [757nm]' 'Rx2-Tx8 [839nm]' 'Rx2-Tx8 [757nm]' 'ADC001' }</span></i></div>
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<i class=""><span style="font-family: 'Courier New';" class="">reading and preprocessing</span></i></div>
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<i class=""><span style="font-family: 'Courier New';" class="">reading and preprocessing trial 1 from 1</span></i></div>
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<i class=""><span style="font-family: 'Courier New';" class=""> </span></i></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<i class=""><span style="font-family: 'Courier New';" class="">the call to "ft_preprocessing" took 2 seconds</span></i></div>
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<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
You also sent another data file with events. The rationale here is equivalent to above. First, check the data for events:</div>
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<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span style="font-size: 10pt; font-family: 'Courier New';" class="">>> cfg = [];</span><span style="font-size: 12pt; font-family: 'Courier New';" class=""></span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span style="font-size: 10pt; font-family: 'Courier New';" class="">>> cfg.dataset =<span class="Apple-converted-space"> </span></span><span style="font-size: 10pt; font-family: 'Courier New'; color: rgb(160, 32, 240);" class="">'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3'</span><span style="font-size: 10pt; font-family: 'Courier New';" class="">;</span><span style="font-size: 12pt; font-family: 'Courier New';" class=""></span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span style="font-size: 10pt; font-family: 'Courier New';" class="">>> cfg.trialdef.eventtype =<span class="Apple-converted-space"> </span></span><span style="font-size: 10pt; font-family: 'Courier New'; color: rgb(160, 32, 240);" class="">'?'</span><span style="font-size: 10pt; font-family: 'Courier New';" class="">;</span><span style="font-size: 12pt; font-family: 'Courier New';" class=""></span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span style="font-size: 10pt; font-family: 'Courier New';" class="">>> ft_definetrial(cfg);</span><span style="font-size: 12pt; font-family: 'Courier New';" class=""></span></div>
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</p>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
With the output being:</div>
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</p>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<i class=""><span style="font-family: 'Courier New';" class="">evaluating trialfunction 'ft_trialfun_general'</span></i></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<i class=""><span style="font-family: 'Courier New';" class="">reading the header from 'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3'</span></i></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<i class=""><span style="font-family: 'Courier New';" class="">reading the events from 'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3'</span></i></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<i class=""><span style="font-family: 'Courier New';" class="">the following events were found in the datafile</span></i></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<i class=""><span style="font-family: 'Courier New';" class="">event type: 'ADC001'</span></i></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<i class=""><span style="font-family: 'Courier New';" class="">with event values: 1.4</span></i></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<i class=""><span style="font-family: 'Courier New';" class=""> </span></i></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<i class=""><span style="font-family: 'Courier New';" class="">event type: 'event'</span></i></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<i class=""><span style="font-family: 'Courier New';" class="">with event values: 'A' 'B' 'C' 'D'</span></i></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<i class=""><span style="font-family: 'Courier New';" class=""> </span></i></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<i class=""><span style="font-family: 'Courier New';" class="">no trials have been defined yet, see FT_DEFINETRIAL for further help</span></i></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<i class=""><span style="font-family: 'Courier New';" class="">found 5 events</span></i></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<i class=""><span style="font-family: 'Courier New';" class="">created 0 trials</span></i></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<i class=""><span style="font-family: 'Courier New';" class="">the call to "ft_definetrial" took 3 seconds</span></i></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<i class=""><span style="font-family: 'Courier New';" class=""> </span></i></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<i class=""> </i></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
I am not sure what your events mean, but you are then able to define trials according to these events, e.g.<span style="font-family: 'Courier New';" class=""></span></div>
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<span style="font-family: 'Courier New';" class=""> </span></p>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span style="font-size: 10pt; font-family: 'Courier New';" class="">>> cfg.trialdef.eventtype =<span class="Apple-converted-space"> </span></span><span style="font-size: 10pt; font-family: 'Courier New'; color: rgb(160, 32, 240);" class="">'event'</span><span style="font-size: 10pt; font-family: 'Courier New';" class="">;</span><span style="font-size: 12pt; font-family: 'Courier New';" class=""></span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span style="font-size: 10pt; font-family: 'Courier New';" class="">>> cfg.trialdef.eventvalue =<span class="Apple-converted-space"> </span></span><span style="font-size: 10pt; font-family: 'Courier New'; color: rgb(160, 32, 240);" class="">'B'</span><span style="font-size: 10pt; font-family: 'Courier New';" class="">;</span><span style="font-size: 12pt; font-family: 'Courier New';" class=""></span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span style="font-size: 10pt; font-family: 'Courier New';" class="">>> cfg.trialdef.prestim = 5;</span><span style="font-size: 12pt; font-family: 'Courier New';" class=""></span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span style="font-size: 10pt; font-family: 'Courier New';" class="">>> cfg.trialdef.prestim = 35;</span><span style="font-size: 12pt; font-family: 'Courier New';" class=""></span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span style="font-size: 10pt; font-family: 'Courier New';" class="">>> cfg = ft_definetrial(cfg);</span><span style="font-size: 12pt; font-family: 'Courier New';" class=""></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class=""> </span></p>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span style="" class="">This would create a trial definition for event B, starting 5 second before event B ending 35 seconds after event B. Reading in the data would then go via:</span></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class=""></span><span style="font-size: 12pt; font-family: 'Courier New';" class=""></span></p>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span style="font-size: 10pt; font-family: 'Courier New';" class="">>> data = ft_preprocessing(cfg);</span><span style="font-size: 12pt; font-family: 'Courier New';" class=""></span></div>
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<span style="font-family: 'Courier New';" class=""> </span></p>
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The usage is 100% equivalent to standard FieldTrip conventions, so you can follow any tutorial on the FieldTrip wiki and try it with your NIRS data (but keep the fundamental difference between EEG and fNIRS in mind). I hope this helps to get started!</div>
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Btw, if someone wants to do a combined EEG-fNIRS analysis using FieldTrip, give me a shout.</div>
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With best regards,</div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
Jörn</div>
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<b class=""><span style="font-size: 9pt; font-family: Verdana, sans-serif;" class="">--<span style="color: rgb(37, 90, 158);" class=""><br class="">
Jörn M. Horschig, PhD</span></span></b><span style="font-size: 9pt; font-family: Verdana, sans-serif; color: rgb(98, 98, 100);" class="">, Project Leader & Software Engineer<br class="">
<a href="http://www.artinis.com/" target="_blank" style="color: purple; text-decoration: underline;" class=""><span style="color: rgb(98, 98, 100);" class="">Artinis Medical Systems</span></a> | +31 481 350 980</span></div>
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up for our NIRS newsletter</a></span><span style="font-size: 13.5pt;" class=""></span></div>
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<b class="">From:</b><span class="Apple-converted-space"> </span>fieldtrip <<a href="mailto:fieldtrip-bounces@science.ru.nl" style="color: purple; text-decoration: underline;" class="">fieldtrip-bounces@science.ru.nl</a>><span class="Apple-converted-space"> </span><b class="">On
Behalf Of<span class="Apple-converted-space"> </span></b>Jörn M. Horschig<br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>Monday, July 30, 2018 15:42<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span>'FieldTrip discussion list' <<a href="mailto:fieldtrip@science.ru.nl" style="color: purple; text-decoration: underline;" class="">fieldtrip@science.ru.nl</a>><br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data</div>
</div>
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Hi Sunny,</div>
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The ADC channels in the tutorial are used as a trigger-channel. I am not sure how you insert the triggers in your experiment, but the Octamon has no direct trigger input (you could add triggers either wirelessly using a PortaSync or directly from within Oxysoft).
The ADC of the Octamon is the battery level and not a trigger input. Depending on what you did, you have to follow different processing steps. If you let me know more about the events and triggers, I can let you know what to do (you could also send me some
example data and I will send you an example script back that reads in the data in FieldTrip).</div>
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With best regards,</div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
Jörn</div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<b class=""><span style="font-size: 9pt; font-family: Verdana, sans-serif;" class="">--<span style="color: rgb(37, 90, 158);" class=""><br class="">
Jörn M. Horschig, PhD</span></span></b><span style="font-size: 9pt; font-family: Verdana, sans-serif; color: rgb(98, 98, 100);" class="">, Project Leader & Software Engineer<br class="">
<a href="http://www.artinis.com/" target="_blank" style="color: purple; text-decoration: underline;" class=""><span style="color: rgb(98, 98, 100);" class="">Artinis Medical Systems</span></a> | +31 481 350 980</span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span style="font-size: 9pt; font-family: Verdana, sans-serif; color: rgb(31, 73, 125);" class=""><a href="http://artinis.us3.list-manage1.com/subscribe?u=6bef931b76193f0e3d1dfe654&id=550bfdab46" style="color: purple; text-decoration: underline;" class="">Sign
up for our NIRS newsletter</a></span><span style="font-size: 13.5pt;" class=""></span></div>
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<b class="">From:</b><span class="Apple-converted-space"> </span>Sunny p <<a href="mailto:sunnypitt1965@gmail.com" style="color: purple; text-decoration: underline;" class="">sunnypitt1965@gmail.com</a>><span class="Apple-converted-space"> </span><br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>Monday, July 30, 2018 15:29<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span>FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl" style="color: purple; text-decoration: underline;" class="">fieldtrip@science.ru.nl</a>>;<span class="Apple-converted-space"> </span><a href="mailto:jorn@artinis.com" style="color: purple; text-decoration: underline;" class="">jorn@artinis.com</a><br class="">
<b class="">Cc:</b><span class="Apple-converted-space"> </span>Arana, S.L. (Sophie) <<a href="mailto:S.Arana@donders.ru.nl" style="color: purple; text-decoration: underline;" class="">S.Arana@donders.ru.nl</a>><br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data</div>
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Hello Jorn,</div>
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Thanks a lot for your response. I am working with Octamon data (4*2 Channel). I am trying to visualize the data using topo plot on head based image following <a href="http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel#epoch" style="color: purple; text-decoration: underline;" class="">http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel#epoch</a><span class="Apple-converted-space"> </span>(nirs
multi channel tutorial based on Oxymon which has 48 channel). I am wondering what parameter changes should I make to get the data for OCTAMON visualization as my data has only ADC001 and there is no ADC002 in data for epoch section. As I am not an NIRS expert,
its difficult to figure out which parameters gives me the visualization as its throwing errors when following the tutorial.</div>
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Thanks for your understanding and support.</div>
</div>
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Best Regards,</div>
</div>
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Sunny</div>
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On Mon, Jul 30, 2018 at 2:47 AM, Jörn M. Horschig <<a href="mailto:jorn@artinis.com" target="_blank" style="color: purple; text-decoration: underline;" class="">jorn@artinis.com</a>> wrote:</div>
<blockquote style="border-style: none none none solid; border-left-width: 1pt; border-left-color: rgb(204, 204, 204); padding: 0in 0in 0in 6pt; margin: 5pt 0in 5pt 4.8pt;" class="">
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Hi Sunny,</div>
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Yes, the FieldTrip NIRS plugin works for all our devices.</div>
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With best regards,</div>
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Jörn</div>
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<b class=""><span style="font-size: 9pt; font-family: Verdana, sans-serif;" class="">--<span style="color: rgb(37, 90, 158);" class=""><br class="">
Jörn M. Horschig, PhD</span></span></b><span style="font-size: 9pt; font-family: Verdana, sans-serif; color: rgb(98, 98, 100);" class="">, Project Leader & Software Engineer<br class="">
<a href="http://www.artinis.com/" target="_blank" style="color: purple; text-decoration: underline;" class=""><span style="color: rgb(98, 98, 100);" class="">Artinis Medical Systems</span></a> | +31 481 350 980</span></div>
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<span style="font-size: 9pt; font-family: Verdana, sans-serif; color: rgb(31, 73, 125);" class=""><a href="http://artinis.us3.list-manage1.com/subscribe?u=6bef931b76193f0e3d1dfe654&id=550bfdab46" target="_blank" style="color: purple; text-decoration: underline;" class="">Sign
up for our NIRS newsletter</a></span></div>
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<b class="">From:</b><span class="Apple-converted-space"> </span>fieldtrip <<a href="mailto:fieldtrip-bounces@science.ru.nl" target="_blank" style="color: purple; text-decoration: underline;" class="">fieldtrip-bounces@science.ru.nl</a>><span class="Apple-converted-space"> </span><b class="">On
Behalf Of<span class="Apple-converted-space"> </span></b>Sunny p<br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>Friday, July 27, 2018 20:41<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span>Arana, S.L. (Sophie) <<a href="mailto:S.Arana@donders.ru.nl" target="_blank" style="color: purple; text-decoration: underline;" class="">S.Arana@donders.ru.nl</a>><br class="">
<b class="">Cc:</b><span class="Apple-converted-space"> </span>FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl" target="_blank" style="color: purple; text-decoration: underline;" class="">fieldtrip@science.ru.nl</a>><br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data</div>
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Hello Sophie,</div>
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Once this tutorial is fully developed, Can we use this for OCTAMON (<a href="https://www.artinis.com/octamon/" target="_blank" style="color: purple; text-decoration: underline;" class="">https://www.artinis.com/octamon/</a>) ?</div>
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Thanks for your understanding and support.</div>
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Best Regards,</div>
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Sunny</div>
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On Wed, Jul 25, 2018 at 12:35 PM, Sunny p <<a href="mailto:sunnypitt1965@gmail.com" target="_blank" style="color: purple; text-decoration: underline;" class="">sunnypitt1965@gmail.com</a>> wrote:</div>
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Hello Sophie,</div>
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Thanks a lot for providing this code. I am making some changes that are useful. Can you please inform what is the variable 'data_func' in the code relates to. This is the last undefined variable in code.</div>
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Thanks for your understanding and support.</div>
</div>
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Best Regards,</div>
</div>
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<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
Sunny</div>
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On Wed, Jul 25, 2018 at 8:22 AM, Sunny p <<a href="mailto:sunnypitt1965@gmail.com" target="_blank" style="color: purple; text-decoration: underline;" class="">sunnypitt1965@gmail.com</a>> wrote:</div>
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Hello Sophie,</div>
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Thanks a lot for your clarification. This is very useful.</div>
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<span style="color: rgb(136, 136, 136);" class=""> </span></p>
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<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span class="m5783873371524165625m2638943381933682025hoenzb"><span style="color: rgb(136, 136, 136);" class="">Sunny</span></span></div>
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<br class="">
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On Wednesday, July 25, 2018, Arana, S.L. (Sophie) <<a href="mailto:S.Arana@donders.ru.nl" target="_blank" style="color: purple; text-decoration: underline;" class="">S.Arana@donders.ru.nl</a>> wrote:</div>
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<span style="font-size: 10pt; font-family: Tahoma, sans-serif;" class="">Dear Sunny,</span></div>
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<span style="font-size: 10pt; font-family: Tahoma, sans-serif;" class="">the multi-channel NIRS data tutorial is currently under construction and will hopefully be fully available in a couple of weeks. Until then, there might still be some inconsistencies such
as the one you have encountered.</span></div>
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<span style="font-size: 10pt; font-family: Tahoma, sans-serif;" class="">The variable you refer to is indeed missing. It refers to a filtered version of the data, and you can created it by running the following code before the epoching.</span></div>
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<div style="margin: 0in 0in 0.0001pt; text-align: justify;" class=""><span style="font-size: 10pt; font-family: Courier;" class="">cfg = [];</span></div>
<div style="margin: 0in 0in 0.0001pt; text-align: justify;" class=""><span style="font-size: 10pt; font-family: Courier;" class="">cfg.hpfilter = 'yes';</span></div>
<div style="margin: 0in 0in 0.0001pt; text-align: justify;" class=""><span style="font-size: 10pt; font-family: Courier;" class="">cfg.hpfreq = 0.01;</span></div>
<div style="margin: 0in 0in 0.0001pt; text-align: justify;" class=""><span style="font-size: 10pt; font-family: Courier;" class="">data_flt = ft_preprocessing(cfg,data_down);</span></div>
<p style="margin: 0in 0in 0.0001pt; text-align: justify;" class=""><span style="font-size: 10pt; font-family: Tahoma, sans-serif;" class=""> </span></p>
<div style="margin: 0in 0in 0.0001pt; text-align: justify;" class=""><span style="font-size: 10pt; font-family: Tahoma, sans-serif;" class="">This should help you to continue with the tutorial, but please do keep in mind that we are currently working on it
and you might encounter some other inconsistencies still later on.</span></div>
<p style="margin: 0in 0in 0.0001pt; text-align: justify;" class=""><span style="font-size: 10pt; font-family: Tahoma, sans-serif;" class=""> </span></p>
<div style="margin: 0in 0in 0.0001pt; text-align: justify;" class=""><span style="font-size: 10pt; font-family: Tahoma, sans-serif;" class="">Best,</span></div>
<div style="margin: 0in 0in 0.0001pt; text-align: justify;" class=""><span style="font-size: 10pt; font-family: Tahoma, sans-serif;" class="">Sophie</span></div>
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<b class=""><span style="font-size: 10pt; font-family: Tahoma, sans-serif;" class="">From:</span></b><span style="font-size: 10pt; font-family: Tahoma, sans-serif;" class=""><span class="Apple-converted-space"> </span>fieldtrip [<a href="mailto:fieldtrip-bounces@science.ru.nl" target="_blank" style="color: purple; text-decoration: underline;" class="">fieldtrip-bounces@science.ru.nl</a>]
on behalf of Sunny p [<a href="mailto:sunnypitt1965@gmail.com" target="_blank" style="color: purple; text-decoration: underline;" class="">sunnypitt1965@gmail.com</a>]<br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>Tuesday, July 24, 2018 9:24 PM<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span><a href="mailto:fieldtrip@science.ru.nl" target="_blank" style="color: purple; text-decoration: underline;" class="">fieldtrip@science.ru.nl</a><br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>[FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data</span></p>
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<span style="font-size: 9.5pt; font-family: 'Times New Roman', serif;" class="">Hello All Good Day,</span><span style="font-size: 12pt; font-family: 'Times New Roman', serif;" class=""></span></div>
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<span style="font-size: 9.5pt; font-family: 'Times New Roman', serif;" class="">Hope you are doing fine,</span></div>
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<span style="font-size: 9.5pt; font-family: 'Times New Roman', serif;" class="">Thanks a lot for providing with fieldtrip which is really useful to analyze fNIRS data. I have an issue in the "Preprocessing and averaging of multi-channel NIRS data" tutorial.
Can you please help me with this issue?</span></div>
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<span style="font-size: 9.5pt; font-family: 'Times New Roman', serif;" class="">Issue: In the "</span><span style="font-size: 12pt; font-family: 'Times New Roman', serif; background-color: white;" class="">Preprocessing and averaging of multi-channel NIRS
data" tutorial " <a href="http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel" target="_blank" style="color: purple; text-decoration: underline;" class=""><span style="color: rgb(17, 85, 204);" class="">http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel</span></a></span></div>
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<span style="font-size: 12pt; font-family: 'Times New Roman', serif; background-color: white;" class="">The "Epoch" section consists of a variable "data_flt.fsample" where "data_flt" variable is not defined. Can you please inform what is this variable related
to? as this is needed to complete my analysis. </span></div>
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<span style="font-size: 12pt; font-family: 'Times New Roman', serif; background-color: white;" class="">Thanks for your understanding and support</span></div>
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<span style="font-size: 12pt; font-family: 'Times New Roman', serif; background-color: white;" class="">Best Regards,<br class="">
Sunny</span></div>
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