[FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data

Mon Jul 30 15:41:40 CEST 2018

Hi Sunny,

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).

With best regards,

Jörn

--
Jörn M. Horschig, PhD, Project Leader & Software Engineer
 <http://www.artinis.com/> Artinis Medical Systems  |  +31 481 350 980 

Sign up for our NIRS newsletter <http://artinis.us3.list-manage1.com/subscribe?u=6bef931b76193f0e3d1dfe654&id=550bfdab46> 

From: Sunny p <sunnypitt1965 at gmail.com> 
Sent: Monday, July 30, 2018 15:29
To: FieldTrip discussion list <fieldtrip at science.ru.nl>; jorn at artinis.com
Cc: Arana, S.L. (Sophie) <S.Arana at donders.ru.nl>
Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data

Hello Jorn,

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 http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel#epoch (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.

Thanks for your understanding and support.

Best Regards,

Sunny

On Mon, Jul 30, 2018 at 2:47 AM, Jörn M. Horschig <jorn at artinis.com <mailto:jorn at artinis.com> > wrote:

Hi Sunny,

Yes, the FieldTrip NIRS plugin works for all our devices. 

With best regards,

Jörn

--
Jörn M. Horschig, PhD, Project Leader & Software Engineer
 <http://www.artinis.com/> Artinis Medical Systems  |  +31 481 350 980 

Sign up for our NIRS newsletter <http://artinis.us3.list-manage1.com/subscribe?u=6bef931b76193f0e3d1dfe654&id=550bfdab46> 

From: fieldtrip <fieldtrip-bounces at science.ru.nl <mailto:fieldtrip-bounces at science.ru.nl> > On Behalf Of Sunny p
Sent: Friday, July 27, 2018 20:41
To: Arana, S.L. (Sophie) <S.Arana at donders.ru.nl <mailto:S.Arana at donders.ru.nl> >
Cc: FieldTrip discussion list <fieldtrip at science.ru.nl <mailto:fieldtrip at science.ru.nl> >
Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data

Hello Sophie,

Once this tutorial is fully developed, Can we use this for OCTAMON (https://www.artinis.com/octamon/)  ?

Thanks for your understanding and support.

Best Regards,

Sunny

On Wed, Jul 25, 2018 at 12:35 PM, Sunny p <sunnypitt1965 at gmail.com <mailto:sunnypitt1965 at gmail.com> > wrote:

Hello Sophie,

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.

Thanks for your understanding and support.

Best Regards,

Sunny

On Wed, Jul 25, 2018 at 8:22 AM, Sunny p <sunnypitt1965 at gmail.com <mailto:sunnypitt1965 at gmail.com> > wrote:

Hello Sophie,

Thanks a lot for your clarification. This is very useful.

Sunny

On Wednesday, July 25, 2018, Arana, S.L. (Sophie) <S.Arana at donders.ru.nl <mailto:S.Arana at donders.ru.nl> > wrote:

Dear Sunny, 

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.

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.

cfg                 = [];

cfg.hpfilter        = 'yes';

cfg.hpfreq          = 0.01; 

data_flt            = ft_preprocessing(cfg,data_down);

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.

Best,

Sophie

  _____  

From: fieldtrip [fieldtrip-bounces at science.ru.nl <mailto:fieldtrip-bounces at science.ru.nl> ] on behalf of Sunny p [sunnypitt1965 at gmail.com <mailto:sunnypitt1965 at gmail.com> ]
Sent: Tuesday, July 24, 2018 9:24 PM
To: fieldtrip at science.ru.nl <mailto:fieldtrip at science.ru.nl> 
Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data

Hello All Good Day, 

Hope you are doing fine,

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?

Issue: In the  "Preprocessing and averaging of multi-channel NIRS data" tutorial "  <http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel> http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel

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. 

Thanks for your understanding and support

Best Regards,
Sunny

 <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=emailclient> 

Virus-free.  <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=emailclient> www.avg.com 

_______________________________________________
fieldtrip mailing list
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
https://doi.org/10.1371/journal.pcbi.1002202

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20180730/e2cbbd71/attachment-0002.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image001.png
Type: image/png
Size: 4228 bytes
Desc: not available
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20180730/e2cbbd71/attachment-0002.png>