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

Mon Jul 30 16:44:40 CEST 2018

Hello Jorn,

Thanks a lot for your response. Yes, I just collected the data samples, My
primary aim is to visualize this data on a head model using field trip. so
that it will be easy to understand. Please find attached data set collected
using Octamon in this email. I also created layout for this. I attached
data, layout and image in this email. Thanks a lot for your support. Its
very useful for my research.

Best Regards,
Sunny

On Mon, Jul 30, 2018 at 9:41 AM, Jörn M. Horschig <jorn at artinis.com> wrote:

> 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
> Artinis Medical Systems <http://www.artinis.com/>  |  +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>
> 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
> Artinis Medical Systems <http://www.artinis.com/>  |  +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> *On Behalf Of *Sunny p
> *Sent:* Friday, July 27, 2018 20:41
> *To:* Arana, S.L. (Sophie) <S.Arana at donders.ru.nl>
> *Cc:* FieldTrip discussion list <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> 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> 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>
> 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] on behalf of Sunny p [
> sunnypitt1965 at gmail.com]
> *Sent:* Tuesday, July 24, 2018 9:24 PM
> *To:* 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
>
>
>
> 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. www.avg.com
> <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=emailclient>
>
>
>
>
> _______________________________________________
> fieldtrip mailing list
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> https://doi.org/10.1371/journal.pcbi.1002202
>
>
>
> _______________________________________________
> 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/a92534a0/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/a92534a0/attachment-0004.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: OCTAMON.oxy3
Type: application/octet-stream
Size: 417156 bytes
Desc: not available
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20180730/a92534a0/attachment-0004.obj>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: OCTA_layout_MAIN.mat
Type: application/octet-stream
Size: 1493 bytes
Desc: not available
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20180730/a92534a0/attachment-0005.obj>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Brain_PreFrontal_Cortex.PNG
Type: image/png
Size: 88327 bytes
Desc: not available
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20180730/a92534a0/attachment-0005.png>