[FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data
Herbert J Gould (hgould)
hgould at memphis.edu
Tue Jul 31 15:37:06 CEST 2018
Please eliminate me from the mailing list. I have retired.
Thank you.
Sent from my Verizon Wireless 4G LTE smartphone
-------- Original message --------
From: "Jörn M. Horschig"
Date:07/31/2018 2:18 AM (GMT-06:00)
To: 'FieldTrip discussion list'
Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data
Hi Sunny,
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:
>> cfg = [];
>> cfg.dataset = 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3';
>> cfg.trialdef.eventtype = '?';
>> ft_definetrial(cfg);
The output will be:
Warning: no trialfun was specified, using ft_trialfun_general
In ft_definetrial at line 138
evaluating trialfunction 'ft_trialfun_general'
reading the header from 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3'
reading the events from 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3'
the following events were found in the datafile
event type: 'ADC001'
with event values: 1.5
no trials have been defined yet, see FT_DEFINETRIAL for further help
found 1 events
created 0 trials
the call to "ft_definetrial" took 1 seconds
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).
You can still read in the oxy3-data running this code:
>> cfg = [];
>> cfg.dataset = 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3';
>> data = ft_preprocessing(cfg);
The output will be:
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' }
reading and preprocessing
reading and preprocessing trial 1 from 1
the call to "ft_preprocessing" took 2 seconds
You also sent another data file with events. The rationale here is equivalent to above. First, check the data for events:
>> cfg = [];
>> cfg.dataset = 'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3';
>> cfg.trialdef.eventtype = '?';
>> ft_definetrial(cfg);
With the output being:
evaluating trialfunction 'ft_trialfun_general'
reading the header from 'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3'
reading the events from 'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3'
the following events were found in the datafile
event type: 'ADC001'
with event values: 1.4
event type: 'event'
with event values: 'A' 'B' 'C' 'D'
no trials have been defined yet, see FT_DEFINETRIAL for further help
found 5 events
created 0 trials
the call to "ft_definetrial" took 3 seconds
I am not sure what your events mean, but you are then able to define trials according to these events, e.g.
>> cfg.trialdef.eventtype = 'event';
>> cfg.trialdef.eventvalue = 'B';
>> cfg.trialdef.prestim = 5;
>> cfg.trialdef.prestim = 35;
>> cfg = ft_definetrial(cfg);
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:
>> data = ft_preprocessing(cfg);
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!
Btw, if someone wants to do a combined EEG-fNIRS analysis using FieldTrip, give me a shout.
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 Jörn M. Horschig
Sent: Monday, July 30, 2018 15:42
To: 'FieldTrip discussion list' <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data
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<mailto:sunnypitt1965 at gmail.com>>
Sent: Monday, July 30, 2018 15:29
To: FieldTrip discussion list <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>>; jorn at artinis.com<mailto:jorn at artinis.com>
Cc: Arana, S.L. (Sophie) <S.Arana at donders.ru.nl<mailto: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
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<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
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.
[cid:image001.png at 01D428AE.213F63D0]
Thanks for your understanding and support
Best Regards,
Sunny
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