[FieldTrip] Adding Manual Markers

Stephen Whitmarsh stephen.whitmarsh at gmail.com
Wed Nov 25 07:56:42 CET 2020


Hi Mustafa,

Okay, great! I would first see if ft_databrowser won't just be able to
treat your data as continuous (note cfg.continuous option in it's cfg), and
then giving it your start-end markers as a Nx2 matrix in (e.g.)
cfg.artfctdef.mymarker.artifact when you call it. Pretty sure that'll work,
and it would remove the need of restructuring your data. You'll only need
to add cumulative samples to your label samples at each trial, if you get
my drift.

Hope it works out for you,
Stephen





Op wo 25 nov. 2020 om 02:35 schreef MUSTAFA YAVUZ <m.yavuz.18 at ogr.iu.edu.tr
>:

> Merhaba Stephen :),
>
> Thank you for your informative response! Indeed, I already have data as
> separate segments (trials) before any initiation with Fieldtrip. I was just
> wondering if I can plot the event markers just for visualization purposes.
> However, I've learnt why it is the case now. In my case, I believe a
> solution would be ; concatenating the trials and manipulating the time axis
> to arbitrarily create a single trial (continuous?) data  structure and then
> building a custom trialfun to be able to visualize markers in
> ft_databrowser.
>
> Thank you again,
> All the best,
> Mustafa
>
> Stephen Whitmarsh <stephen.whitmarsh at gmail.com>, 24 Kas 2020 Sal, 11:04
> tarihinde şunu yazdı:
>
>> Merhaba Mustafa,
>>
>> Welcome to FieldTrip!
>> Just to be clear - I assume you segmented your continuous data into
>> trials by passing your marker timing as a cfg.trl in ft_preprocessing,
>> right?
>> When you did, the temporal information about the markers became
>> irrelevant, because the trials are then expressed *not *in samples from
>> the onset of the continuous data anymore, but instead as time relative to
>> the markers. I.e. each trial now starts at t=0s (-offset), rather and, say
>> [13, 104, 206, ...] samples (i.e. your initial trl). See the resultant
>> data.time field.
>> Secondly, ft_databrowser does not take cfg.trl as the location of
>> markers, rather it does so in cfg.artfctdef.xxx.artifact (yes, a bit
>> strange, partly historical, and because databrowser is typically used to
>> manually scan for artifacts).
>>
>> So, in your case, you could either:
>>
>> Use ft_databrowser to plot the original, unsegmented, continuous, data,
>> and pass your trialinfo (as a Nx2 matrix, with only start and end sample)
>> to cfg.artfctdef.xxx.artifact. Replace xxx with whatever your want, e.g.
>> "trialnumber"
>> Use ft_databrowser to plot the segmented data, as trials, with new
>> time-axis, without the markers.
>>
>> Note that ft_databrowser will try to fit your cfg.artfctdef.xxx.artifact
>> to your segmented trial data as well, by doing some intelligent checking of
>> your past cfg (which is tracked in your segmented data structure and
>> beyond), and treating your data as continuous data. That might work, or it
>> might not, but now you know why!
>>
>> Happy fieldtripping,
>> Stephen
>>
>>
>>
>> Op di 24 nov. 2020 om 02:29 schreef MUSTAFA YAVUZ <
>> m.yavuz.18 at ogr.iu.edu.tr>:
>>
>>> Hi all,
>>>
>>> I've been trying to adjust my EEG data (segmented and .mat file) to be
>>> analyzed by FT. I already have separate trials and have temporal
>>> information about the event markers' time courses. I constructed a Nx3 trl
>>> structure and passed it as cfg.trl while calling ft_preprocessing. Whilst
>>> the function worked and I can see the cfg.trl field in the output
>>> structure, when I call ft_databrowser, the event markers are not displayed
>>> on trials. Do you have any idea/solution for this situation?
>>>
>>> Thank you in advance,
>>> Mustafa
>>>
>>> --
>>> *Mustafa Yavuz *
>>>
>>> Ph.D. Candidate in Neuroscience
>>>
>>> Department of Neuroscience
>>> İstanbul University
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>> https://doi.org/10.1371/journal.pcbi.1002202
>>>
>> _______________________________________________
>> fieldtrip mailing list
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>> https://doi.org/10.1371/journal.pcbi.1002202
>>
>
>
> --
> *Mustafa Yavuz *
>
> M.Sc. Candidate in Neuroscience
>
> Department of Neuroscience
> İstanbul University
>
> _______________________________________________
> fieldtrip mailing list
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> https://doi.org/10.1371/journal.pcbi.1002202
>
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