[FieldTrip] ft redefine trials: how to change trigger?
KatrinH Heimann
katrinheimann at gmail.com
Tue May 27 23:02:41 CEST 2014
Hi! Guys, your help is so much appreciated!
So I try to be more clear!:
So, yeah, Max, you are right! At the end I would like to use two different
triggervalues.
If I would use twice ft_definetrial then it would look like this:
cfg = [];
cfg.dataset = '1.raw';
cfg.trialfun = 'ft_trialfun_general';
cfg.trialdef.eventtype = 'trigger';
cfg.trialdef.eventvalue = 'stim'; % the value of the stimulus trigger for
the beginning of baseline
cfg.trialdef.prestim = 0.5; %the time of the fixation cross
cfg.trialdef.poststim = 1.5; %the time of the baseline (plus 0.5 buffer)
cfg = ft_redefinetrial(cfg);
This baselinedata I could easily baselinecorrect using 100 ms of the
fixationcrossperiod:
cfg.channel = 'all';
cfg.preproc.demean = 'yes';
cfg.preproc.baselinewindow = [-0.1 0]
cfg.preproc.bpfilter = 'yes';
cfg.preproc.bpfreq = [6 32];
The stimulusdata would be defined using a trigger that corresponds to a
button press:
cfg = [];
cfg.dataset = '1.raw';
cfg.trialfun = 'ft_trialfun_general';
cfg.trialdef.eventtype = 'trigger';
cfg.trialdef.eventvalue = 'resp'; % the value of the stimulus trigger for
the beginning of baseline
cfg.trialdef.prestim = 0.5; % 0.5 sec before button press
cfg.trialdef.poststim = 1.5; % 1.5 sec after button press (time that I
wanna analyse)
cfg = ft_redefinetrial(cfg);
However here I have the problem that I cannot correct with the same
baseline than before as the buttonpress is not always at the same time so I
don't know when the fixationcrossperiod is located...
So I thought I could first "cut" bigger pieces and then redefine trials by
cutting again (after the preprocessing), then with different eventvalues
...
But you say that is not possible?
Thanks a lot for your help!!!
Katrin
2014-05-27 21:05 GMT+02:00 Max Cantor <mcantor at umich.edu>:
> Ya, it would definitely help if we could see your code, but I might have
> another idea.
>
> When you say you have a fixation cross trigger, is this trigger being
> recorded from your EEG recording equipment in such a way that it can be
> represented as an event value in cfg.trialdef for ft_definetrial? If so, I
> think you may be right that it can't be changed through ft_redefinetrial
> (at least, as far as I can tell, no mention of this is made in the help
> section of the function). That being said, if you run ft_definetrial
> separately for both event values that should work.
>
> That being said, I may still be slightly confused about what you mean when
> you say you want to change the trigger. Do you mean you want to create a
> new trigger for your data off-line? I think it may be possible to create
> custom triggers off-line through fieldtrip, but it's not something I've
> tried personally, but if that is what you are trying to do, I could look
> into it.
>
>
> On Tue, May 27, 2014 at 2:44 PM, kousik sarathy <sarathykousik at gmail.com>wrote:
>
>> Hey Katrin,
>>
>> It seems to me that Max's suggestion would suffice. But you seem to be
>> looking for something else. Could you elaborate a little bit as to what you
>> need?
>>
>> --
>> Regards,
>> Kousik Sarathy, S
>>
>>
>>
>> On Tue, May 27, 2014 at 8:30 PM, KatrinH Heimann <katrinheimann at gmail.com
>> > wrote:
>>
>>> Dear Max, thanks a lot for your prompt answer. Unfortunately this is not
>>> what I am looking for (I found an example like this in the tutorial). I
>>> would like to change the trigger for one of the two conditions, let it be
>>> now the response of the subject, as this is where the stimulus actually
>>> starts... Defining two different timewindows is not enough... Can you also
>>> help me with that? Thanks a million! Katrin
>>>
>>>
>>> 2014-05-27 18:58 GMT+02:00 Max Cantor <mcantor at umich.edu>:
>>>
>>> Hi Katrin,
>>>>
>>>> It may help to see your code, but hopefully this will help. It should
>>>> be as simple as taking your epoched data from ft_definetrial and
>>>> ft_preprocessing, then creating two configurations for your timewindows and
>>>> running ft_redefinetrial.
>>>>
>>>> For example (from the fieldtrip tutorial, slightly simplified by me for
>>>> explanatory purposes):
>>>>
>>>> ***
>>>>
>>>> % find the interesting segments of data
>>>>
>>>> cfg = [];
>>>> % empty configuration
>>>> cfg.dataset = 'Subject01.ds';
>>>> % name of CTF dataset
>>>> cfg.trialdef.eventtype = 'backpanel trigger';
>>>> cfg.trialdef.prestim = 1;
>>>> cfg.trialdef.poststim = 2;
>>>> cfg.trialdef.eventvalue = 3;
>>>> % event value of FIC
>>>> cfg = ft_definetrial(cfg);
>>>>
>>>> % preprocess the data
>>>>
>>>> cfg.channel = {'MEG'};
>>>> dataFIC = ft_preprocessing(cfg);
>>>>
>>>> % define time window
>>>>
>>>> cfg = [];
>>>>
>>>> cfg.toilim = [-0.5 0];
>>>> dataPre = ft_redefinetrial(cfg, dataFIC);
>>>>
>>>> cfg.toilim = [0.8 1.3];
>>>> dataPost = ft_redefinetrial(cfg, dataFIC);
>>>>
>>>> ***
>>>>
>>>> So if your code resembles this, you are defining in
>>>> cfg.trialdef.prestim and cfg.trialdef.poststim a timewindow that
>>>> encompasses both your baseline period and stimulus period, then for
>>>> cfg.toilim in the ft_redefinetrial section you are setting one to your
>>>> baseline period and the other to your stimulus period, and outputting them
>>>> into separate variables.
>>>>
>>>> Hopefully this helps. Also, if you haven't done so already, I would
>>>> strongly recommend you run through the tutorial, as it may help answer
>>>> questions like this in the future (assuming I've properly identified the
>>>> issue).
>>>>
>>>> Good luck,
>>>>
>>>> Max
>>>>
>>>>
>>>>
>>>>
>>>> On Tue, May 27, 2014 at 12:10 PM, KatrinH Heimann <
>>>> katrinheimann at gmail.com> wrote:
>>>>
>>>>> Dear all,
>>>>>
>>>>> my name is Katrin Heimann, I am phd student at the University of
>>>>> Parma. New to Fieldtrip.
>>>>> I am doing an EEG analysis, still in the preprocessing phase.
>>>>> It is a within trials design. I would like to compare a baseline
>>>>> period with an experimental condition (visual stimulus).
>>>>>
>>>>> I have a trigger after a fixation cross, then a baseline period
>>>>> (approx 1 sec) , then the period of my stimulus (1 sec- starting with a
>>>>> bottom press (trigger)).
>>>>>
>>>>> As I would like to apply the same baseline correction for both (the
>>>>> fixationcross period) I planned to first define my trials as long trials
>>>>> including the timewindows of baseline and the stimulus period, applying
>>>>> filter and baselinecorrection on those long pieces. However, as I do not
>>>>> wanna do the artifact detection on the whole pieces (but seperately for
>>>>> baseline and stimulus, to avoid that I have to throw away too many trials)
>>>>> I would like to redefine my trials then, cutting out only baseline period
>>>>> and only stimulus period (starting with another trigger
>>>>> (triggervalue=resp)..
>>>>>
>>>>> *Unfortunately I do not understand how I can change the trigger used
>>>>> with ft redefine trial. *
>>>>>
>>>>> Anybody who could give me an example how that is done?
>>>>> Thanks a million
>>>>> Katrin
>>>>>
>>>>> _______________________________________________
>>>>> fieldtrip mailing list
>>>>> fieldtrip at donders.ru.nl
>>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Max Cantor
>>>> Research Assistant
>>>> Computational Neurolinguistics Lab
>>>> University of Michigan
>>>>
>>>> _______________________________________________
>>>> fieldtrip mailing list
>>>> fieldtrip at donders.ru.nl
>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>>
>>>
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
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>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
>
> --
> Max Cantor
> Research Assistant
> Computational Neurolinguistics Lab
> University of Michigan
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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