[FieldTrip] freqanalysis
Victoria Schröder
victorias at dsv.su.se
Wed Feb 5 12:57:31 CET 2014
Dear Eelke and Jörn
Yes, this really answers my question. Really cool!
Thanks
Victoria
2014-02-05 12:49 skrev Jörn M. Horschig:
> Hi Victoria,
>
> see:
>
> http://fieldtrip.fcdonders.nl/faq/why_does_my_tfr_contain_nans?s[]=tfr&s[]=nan
> and: http://fieldtrip.fcdonders.nl/walkthrough#frequency_analysis
>
> These should answer your question ;)
>
> Best,
> Jörn
>
> On 2/5/2014 12:40 PM, Victoria Schröder wrote:
>> Dear Jörn,
>>
>> I still am dealing with finding the right cfg.toi when doing a time
>> frequency analysis. Depending on the time resolution i get NaN values
>> in the first matrixes in the resulting powspctrm and crsspctrm. It
>> seems that for the first times selected there is no data. If i choose
>> a cfg.toi 1:0.05:2 then i get no Nan values but as soon as I start
>> below 1 i get Nan values.
>>
>> This is my code for the analysis. I would appreciate some concrete
>> advice and suggestions why i run into this problem.
>>
>> % time-frequency analysis
>> cfg = [];
>> cfg.output = 'powandcsd'; % different for convol than for fft
>> cfg.channel={'C15' 'C10' 'B23' 'B3'};
>> cfg.method = 'mtmconvol';
>> cfg.taper = 'hanning';
>> cfg.keeptrials = 'yes';
>> cfg.trials=data_clean.trialinfo(:,1) < 20;
>> cfg.channel={'C29' 'C16' 'C31' 'C9' 'C26' 'C13' 'D23' 'B26' 'D29'
>> 'B13' 'D31' 'B11'};
>> cfg.channelcmb={'C29' 'D23'
>> 'C29' 'D31'
>> 'C29' 'D29'
>> 'C31' 'D23'
>> 'C31' 'D31'
>> 'C31' 'D29'
>> 'C26' 'D23'
>> 'C26' 'D31'
>> 'C26' 'D29'
>> 'C16' 'B26'
>> 'C16' 'B11'
>> 'C16' 'B13'
>> 'C13' 'B26'
>> 'C13' 'B11'
>> 'C13' 'B13'
>> 'C9' 'B26'
>> 'C9' 'B11'
>> 'C9' 'B13'} ;
>> cfg.foi = 12:2:30; % analysis 2 to 30 Hz in steps of 2 Hz
>> cfg.t_ftimwin = ones(length(cfg.foi),1).*0.5; % length of time
>> window = 0.5 sec
>> cfg.toi = 0:0.05:1;
>> freq_convol = ft_freqanalysis(cfg, data_clean);
>>
>> Thank you a lot
>> Victoria
>>
>>
>> 2014-02-03 13:40 skrev Jörn M. Horschig:
>>> Hi Victoria,
>>>
>>> On 2/3/2014 12:14 PM, Victoria Schröder wrote:
>>>> Thank Jörn,
>>>>
>>>> Thank for the advice for the tutorials but i have already looked
>>>> at them a lot.
>>>>
>>>> Anyhow, suppose i say cfg.keeptrials = 'yes', then i get the
>>>> averaged power over trials? Well, it might sound obvious, but if you
>>>> say 'yes' to keep trials, you keep the trials, whereas if you say
>>>> 'no' you do not keep the trials and instead get an average.
>>>
>>>> what happens then when the trials do not have the same length?
>>> The average will be made with all data that is available. If some
>>> trials go to 30s but all trials go to 29s, then the average of the
>>> last one second is made of less data then the first 29s. This is a
>>> crucial point for doing statistics as the degrees of freedom,
>>> signal-to noise ration etc. will be different for different time
>>> points.
>>>
>>>>
>>>> and a last question :)
>>>>
>>>> what does cfg.toi depend on ? in the tutorial time frequency
>>>> analysis this is chosen : cfg.toi = -0.5:0.05:1.5; .. why
>>>> is that the case?
>>> it depends on what time you are interested in and how much memory
>>> (and cpu time aka patience) you got.
>>>
>>> Good luck ;)
>>> Best,
>>> Jörn
>>>
>>>>
>>>> I hope this should be it for now
>>>> Best
>>>> Victoria
>>>>
>>>>
>>>> 2014-02-03 11:42 skrev Jörn M. Horschig:
>>>>> Hi Victoria,
>>>>>
>>>>> you might want to read the relevant part of the walkthrough for
>>>>> your
>>>>> questions on mtmconvol and mtmfft:
>>>>> http://fieldtrip.fcdonders.nl/walkthrough#frequency_analysis
>>>>>
>>>>> Then, also doing this tutorial might help in understanding what
>>>>> the
>>>>> different methods are doing:
>>>>> http://fieldtrip.fcdonders.nl/tutorial/timefrequencyanalysis
>>>>>
>>>>> And lastly, to shortly answer your questions, see below ;)
>>>>>
>>>>> On 2/3/2014 11:15 AM, Victoria Schröder wrote:
>>>>>> Dear Jörn,
>>>>> Hi ;)
>>>>>
>>>>>>
>>>>>> the code works but i dont know whether my data is logical and
>>>>>> whether i decided to use the right method etc.
>>>>> maybe you should try to get into one of the FieldTrip courses :)
>>>>> This
>>>>> might tremendously help you in understanding what's being done
>>>>> and
>>>>> why. Otherwise, try to read as much as you can, read methods of
>>>>> papers
>>>>> and discuss with your supervisor and colleagues. Of course, on
>>>>> the
>>>>> mailing list we also like to help a lot.
>>>>>>
>>>>>> My trials are pretty long (approx 30 sec but all are not the
>>>>>> same length) and i am interested in beta frequency.
>>>>>>
>>>>>> First, it is not really clear to me whether i should use
>>>>>> cfg.method=mtmfft or cfg.method=mtmconvol. As i understand , the
>>>>>> latter calculates the FFT for shorter self-specified time windows
>>>>>> to look at changes in power over time. Is that right? yep, about
>>>>>> right.
>>>>>
>>>>>> however, if i have more stimuli for one condition, how is the
>>>>>> time component then taken into account? it depends on how you
>>>>>> segmented your data. FieldTrip is just transforming your
>>>>>> preprocessed data, so whatever you put in is what you get out.
>>>>>
>>>>>> does mtmconvol take all trials of one condition and average the
>>>>>> the power for each time window over all trials? Or is each trial
>>>>>> treated seperatly?
>>>>> depends on whether you specify cfg.keeptrials = 'yes' or 'no'
>>>>>>
>>>>>> Say i would use cfg.method=mtmfft do i need to specify a
>>>>>> cfg.tapsmofrq when using cfg.taper='hanning'? no, a hanning taper
>>>>>> is always a single taper. Only when combining multiple tapers you
>>>>>> can effectively smooth in the frequency domain. this is
>>>>>> implemented as taper='dpss'
>>>>>
>>>>>> As i understand hanning if appropriate for lower freuquencies so
>>>>>> i should use this taper to assess beta frequencies.
>>>>> this is a rule of thumb, but there is nothing wrong with using
>>>>> multitapering for lower frequencies. It depends on what you
>>>>> expect
>>>>> from your data and what you want to achieve.
>>>>>>
>>>>>> Say i use cfg.method=mtmconvol what cfg.t_ftimwin is
>>>>>> appropriate?
>>>>> this depends on the frequencies you are interested in. I wouldn't
>>>>> trust anything below 3 cycles, i.e. for 10Hz alpha at least
>>>>> 300ms.
>>>>>
>>>>>>
>>>>>> Thank you a lot for the help
>>>>> you're welcome, hope this helps
>>>>>> Best
>>>>>> Victoria
>>>>> Likewise,
>>>>> Jörn
>>>>>
>>>>>>
>>>>>>
>>>>>> 2014-02-03 09:19 skrev Jörn M. Horschig:
>>>>>>> Hi Victoria,
>>>>>>>
>>>>>>> is there anything wrong with the code you used below? By
>>>>>>> smoothing,
>>>>>>> do you refer to smoothing in the frequency domain?
>>>>>>>
>>>>>>> Best,
>>>>>>> Jörn
>>>>>>>
>>>>>>>
>>>>>>> On 1/30/2014 11:33 AM, Victoria Schröder wrote:
>>>>>>>> Hello
>>>>>>>>
>>>>>>>> I am currently working on a freqanalysis as a first step to do
>>>>>>>> a connectivityanalysis. I am a bit unsure about the method to
>>>>>>>> use for the freqanalysis. My stimuli are very long: between 29
>>>>>>>> and 30 sec. In total i have 4 stimuli per condition and 2
>>>>>>>> seperate conditions. I am looking at the beta range so fairly
>>>>>>>> low frequencies.
>>>>>>>>
>>>>>>>> this is my code:
>>>>>>>> Am i using the right taper and method. Should i smooth the
>>>>>>>> data? and if so, what should such a smoothing parameter depend
>>>>>>>> on?
>>>>>>>>
>>>>>>>> %fourier analysis
>>>>>>>> cfg=[];
>>>>>>>> cfg.output='fourier';
>>>>>>>> cfg.method='mtmfft';
>>>>>>>> cfg.foi=[12:30];
>>>>>>>> cfg.taper='hanning';
>>>>>>>> cfg.keeptrials='yes';
>>>>>>>> cfg.channel={'C15' 'C10' 'B23' 'B3'};
>>>>>>>> frefourier=ft_freqanalysis(cfg,data_clean);
>>>>>>>>
>>>>>>>>
>>>>>>>> %coherence analysis
>>>>>>>> cfg=[];
>>>>>>>> cfg.method='coh';
>>>>>>>> cfg.channelcmb={'B3' 'C15'
>>>>>>>> 'B3' 'C10'
>>>>>>>> 'B23' 'C15'
>>>>>>>> 'B23' 'C10'}
>>>>>>>> coherence=ft_connectivityanalysis(cfg, frefourier);
>>>>>>>>
>>>>>>>>
>>>>>>>> Thank you very much for the suggestions!
>>>>>>>> Best
>>>>>>>> Victoria
>>>>>>>> _______________________________________________
>>>>>>>> fieldtrip mailing list
>>>>>>>> fieldtrip at donders.ru.nl
>>>>>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>>>>>
>>>>>>>
>>>>>>> -- Jörn M. Horschig
>>>>>>> PhD Student
>>>>>>> Donders Institute for Brain, Cognition and Behaviour
>>>>>>> Centre for Cognitive Neuroimaging
>>>>>>> Radboud University Nijmegen
>>>>>>> Neuronal Oscillations Group
>>>>>>> FieldTrip Development Team
>>>>>>>
>>>>>>> P.O. Box 9101
>>>>>>> NL-6500 HB Nijmegen
>>>>>>> The Netherlands
>>>>>>>
>>>>>>> Contact:
>>>>>>> E-Mail: jm.horschig at donders.ru.nl
>>>>>>> Tel: +31-(0)24-36-68493
>>>>>>> Web: http://www.ru.nl/donders
>>>>>>>
>>>>>>> Visiting address:
>>>>>>> Trigon, room 2.30
>>>>>>> Kapittelweg 29
>>>>>>> NL-6525 EN Nijmegen
>>>>>>> The Netherlands
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> fieldtrip mailing list
>>>>>>> fieldtrip at donders.ru.nl
>>>>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>>>>
>>>>>
>>>>>
>>>>> -- Jörn M. Horschig
>>>>> PhD Student
>>>>> Donders Institute for Brain, Cognition and Behaviour
>>>>> Centre for Cognitive Neuroimaging
>>>>> Radboud University Nijmegen
>>>>> Neuronal Oscillations Group
>>>>> FieldTrip Development Team
>>>>>
>>>>> P.O. Box 9101
>>>>> NL-6500 HB Nijmegen
>>>>> The Netherlands
>>>>>
>>>>> Contact:
>>>>> E-Mail: jm.horschig at donders.ru.nl
>>>>> Tel: +31-(0)24-36-68493
>>>>> Web: http://www.ru.nl/donders
>>>>>
>>>>> Visiting address:
>>>>> Trigon, room 2.30
>>>>> Kapittelweg 29
>>>>> NL-6525 EN Nijmegen
>>>>> The Netherlands
>>>>>
>>>>> _______________________________________________
>>>>> fieldtrip mailing list
>>>>> fieldtrip at donders.ru.nl
>>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>>
>>>
>>>
>>> -- Jörn M. Horschig
>>> PhD Student
>>> Donders Institute for Brain, Cognition and Behaviour
>>> Centre for Cognitive Neuroimaging
>>> Radboud University Nijmegen
>>> Neuronal Oscillations Group
>>> FieldTrip Development Team
>>>
>>> P.O. Box 9101
>>> NL-6500 HB Nijmegen
>>> The Netherlands
>>>
>>> Contact:
>>> E-Mail: jm.horschig at donders.ru.nl
>>> Tel: +31-(0)24-36-68493
>>> Web: http://www.ru.nl/donders
>>>
>>> Visiting address:
>>> Trigon, room 2.30
>>> Kapittelweg 29
>>> NL-6525 EN Nijmegen
>>> The Netherlands
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
> --
> Jörn M. Horschig
> PhD Student
> Donders Institute for Brain, Cognition and Behaviour
> Centre for Cognitive Neuroimaging
> Radboud University Nijmegen
> Neuronal Oscillations Group
> FieldTrip Development Team
>
> P.O. Box 9101
> NL-6500 HB Nijmegen
> The Netherlands
>
> Contact:
> E-Mail: jm.horschig at donders.ru.nl
> Tel: +31-(0)24-36-68493
> Web: http://www.ru.nl/donders
>
> Visiting address:
> Trigon, room 2.30
> Kapittelweg 29
> NL-6525 EN Nijmegen
> The Netherlands
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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