[FieldTrip] freqanalysis
Victoria Schröder
victorias at dsv.su.se
Wed Feb 5 12:40:56 CET 2014
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
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