[FieldTrip] freqanalysis

"Jörn M. Horschig" jm.horschig at donders.ru.nl
Mon Feb 3 13:40:55 CET 2014 

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

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