[FieldTrip] freqanalysis

["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