# [Eeglablist] Newtimef parameters - window size and number of cycles

Makoto Miyakoshi mmiyakoshi at ucsd.edu
Mon Dec 7 17:45:53 PST 2015

```Dear Katharina,

> If cycles increased in equally spaced steps, I should get about 0.4
cycles more per frequency (I have 28 frequencies in my output).

Katharina, you are right, that's what it means 'linearly'. This is how you
calculate the cycles for each frequency. (14-3)/28 = 0.3929. Good luck for
the revision!

Makoto

On Mon, Dec 7, 2015 at 5:12 AM, Katharina Limbach <
katharina.limbach at uni-jena.de> wrote:

> Dear Makato,
>
> thanks a lot for your response.
>
> I was wondering whether you could be more specific about how I can
> calculate how many cylces are used at a specific frequency (I got asked by
> a reviewer to supply this information).
>
> As mentioned before, I use 3 cycles at the lowest and 14 cycles at the
> highest frequency. If cycles increased in equally spaced steps, I should
> get about 0.4 cycles more per frequency (I have 28 frequencies in my
> output).
> However in the documentation I could only find, that cycles increase
> 'linerarily'.
>
> I am not sure, whether that helps, but I found out that 'cycles', [3 14],
> 'freqs' [5 60] and  'cycles', [3 0.611], 'freqs' [5 60] lead to very
> similar results.
>
> Thanks heaps, Katharina
>
> 2015-11-27 1:47 GMT+01:00 Makoto Miyakoshi <mmiyakoshi at ucsd.edu>:
>
>> Dear Katharina,
>>
>> > How exactly is the window size computed? In the archives I read a
>> couple of times, that it should be close to 1000/(lowest frequency) x
>> (number of cycles). In my example that should lead to a window size of 600
>> and not 668. Where do those 'extra' 68 ms come from?
>>
>> I don't know this in detail, but the extra 68 ms must be for adjustments.
>>
>> > How can I calculate how many cycles were used at specific frequencies?
>> I have 3 cycles at the lowest and 14 cycles at the highest frequency and I
>> am getting estimates for 28 frequencies. Does that mean that I get  ~ 0.4
>> cycles more per frequency step? (3.4 cycles at  5.48 Hz; 3.8 cycles at 6.01
>> Hz)?
>>
>> If I use 'cycles', [3 0.85], 'freqs', [3 50], then the smallest number of
>> cycles is 3 at 3Hz, and the largest number of cycles is something like 50 *
>> (1-0.85) =  7.5 cycles at 50 Hz.
>>
>> Makoto
>>
>> On Mon, Nov 2, 2015 at 7:19 AM, Katharina Limbach <
>> katharina.limbach at uni-jena.de> wrote:
>>
>>> Dear all,
>>>
>>> I have two questions regarding the description of a time frequency
>>> analysis using  the newtimef function.
>>>
>>> This the is command that I am using:
>>>
>>> *[ersp itc powbase times frequencies boot1 boot2 tfdata] = pop_newtimef(
>>> EEG, 1, chani, [-1460   596], [3  14] , 'baseline',[NaN], 'freqs', [5 60],
>>> 'plotitc' , 'off', 'plotersp', 'off', 'plotphase', 'off','freqscale',
>>> 'log', 'scale', 'abs', 'padratio', 1);*
>>>
>>> Which leads to the following output in the Command window:
>>>
>>> *Computing Event-Related Spectral Perturbation (ERSP) and*
>>> *  Inter-Trial Phase Coherence (ITC) images based on 1031 trials*
>>> *  of 514 frames sampled at 250 Hz.*
>>> *Each trial contains samples from -1460 ms before to*
>>> *  596 ms after the timelocking event.*
>>> *  Image frequency direction: normal*
>>> *Using 3 cycles at lowest frequency to 14 at highest.*
>>> *Generating 200 time points (-1125.3 to 261.3 ms)*
>>> *Finding closest points for time variable*
>>> *Time values for time/freq decomposition is not perfectly uniformly
>>> distributed*
>>> *The window size used is 167 samples (668 ms) wide.*
>>> *Estimating 28 log-spaced frequencies from 5.0 Hz to 60.0 Hz.*
>>> *Processing time point (of 200): 10 20 30 40 50 60 70 80 90 100 110 120*
>>> * 130 140 150 160 170 180 190 200*
>>> *Computing the mean baseline spectrum*
>>> *Note: Add output variables to command line call in history to*
>>> *      retrieve results and use the tftopo function to replot them*
>>>
>>>
>>> How exactly is the window size computed? In the archives I read a couple
>>> of times, that it should be close to 1000/(lowest frequency) x (number
>>> of cycles). In my example that should lead to a window size of 600 and not
>>> 668. Where do those 'extra' 68 ms come from?
>>>
>>> How can I calculate how many cycles were used at specific frequencies? I
>>> have 3 cycles at the lowest and 14 cycles at the highest frequency and I am
>>> getting estimates for 28 frequencies. Does that mean that I get  ~ 0.4
>>> cycles more per frequency step? (3.4 cycles at  5.48 Hz; 3.8 cycles at 6.01
>>> Hz)?
>>>
>>> Thanks a lot for your help,
>>> Katharina
>>>
>>>
>>>
>>>
>>>
>>>
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>>
>>
>>
>> --
>> Makoto Miyakoshi
>> Swartz Center for Computational Neuroscience
>> Institute for Neural Computation, University of California San Diego
>>
>
>

--
Makoto Miyakoshi
Swartz Center for Computational Neuroscience
Institute for Neural Computation, University of California San Diego
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