[Eeglablist] Some confusion about ERSPs/ITC precomputing

Thu Jul 12 11:55:39 PDT 2012

Dear PengMin,

>  *"It is currently not possible to plot ERSP in linear frequency scale in
study. We are working on fixing this issue."*

Sorry but this means linear scaling is not supported in the current version.

> Could you briefly talk about the difference between two parameters:
linear and log?

Linear 10 scales from 1 to 100: 1 12 23 34 45 56 67 78 89 100
Log 10 scales from 1 to 100: 1 1.6 2.7 4.6 7.7 12.9 21.5 35.9 59.9 100

If you use log scale, you have more resolution in lower frequencies.

Makoto

2012/7/12 PengMin Qin <qin.pengmin at gmail.com>

>  Dear Makoto,
>
> Thank you very much! I have tried your suggestions. I used the parameters:
> 'freqs', [3 45], 'nfreqs', 14; but I did not give the 'freqscale'. I run
> the precompute, I did not get the equal freqscale space. So I tried to give
> the 'freqscale', first, I give parameters in the following way: 'freqs', [3
> 45], 'nfreqs', 14, 'freqscale', 'linear' (this is the default option in the
> help file), but I meet one error report: *"It is currently not possible
> to plot ERSP in linear frequency scale in study. We are working on fixing
> this issue."* When I try 'freqscale', 'log', this worked well. I have
> used two versions: 11_0_2_1b and 11_0_1_1b, both of them show the same
> problem. Could you tell me how to figure this question out? Could you
> briefly talk about the difference between two parameters: linear and log?
> Thank you very much!
>
> Best,
> Pengmin
>
>
>
>
>
>
>
>
>
> 2012/7/11 Makoto Miyakoshi <mmiyakoshi at ucsd.edu>
>
>> Dear PengMin,
>>
>> > How could I get the results with frequency in the following way: 3 6 9
>> 12 15 18 ......45? Thanks a lots!
>>
>> 'freqs', [3 45], 'nfreqs', 14
>>
>> The second options specifies the resolution of your frequency range. In
>> the example above, 3-45 Hz will be divided by 14, which is (45-3)/14 = 3
>> (assuming you use the default freqscale option). You can fine-tune the
>> parameter by cut-and-try then if necessary.
>>
>> Makoto
>>
>>
>> 2012/7/10 PengMin Qin <qin.pengmin at gmail.com>
>>
>>> Dear all,
>>>
>>> Thank you very much! Your talk is very useful.
>>>
>>> I have a similar question. I make a study file, and  then then use the
>>> precompute channel measure to calculate the ERSP and ITC. In this study
>>> file including 22 participants, each participants have two conditions. The
>>> epoch for each condition is 1100 ms (-200 to 900). when I calculate the
>>> ERSP and ITC, I use three kinds of parameters for cycles: [1 0], [1 1] and
>>> [1 0.5]; frequency [3 45], baseline [0].  When I check the results of these
>>> three analysis, the frequency of the results are same: 3.00    3.93
>>> 5.15   6.76    8.86    11.61   15.23    19.97    26.18    34.32   45.00. Is
>>> this right? How could I get the results with frequency in the following
>>> way: 3 6 9 12 15 18 ......45? Thanks a lots!
>>>
>>> Best,
>>> Pengmin
>>>
>>>
>>>
>>> 2012/7/10 Makoto Miyakoshi <mmiyakoshi at ucsd.edu>
>>>
>>>> Dear Mengyan,
>>>>
>>>> If you want to have 3 Hz to 30 Hz range after wavelet transform, the
>>>> problem is that you have only -200 to 800 ms so that it is extremely
>>>> difficult to have 3 Hz.
>>>>
>>>> If you use 3 cycles at 3 Hz, your window side is (1000ms/3Hz)*3cycles =
>>>> 1000ms, meaning that 1000ms length data generates 1 datapoint after wavelet
>>>> transform. So your epoch can allow to generate only 1 datapoint!
>>>>
>>>> You can either
>>>>
>>>> 1. prepare longer epoch (from -1000 ms to 2000 ms relative to stimulus
>>>> onset) and use 3 Hz 3 cycle at the lowest: then you'll have -500 to 1500 ms
>>>> after wavelet transform. You lose 500 ms from both sides of your epoch,
>>>> because your window side is 1000 ms. It does not matter very much if your
>>>> epoch overlaps each other if it is not too much.
>>>>
>>>> 2. Give up the lowest frequency range of 3 Hz and use 5 Hz instead with
>>>> 2 cycles (decreasing the cycle number reduces sensitivity though). Then
>>>> you'll have 0 to 800 ms after wavelet transform. You lose 200 ms from both
>>>> sides of your epoch since your window size is (1000ms/5Hz)*2cycles = 400ms.
>>>>
>>>> You can try No.2 immediately. Use the following options to see what
>>>> happens.
>>>>
>>>> 'cycles', [2 0.5], 'freqs', [5 30], 'nfreqs', 50
>>>>
>>>> Makoto
>>>>
>>>>
>>>>
>>>> 2012/7/9 诸梦妍 <bj12116 at gmail.com>
>>>>
>>>>>  Dear eeglablist,
>>>>>
>>>>> I'm just computing EEG data using EEGLAB. However, I met some problems
>>>>> about pre-computing ERSPs/ITC (channel measures) and hope someone could
>>>>> help me.
>>>>>
>>>>> In my experiment, I had 43 subjects, 500Hz sampling rate. It was a 2
>>>>> by 2 repeated measures design, and each condition had about 30 trials and
>>>>> the same 43 channels for each subject after rejecting. I pre-processed the
>>>>> raw data in Brain Vision Analyzer until I extracted epochs for each
>>>>> condition which was -200 to 800ms. I exported the epoched data to EEGLAB,
>>>>> re-saved it as .set and .fdt files for each condition each subject, and
>>>>> created a STUDY using those data. Then I just used the GUI and tried to
>>>>> pre-compute the data.
>>>>>
>>>>> For ERP part, it worked well and got the same result with Analyzer.
>>>>> But for ERSPs/ITS part, it didn't. Actually, I do not quite understand the
>>>>> parameters of ERSPs/ITC processing, so I just used the default. However, I
>>>>> found that it only computed 23.4Hz to 250Hz's data, which do not include my
>>>>> interest Frequency(3 to 30Hz). I tried to add options in GUI like "
>>>>> 'cycles',[3 0.5], 'nfreqs', 100, 'freqs',[3 30] ",but it turned out as a
>>>>> wrong syntax.
>>>>>
>>>>> When I used the default parameter, it showed in the MATLAB command
>>>>> window like this below. I was just wondering what the red sentence means ( 1)
>>>>> to 4) ) and hope that someone could tell me what should I do if I
>>>>> just want it to compute 3Hz to 30Hz frequency.
>>>>>
>>>>> Computing Event-Related Spectral Perturbation (ERSP) and
>>>>>
>>>>>   Inter-Trial Phase Coherence (ITC) images based on 31 trials
>>>>>
>>>>>    of 500 frames sampled at 500 Hz.
>>>>>
>>>>> Each trial contains samples from -200 ms before to
>>>>>
>>>>>   798 ms after the timelocking event.
>>>>>
>>>>>   Image frequency direction: normal
>>>>>
>>>>> [?]1) Using 3 cycles at lowest frequency to 16 at highest.
>>>>>
>>>>> [?]2) Generating 200 time points (-129.0 to 727.0 ms)
>>>>>
>>>>> Finding closest points for time variableTime values for time/freq
>>>>> decomposition is not perfectly uniformly distributed
>>>>>
>>>>>  [?]3) The window size used is 71 samples (142 ms) wide.
>>>>>
>>>>> [?]4) Estimating 100 log-spaced frequencies from 23.4 Hz to 250.0 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
>>>>>
>>>>>
>>>>> Thanks in advance,
>>>>>
>>>>> Zhu Mengyan
>>>>>
>>>>>
>>>>> --
>>>>> Mengyan Zhu
>>>>> Psychology department, Peking University
>>>>> Dormitory 2061, Building 48,No.5 Yiheyuan Road, Haidian District,
>>>>> Beijing 100871, China
>>>>>  E-mail: bj12116 at gmail.com
>>>>>
>>>>> _______________________________________________
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>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Makoto Miyakoshi
>>>> JSPS Postdoctral Fellow for Research Abroad
>>>> Swartz Center for Computational Neuroscience
>>>> Institute for Neural Computation, University of California San Diego
>>>>
>>>>
>>>> _______________________________________________
>>>> Eeglablist page: http://sccn.ucsd.edu/eeglab/eeglabmail.html
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>>>
>>>
>>
>>
>> --
>> Makoto Miyakoshi
>> JSPS Postdoctral Fellow for Research Abroad
>> Swartz Center for Computational Neuroscience
>> Institute for Neural Computation, University of California San Diego
>>
>>
>

-- 
Makoto Miyakoshi
JSPS Postdoctral Fellow for Research Abroad
Swartz Center for Computational Neuroscience
Institute for Neural Computation, University of California San Diego
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