[Eeglablist] Some confusion about ERSPs/ITC precomputing

Thu Jul 12 11:45:32 PDT 2012

Dear  Mengyan,

> I found that the plot didn't at the baseline and I think that is due to
my 10Hz filter. Is that a bug?

I believe it is a known bug I have reported previously. I'll post it again
to Bugzilla. What's happening is that it seems filter is applied *after*
baseline correction for plotting. When you run statistics the results must
be correct (because the filtering is only for plotting and does not take
effect in statistics). Sorry for inconvenience.

Makoto

2012/7/12 诸梦妍 <bj12116 at gmail.com>

> Dear Makoto and eeglablists,
>
> Thanks very much!
>
> I have tried solution No.2, and it works well. I will try solution No.1
> after I export longer epoch from BP analyzer since I'm interested in ERSPs
> of 400-800ms.
>
> By the way, I have another question. I precomputed ERPs at baseline of
> -200 to 0ms. When I plot it, I added a high cut-off filter of 10Hz in
> parameter settings.However, I found that the plot didn't at the baseline
> and I think that is due to my 10Hz filter. Is that a bug? I just don't want
> to do the filter before precomputing.....
>
> Hope you could answer my question.
>
> Sincerely,
>
> Zhu Mengyan
>
>
>
>
>
> 2012/7/11 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
>>
>>
>
>
> --
> 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
>

-- 
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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