[Eeglablist] Repairing non-stereotyped artifacts using using the Automatic Artifact Removal (AAR) toolbox

Makoto Miyakoshi mmiyakoshi at ucsd.edu
Mon May 12 08:50:40 PDT 2014


Dear Lars,

> For example, how do I run a spectro-analysis with a 90% overlapping
Hanning window of 1 s (512-point short-time Fourier transform) including a
baseline (mean baseline power) within the stimulus, and with log-converted
power values (dB)?

Go to http://sccn.ucsd.edu/pipermail/eeglablist/2014/thread.html and find
this thread
[Eeglablist] How to change FFT parameters?
See what Arno says there.

> How would I caluclate relative (vs. absolute) dB?

In EEGLAB, 1uV peak-to-peak sine wave power is defined to be 0dB;, 10uV is
20dB, 0.1uV is -20dB etc.

> Is it possible to run the spectro-analysis in grouped frequency ranges
(e.g., delta, theta, alpha, beta, gamma) seperately? What would be the code
I would have to add in the interface? I am a bit confused, since the
Freq.range [Hz] on the "Build preclustering array"interface is by default
"3 25" and by changing it would not change the output.

Go to http://sccn.ucsd.edu/pipermail/eeglablist/2014/thread.html and find
this thread
[Eeglablist] Extracting data in frequency ranges from dataset
Find my replies. You can find code for that.

> And two questions concerning statistics: Does the sampling rate have an
impact on (permutation) statistics? Currently, I am using a sampling rate
of 500. I would probably have to down-sample if it increases multiple
corrections.

Although I don't have mathematical proof, I would say no.

> And finally, I can't find a file with the statistical values. I assume I
would just have to click on the cluster I am interested and select the
statistics ("STATS") and plot spectra. Then matlab should create a new
file, right?

If you want to extract statistics results, you need to run it from command
line. I strongly believe that this should be fixed so that users can access
result values. Let me show you a temporally solution for a workaround. In
STUDY edit/plot GUI, show spectra for all clusters. Press 'ok' and close
the edit/plot GUI to make EEGLAB updated. In the Matlab workspace, click
'STUDY-cluster(1,x) where x is your desired cluster - spectra (or something
like that). You can find stacked arrays of spectra in the order of
conditions (conditions are separated as cell), frequency, and ICs. You can
run statistics on your own using these values.

Makoto

2014-05-12 4:20 GMT-07:00 <lars.rogenmoser at psychologie.uzh.ch>:

> Dear Makoto
>
> Thank you very much for your help on the time-frequency analysis. However,
> since EEGlab has been updated recently, the problem ("Inner matrix
> dimensions must agree") did not occur anymore. Thus, the problem is solved.
>
> Currently, I am analyzing spectra on the level of IC clusters. However,
> even though I studied the manual carefully, I don t fully understand how to
> use these spectopo parameters provided on the interface “Precompute
> component measures ”(Power spectrum). I was wondering whether you could share
> your knowledge on this. I would be really thankful!
>
> For example, how do I run a spectro-analysis with a 90% overlapping
> Hanning window of 1 s (512-point short-time Fourier transform) including
> a baseline (mean baseline power) within the stimulus, and with
> log-converted power values (dB)?
>
> How would I caluclate relative (vs. absolute) dB?
>
> Is it possible to run the spectro-analysis in grouped frequency ranges
> (e.g., delta, theta, alpha, beta, gamma) seperately? What would be the code
> I would have to add in the interface? I am a bit confused, since the
> Freq.range [Hz] on the "Build preclustering array"interface is by default
> "3 25" and by changing it would not change the output.
>
> And two questions concerning statistics: Does the sampling rate have an
> impact on (permutation) statistics? Currently, I am using a sampling rate
> of 500. I would probably have to down-sample if it increases multiple
> corrections. And finally, I can't find a file with the statistical values.
> I assume I would just have to click on the cluster I am interested and
> select the statistics ("STATS") and plot spectra. Then matlab should create
> a new file, right?
>
> I hope these arent too many questions. Thousand thanks!!!
>
> best, Lars
>
>
>
>
>
>
> -----Makoto Miyakoshi <mmiyakoshi at ucsd.edu> schrieb: -----
> An: lars.rogenmoser at psychologie.uzh.ch
> Von: Makoto Miyakoshi <mmiyakoshi at ucsd.edu>
> Datum: 15.04.2014 17:34
>
> Betreff: Re: [Eeglablist] Repairing non-stereotyped artifacts using using
> the Automatic Artifact Removal (AAR) toolbox
>
> Dear Lars,
>
> Sorry for delay.
> I found you sent me the document that says your size(EEG.icaact,1) == 0,
> which is a problem. This means that you don't have independent component
> activation.
>
> Do you have ICA matrix? Check your main EEGLAB GUI to see whether ICA is
> yes. If it's yes AND size(EEG.icaact,1) == 0, that is pathological. You
> should try this code
>
> EEG = eeg_checkset(EEG, 'ica');
>
> although I don't understand why you don't have EEG.icaact... and if you
> don't have EEG.icaact you should not have been able to compute component
> cross coherence.
>
> Could you check you EEG.data also? Does it say 'mmo' (memory mapping
> object) by any chance? If that's the case, then you should do
>
> EEG.data = EEG.data(:,:,:);
>
> to retrieve all data into RAM. I hate this memory mapping object since
> this is not compatible with many EEGLAB functionis and causes troubles
> everywhere. This memory mapping option comes with (I believe) Mobilab. In
> the EEGLAB set up option you may find an item for this memory mapping
> object. TURN IT OFF if it is ever checked 'on'!
>
> Makoto
>
> Makoto
>
>
> 2014-04-07 3:01 GMT-07:00 <lars.rogenmoser at psychologie.uzh.ch>:
>
>> Dear Makoto
>>
>> I pasted the following code and received a large message. I copied it in
>> a word file and attached it. I further attached my dataset for
>> toubleshooting.
>> I am still struggling with this error. I really appreciate your help.
>>
>> Best regards,
>> Lars
>>
>>
>> -----Makoto Miyakoshi <mmiyakoshi at ucsd.edu> schrieb: -----
>> An: lars.rogenmoser at psychologie.uzh.ch
>> Von: Makoto Miyakoshi <mmiyakoshi at ucsd.edu>
>> Datum: 05.04.2014 04:26
>>
>> Betreff: Re: [Eeglablist] Repairing non-stereotyped artifacts using using
>> the Automatic Artifact Removal (AAR) toolbox
>>
>> Dear Lars,
>>
>> Check the following, copy and paste what you find. I may be able to find
>> something there.
>>
>> EEG.icachansind
>> size(EEG.icaact,1)
>> EEG.nbchan
>> EEG.history
>>
>> If this does not work... you may need to send me a sample data for
>> troubleshooting. It's highly likely that this is not an EEGLAB bug, but I'd
>> be happy to help you anyways!
>>
>> Makoto
>>
>>
>>
>> 2014-04-03 5:05 GMT-07:00 <lars.rogenmoser at psychologie.uzh.ch>:
>>
>>> As I mentioned, on channel level I am able to plot time-frequency and
>>> also cross-coherence. In fact, I am also able to run component
>>> cross-coherence, but unfortunately no component time-frequency which seems
>>> to be quite strange. I receive the error "Inner matrix dimensions must
>>> agree".
>>>
>>> I imported vhdr-files recorded from Geodesics-system. I used a
>>> self-generated channel location (please find attached), however I read this
>>> template over "read locations" and chose the "BESA or EGI-3D cartesian .sfp
>>> file" format, ending up with 109 channels. My sampling rate is 500 Hz. I
>>> tried lowering the sampling rate (250 Hz) but the problem remained. I
>>> re-referenced using an averaged reference. I filtered 1-100 Hz (Basic FIR
>>> filter) and used the cleanline algorithm. I removed segemnts on which the
>>> subjects responded (select data using events), ending up with a dataset
>>> with segemnts of interest. I ran ASR and then ICA (extended), of course
>>> excluding noisy channels before. I then epoched the segemnts (extract
>>> epoches) beloning to the same conditions. Precisely, I have 4 segements per
>>> conditions however with a lenght of 1 minute (+5 sec pre-stimulus). I haven
>>> t removed the baseline or corrected anything in this circumstance.
>>>
>>> Furthermore, I re-named the types of the triggers (Event values) and
>>> also co-registered channel location with head mesh (colin27headmesh). I am
>>> using the latest version of EEGlab and Matlab R2013b.
>>>
>>> I really hope this helps.
>>>
>>> Best, Lars
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>
>
> --
> 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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