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

Makoto Miyakoshi mmiyakoshi at ucsd.edu
Wed May 14 16:20:55 PDT 2014


> I was curious about whether it is possible to include different frequency
ranges (delta, alpha...) in component clustering seperately.

You can specify the freq range in ERSP when preclustering. However, if you
want to include multiple ranges, that's impossible. Also, if you want to
test the difference across freq ranges, you need to repeat preclustering
separately for each range, and the results should be treated as separate
too. You can't do multiple frequency range clustering with different
weights etc.

> I am confused since the spectra (plot spectra) remains the same
independently of the 'frequrange'(?) I add. However, on the matlab file
(Study-cluster, specdata) the frequency-bins change correspondingly.

I don't understand this. Is this a spectrum curve or ERSP? Please tell us
more details.

> By the way, what information does the file "specfreqs" contain?

I don't to know off the top of my head...Which function takes this option,
do you know?

Makoto

2014-05-14 14:02 GMT-07:00 <lars.rogenmoser at psychologie.uzh.ch>:

> Dear Makoto
>
> Thanks for the insightful inputs.
>
> I guess 'timerange' [min max] is the spectopo parameter for including a
> power baseline.
>
> Thanks for referring to the code for exporting grouped frequency values.
> However, I was curious about whether it is possible to include different
> frequency ranges (delta, alpha...) in component clustering seperately. This
> might be advantageous since less tests (per Hz) have to be done,
> decrasing the number of multiple corrections. I am confused since the
> spectra (plot spectra) remains the same independently of the
> 'frequrange'(?) I add. However, on the matlab file (Study-cluster,
> specdata) the frequency-bins change correspondingly.
>
> By the way, what information does the file "specfreqs" contain?
>
> Lars
>
>
>
>
>
> -----Makoto Miyakoshi <mmiyakoshi at ucsd.edu> schrieb: -----
> An: lars.rogenmoser at psychologie.uzh.ch
> Von: Makoto Miyakoshi <mmiyakoshi at ucsd.edu>
> Datum: 12.05.2014 17:52
> Kopie: EEGLAB List <eeglablist at sccn.ucsd.edu>
>
> Betreff: Re: [Eeglablist] Repairing non-stereotyped artifacts using using
> the Automatic Artifact Removal (AAR) toolbox
>
> 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
>



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