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

Makoto Miyakoshi mmiyakoshi at ucsd.edu
Fri May 16 08:32:44 PDT 2014


Dear Lars,

> By default, I would pre-cluster with "3 25". However, I am confused since
the whole frequency range (0-250 Hz) is alway calculated anyway.

Imagine your experimental paradigm is SSVEP or Kanizsa triangle
presentation targeting at gamma-band activities. You want to use 40-80Hz in
this case, in stead of 3-25Hz. This allows users to focus on specific
frequency ranges for clustering criteria.

> Do you know how to include a mean baseline power deriving from a specific
time period (at the level of clusters)? I am not sure whether its
'baseline' or 'powbase'. Both are discussed in terms of spectral analysis.

I checked std_preclust() help but did not see 'baseline' or 'powbase'...
aren't they options for ERSP?

Makoto

2014-05-16 7:37 GMT-07:00 <lars.rogenmoser at psychologie.uzh.ch>:

> I am just interested in the spectra (no ERSP). thats why I am
> pre-computing that only. Concerning pre-clustering, it is also possible to
> specify the freq. range [Hz]. By default, I would pre-cluster with "3 25".
> However, I am confused since the whole frequency range (0-250 Hz) is alway
> calculated anyway.
>
>
> Do you know how to include a mean baseline power deriving from a specific
> time period (at the level of clusters)? I am not sure whether its
> 'baseline' or 'powbase'. Both are discussed in terms of spectral analysis.
>
> best, Lars
>
>
>
>
> -----Makoto Miyakoshi <mmiyakoshi at ucsd.edu> schrieb: -----
>  An: lars.rogenmoser at psychologie.uzh.ch
> Von: Makoto Miyakoshi <mmiyakoshi at ucsd.edu>
> Datum: 15.05.2014 01:21
>
> Kopie: EEGLAB List <eeglablist at sccn.ucsd.edu>
> Betreff: Re: [Eeglablist] Repairing non-stereotyped artifacts using using
> the Automatic Artifact Removal (AAR) toolbox
>
> > 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
>



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