[Eeglablist] Error in running ICA
Makoto Miyakoshi
mmiyakoshi at ucsd.edu
Wed Jul 11 11:35:16 PDT 2018
Dear Edwige,
> I have no idea what this means and at this point I am quite desperate
because I really need this participant…
Don't worry Edwige, this data will be fine.
In the worst case, you can still send it to me for re-processing.
> 1: the number of channels is: 55
Ok it means you do have 55 channels.
> 2: the number of rows is I think: 53 (?)
Sorry, I should have asked you to do it in this way: Could you please copy
and paste all the output from typing 'EEG'? It's like this.
EEG =
setname: '5022'
filename: '5022.set'
filepath: '/data/data/data/data/data/data/data'
subject: '5022'
group: ''
condition: ''
session: []
comments: ''
nbchan: 128
trials: 1
pnts: 540914
srate: 250
xmin: 0
xmax: 2.1637e+03
times: [1x540914 double]
data: [128x540914 single]
icaact: [123x540914 single]
icawinv: [128x123 double]
icasphere: [123x128 double]
icaweights: [123x123 double]
icachansind: [1x128 double]
chanlocs: [1x128 struct]
urchanlocs: []
chaninfo: [1x1 struct]
ref: 'averef'
event: [1x1096 struct]
urevent: [1x1015 struct]
eventdescription: {'' '' '' ''}
epoch: []
epochdescription: {}
reject: [1x1 struct]
stats: [1x1 struct]
specdata: []
specicaact: []
splinefile: ''
icasplinefile: ''
dipfit: [1x1 struct]
history: [1x432 char]
saved: 'yes'
etc: [1x1 struct]
datfile: '5022.fdt'
I made a mistake, I should have asked to tell me the number of columns
instead of rows (i.e., the second dimension of the n x m matrix; m must be
the same as the number of channels).
Makoto
On Tue, Jul 10, 2018 at 1:56 AM E. Sijyeniyo <e.sijyeniyo at student.rug.nl>
wrote:
> Dear Makoto,
>
> I have been spending some time now trying to figure out what your
> suggestion means, but I am afraid I don’t really understand what you mean.
>
> In our previous correspondence you answered the following:
>
> “*You mean this error message again?*
>
>
> *"eeg_checkset error: number of elements in ‘icachansind’ (55) does not
> match the number of columns in the sphere array (54). Should EEGlab remove
> ICA information (press cancel to fix the problem from the command line)”. *
>
> *That's pretty strange...*
> *One think you can try quickly is that when you use infomax, use 'pca',
> 58; If your current number of channels is 60, you try 59, 58, 57... I'm
> testing here the possibility of dimension reduction happened to your data
> in an unexpected reason.*
>
> *EEG.icasphere has the dimension of the data decomponsed and the number of
> channels used, where nbchan >= data rank. When this is equal, it is called
> 'full rank' which is the basic assumption. Runica() has its own rank
> detection stage to estimate the right rank of the data, which sometimes
> fails.*
>
>
> *I still suspect that some type of user operation caused the channel
> inconsistency. Are you sure you did not do any channel manipulation after
> ICA?*
>
> *Makoto*”
>
> I typed in what you suggested:
>
> Sorry for the trouble.
> I want to know
>
> 1. The number of channels (EEG.nbchan)
> 2. The number of rows in EEG.icasphere *right after* ICA
>
> 1: the number of channels is: 55
> 2: the number of rows is I think: 53 (?) I get a lot of data with zeros
> and the last bit of data says: Colums 53 through 55.
>
> I have no idea what this means and at this point I am quite desperate
> because I really need this participant…
>
> Thank you.
>
> Best,
> Edwige
>
>
>
>
> On Wed, Jul 4, 2018 at 12:58 AM E. Sijyeniyo <e.sijyeniyo at student.rug.nl>
> wrote:
>
>> Dear Makoto,
>>
>> I performed ICA on the dataset on which I got the error message, this
>> time I excluded the EOG channels before ICA and therefore I didn’t click on
>> the "…channels thing". However, surprisingly, I received the same error
>> again.
>>
>> Now I really don’t know what might have gone wrong.
>>
>> Any insights on this?
>>
>> Thank you so much for your time!
>>
>> Best,
>> Edwige
>>
>> Op 3 jul. 2018, om 19:43 heeft Makoto Miyakoshi <mmiyakoshi at ucsd.edu>
>> het volgende geschreven:
>>
>> Dear Edwige,
>>
>> My guess is that that's a bug in EEGLAB and caused by using that
>> 'channels' thing.
>>
>> > Click on the button ... channels to select all the channels except
>> EOGh and EOGvl. The eye electrodes need to be excluded, because they
>> don’t have the same reference as the other electrodes in our dataset. The
>> eye electrodes are bipolar, meaning that they are referenced to each other.
>> The other electrodes, however, are referenced to the average of all
>> electrodes.
>>
>> This kind of thing is poorly supported. I'm pretty sure that if you don't
>> do it, it'll run fine. Try it.
>>
>> If you don't include channels to ICA, what's the point of having
>> channels... that's our way of thinking. So, if you can't include the EOG
>> channels, reject them before ICA. Eye blinks and saccades are the things
>> ICA can detect most dramatically, so withouot EOG channels it'll be done
>> fine--I have absolutely no worry there.
>>
>> By the way I like your name contains 'ewig'. Nice name.
>>
>> *Weh spricht 'Vergeh!'*
>> *Doch alle Lust will Ewigkeit,*
>> *will tiefe tiefe Ewigkeit!*
>>
>> Makoto
>>
>> On Tue, Jul 3, 2018 at 5:04 AM E. Sijyeniyo <e.sijyeniyo at student.rug.nl>
>> wrote:
>>
>>> Dear Makoto,
>>>
>>> I tried running ICA for a dataset. Since now: I have been doing this in
>>> this order:
>>>
>>> - Go to Tools > Run ICA
>>> - Set ICA algorithm to use to runica
>>> - Click on the button ... channels to select all the channels except
>>> EOGh and EOGvl. The eye electrodes need to be excluded, because they don’t
>>> have the same reference as the other electrodes in our dataset. The eye
>>> electrodes are bipolar, meaning that they are referenced to each other. The
>>> other electrodes, however, are referenced to the average of all electrodes.
>>> - Set the Commandline options to ‘extended’, 1, ‘pca’, [number of
>>> channels -3] (Two of these three channels are the eye electrodes
>>> that you excluded. The third channel needs to be subtracted because we used
>>> average reference, which changes the rank of the data.)
>>> - Click Ok
>>>
>>> Based on your tutorial, I do not include the eye electrodes in since
>>> they were not included in the average reference: see
>>>
>>> - Include EOG, ECG, and other channels as long as they share the
>>> initial reference electrode with scalp electrodes. If EOG channels are
>>> referenced to each other (i.e., bipolar), *exclude them.*
>>>
>>>
>>> This procedure went well and I have been able to get ICs for 6
>>> participants. However, I have done the exact procedure but now I get the
>>> warning:
>>> *"eeg_checkset error: number of elements in ‘icachansind’ (55) does not
>>> match the number of columns in the sphere array (54). Should EEGlab remove
>>> ICA information (press cancel to fix the problem from the command line)”. *
>>>
>>> What does this error mean? I have looked online, but I can't seem to
>>> find what I have done wrong especially because all other datasets went well
>>> with the same procedure….
>>>
>>> I can definitely use your expertise on this issue.
>>>
>>> Thank you so much in advance.
>>>
>>> Best,
>>> Edwige
>>>
>>> Op 27 jun. 2018, om 09:53 heeft E. Sijyeniyo <e.sijyeniyo at student.rug.nl>
>>> het volgende geschreven:
>>>
>>> Dear Makoto,
>>>
>>> Thank you very much for your response! Ok, now I know for sure that I
>>> don’t have to reject these channels!
>>>
>>>
>>> Best,
>>> Edwige
>>>
>>> Op 26 jun. 2018, om 20:02 heeft Makoto Miyakoshi <mmiyakoshi at ucsd.edu>
>>> het volgende geschreven:
>>>
>>> Dear Edwige,
>>>
>>> I don't recommend to reject alpha. Alpha is a great brain component and
>>> explains most part of early visual potentials, for example. If you run ICA,
>>> it will nicely decompose it.
>>>
>>> > a second year research master student
>>>
>>> Very good! Good luck.
>>>
>>> Makoto
>>>
>>> On Tue, Jun 26, 2018 at 10:06 AM E. Sijyeniyo <
>>> e.sijyeniyo at student.rug.nl> wrote:
>>>
>>>> Dear Makoto,
>>>>
>>>> I am Edwige Sijyeniyo, a second year research master student in
>>>> Language and Cognition at the University of Groningen (the Netherlands).
>>>>
>>>> Currently, I am preprocessing my EEG data that I collected for my
>>>> thesis project (name of project: Syntactic Priming in Comprehension).
>>>>
>>>> I am following some of your steps at:
>>>> https://sccn.ucsd.edu/wiki/Makoto%27s_preprocessing_pipeline#To_learn_how_to_evaluate_EEG_and_artifact_ICs_.2801.2F24.2F2017_updated.29
>>>>
>>>>
>>>> I had a question regarding interpolation of bad channels, some
>>>> participants show a lot of alpha waves (especially in the posterior
>>>> electrodes like PO9, PO10, PO7, PO8 etc). I was wondering whether channels
>>>> that contain a lot of alpha waves can be interpolated, therefore marking
>>>> these channels as noisy
>>>>
>>>> Would alpha waves distort the data to a large extent if these are not
>>>> interpolated?
>>>>
>>>> Thank you so much for your time and am looking forward to your response!
>>>>
>>>> Best,
>>>> Edwige
>>>>
>>>>
>>>>
>>>
>>> --
>>> 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
>>
>>
>>
>
>
> Op 6 jul. 2018, om 21:03 heeft Makoto Miyakoshi <mmiyakoshi at ucsd.edu> het
> volgende geschreven:
>
> Dear Edwige,
>
> Sorry for the trouble.
> I want to know
>
> 1. The number of channels (EEG.nbchan)
> 2. The number of rows in EEG.icasphere *right after* ICA
>
> They should match. If they don't, it must be EEGLAB bug--in that case, we
> may need to ask you to send us the dataset. Let us know what you get.
>
> Makoto
>
> On Fri, Jul 6, 2018 at 10:32 AM E. Sijyeniyo <e.sijyeniyo at student.rug.nl>
> wrote:
>
>> Dear all,
>>
>> While running ICA for one of my participants, I received the following
>> error message:
>>
>> *"eeg_checkset error: number of elements in ‘icachansind’ (55) does not
>> match the number of columns in the sphere array (54). Should EEGlab remove
>> ICA information (press cancel to fix the problem from the command line)”. *
>>
>> I have done the preprocessing procedure for this participant the same way
>> in which I have done others. However, for my other participants, I did not
>> get this message, only for this one participant.
>>
>> What I typed in the *Commandline* after selecting for runica is -> ‘extended’,
>> 1, ‘pca’, [number of channels -1] (-1 is because I used average
>> reference which changes the rank of the data).
>>
>> Does anyone know what this error mean? I tried running ICA for the same
>> participant again, but I keep getting the same error…could this be a bug?
>>
>> Thank you so much in advance!
>>
>> Best,
>> Edwige
>>
>>
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>
>
>
> --
> 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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