[Eeglablist] For Marjan

[Makoto Miyakoshi]

Dear madam Marjan,

> My data is ERP and I want to run Amica on my data because running ICA
(runica) on ERP data takes too time.

Now it has become interesting.
Why don't you tell me the detail of your input data? The number of the
channels, data sampling rate, data length, etc. You should also check the
data by using trimOutlier plugin. Send me a screenshot of the first plot it
generates.

Nowadays, it is hard to believe that runcia() does not run very fast unless
you have > 200 ch and > 1 hour data with very bad stationarity. There must
be an obvious problem in your input data--that's my initial guess.

Makoto


On Sat, Jul 9, 2022 at 7:35 AM m za <ma.zamani.20 at gmail.com> wrote:

> Dear Sir Makoto
> My data is ERP and I want to run Amica on my data because running ICA
> (runica) on ERP data takes too time.I used your instuction on your pipeline
> and I used codes you wrote on pipeline and changed the mfile of runica
> based on those codes. I also recieved result (I mean runica)and it worked(I
> had no problem with ranking of my data). However, I did your pipeline
> instruction(I mean runica on my data) on data that has not epoch(I don't
> know if it was a right action).
> Inaddition, Amica didn't work on both data(ERP data and EEG data) and the
> rank of data has problem. I would appriciate it if you could help me with a
> code that can change the mfile of Amica.
> Best regards
> Marjan
>
>
>
> On Sat, 9 Jul 2022, 02:54 Makoto Miyakoshi via eeglablist, <
> eeglablist at sccn.ucsd.edu> wrote:
>
>> Dear Madam Marjan,
>>
>> > First of all, I used the ASR section of EEG Lab and rejected the bad
>> channels, and after that I applied an interpolate channels and then
>> average
>> reference to my data as you said on your pipeline. But, unfortunately,
>> when
>> I wanted to run Amica to my data, the number of components were less than
>> channels(the number of channels were 14 and components were 2 or 3). I
>> struggled with this issue for a long time but I failed to find an
>> effective
>> solution.
>>
>> That is because when scalp electrodes were interpolated, your data rank
>> dropped to the number of the remaining electrodes. ICA knows how many
>> electrodes were there before interpolation by calculating the data rank.
>> See this article for more information.
>>
>>
>> https://sccn.ucsd.edu/wiki/Makoto%27s_preprocessing_pipeline#What_is_rank.3F_.28Updated_06.2F06.2F2016.29
>>
>> > I also investigated the amount of EIG value, but I have no idea which
>> change I should apply to my data to obtain the required component's
>> amount.
>> I was wondering if you could help me with my problem.
>>
>> See these articles.
>>
>> https://sccn.ucsd.edu/wiki/Makoto%27s_useful_EEGLAB_code#How_to_avoid_the_effect_of_rank-deficiency_in_applying_ICA_.2803.2F31.2F2021_added.29
>> https://sccn.ucsd.edu/wiki/Shannon%27s_ICA_rank_project
>>
>> Makoto
>>
>>
>>
>> Original message:
>> %%%%%%%%%%%%%%%%%%%%%%%%
>> Dear Sir Makoto
>> I would appreciate it if you could guide me about the problem I have with
>> the EEG lab. First of all, I used the ASR section of EEG Lab and rejected
>> the bad channels, and after that I applied an interpolate channels and
>> then
>> average reference to my data as you said on your pipeline. But,
>> unfortunately, when I wanted to run Amica to my data, the number of
>> components were less than channels(the number of channels were 14 and
>> components were 2 or 3). I struggled with this issue for a long time but I
>> failed to find an effective solution. I do not know if the problem is
>> because of the W (Weight matrix) or another reason. I also investigated
>> the
>> amount of EIG value, but I have no idea which change I should apply to my
>> data to obtain the required component's amount. I was wondering if you
>> could help me with my problem.
>> Best regards
>> Marjan
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>