[Eeglablist] Adjust data rank for ICA?

[Anna Bánki]

Hi Daniele, Julia,


I am also interpolating some bad channels (max 3-4) before running ICA. Could you help, apart from changing max to min in the pop_runica[] script, would you also set back the full rank before running ICA with this code?


channelSubset = loc_subsets(EEG.chanlocs, yourDataRankHere);
EEG = pop_select( EEG,'channel', channelSubset{1});
EEG = pop_chanedit(EEG, 'eval','chans = pop_chancenter( chans, [],[]);');


https://sccn.ucsd.edu/wiki/Makoto%27s_preprocessing_pipeline#Interpolate_all_the_removed_channels_.2803.2F05.2F2021_updated.29

In my layout, there are 3 gyroscope channels on top of the 24 scalp channels, so for now, I only selected my channels as 1:24 before ICA, but did not consider the rank-deficiency issue.


Thanks,

Anna

________________________________
From: eeglablist <eeglablist-bounces at sccn.ucsd.edu> on behalf of Daniele Scanzi <dsca347 at aucklanduni.ac.nz>
Sent: 16 February 2023 21:47
To: Julia Basso
Cc: eeglablist at sccn.ucsd.edu
Subject: Re: [Eeglablist] Adjust data rank for ICA?

Hi Julia,

>From my understanding, you should still change that line (I think it is
line 624) from max to min, otherwise 'runica' most likely won't adjust for
rank-deficient data.

Cheers,

Daniele

On Fri, 17 Feb 2023 at 09:34, Julia Basso <jbasso at vt.edu> wrote:

> Hi,
>
> We are reading Makato's preprocessing pipeline and utilizing the general
> pipeline for our dataset. We have interpolated across some bad channels and
> have taken note of the section on "Adjust data rank for ICA". We see that
> he recommends changing one line of code in pop_runica() from max to min, to
> adjust for the number of interpolated channels. However, this was a note
> from 5/17/19. Has anything been adjusted in the current code to adjust for
> this problem?
>
> Do you recommend doing this or should we leave it at max?
>
> Thank you for any help you can provide!
>
> Best,
>
> Dr. Basso
>
> --
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