[Eeglablist] How much data is interpolated for ASR cleaning

[Dickinson, Abigail]

Thanks for the helpful suggestions.


>Apply the cleaning mask you have in EEG.etc.clean_data_points to the data that are BEFORE applying ASR.

>Now you have two data sets with the identical length, but one is before and the other is after cleaning. You can perform simple subtraction to obtain the difference waves for visual inspection, performing statistics, etc.


This is great, so I could work out channel by channel the % of identical data between the two - and from that work out how much data was interpolated.


>One convenient measure I recommend you to try is percent variance accounted for (PVAF) which is computed in this way.
>PVAF = 100-100*mean(var(beforeASR-afterASR))/mean(var(beforeASR))

Thanks, this is also super helpful. I just wondered what PVAF you would think appropriate (roughly) - its seems that from trying this approach with a few datasets (and using different parameters) the PVAF for some participants seems reasonable to me (30-40%) - whereas for others its really low (<1%)?

Best,

Abby

________________________________
From: Makoto Miyakoshi <mmiyakoshi at ucsd.edu>
Sent: Wednesday, October 3, 2018 11:00 AM
To: Dickinson, Abigail
Cc: EEGLAB List
Subject: Re: [Eeglablist] How much data is interpolated for ASR cleaning

Dear Abby,


> I understand how to extract how many channels/samples are kept in the cleaned dataset using EEG.etc.

Exactly... well, to be really exact, you calculate sum(EEG.etc.clean_data_points)/length(EEG.etc.clean_data_points) to compute the ratio of the rejected data points.

> However, I'd like to keep track of how much data had to be interpolated while batch processing. While this information is easily accessible from the command line (ie. Keeping 82.5% (132 seconds) of the data) - I'm not sure where this data is saved in the data structure?

  1.  Apply the cleaning mask you have in EEG.etc.clean_data_points to the data that are BEFORE applying ASR.
  2.  Now you have two data sets with the identical length, but one is before and the other is after cleaning. You can perform simple subtraction to obtain the difference waves for visual inspection, performing statistics, etc.
  3.  One convenient measure I recommend you to try is percent variance accounted for (PVAF) which is computed in this way.

PVAF = 100-100*mean(var(beforeASR-afterASR))/mean(var(beforeASR))

Note that the variance should be computed ACROSS CHANNELS (i.e., variance across scalp maps, for each frame!)
For the reference of this calculation, see https://www.ncbi.nlm.nih.gov/pubmed/26738014<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ncbi.nlm.nih.gov_pubmed_26738014&d=DwMFaQ&c=UXmaowRpu5bLSLEQRunJ2z-YIUZuUoa9Rw_x449Hd_Y&r=zgt47dO6mAzDhi4xI_zg4qBpgMHFQTErqFxzJ1dunyI&m=ybdIixh_G8wXWPQLr6jjNMBbCq_4f7XuWpezugMLL80&s=syQuegQkYG-zj1J9lbGer3t5qr88Efs7WP5pp01dfzQ&e=>

I have one paper under review, a collaboration with UCLA Sandra Loo, in which I calculated and reported all of the cleaning parameters and results... but it is not accepted yet.

Makoto



On Wed, Oct 3, 2018 at 4:23 AM Dickinson, Abigail <ADickinson at mednet.ucla.edu<mailto:ADickinson at mednet.ucla.edu>> wrote:

Hi all,


I'm hoping to use ASR cleaning, but also want to quantify the amount of data that is interpolated for each participant.


I understand how to extract how many channels/samples are kept in the cleaned dataset using EEG.etc.


However, I'd like to keep track of how much data had to be interpolated while batch processing. While this information is easily accessible from the command line (ie. Keeping 82.5% (132 seconds) of the data) - I'm not sure where this data is saved in the data structure?


Any help would be greatly appreciated!


Thanks in advance,


Abby

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