[Eeglablist] ICA Transformation on non-ASR or ASR cleaned data

[Makoto Miyakoshi]

Dear Srinivas,

> 1.  high pass filter (1Hz)
2.  line noise filter
3.  bad channel rejection
4. common average reference
5. Artifact subspace reconstruction
6. AMICA
7. Apply ICA sphering and weighting matrices to data

I recommend average reference AFTER ASR (and before AMICA, reject 1 channel
or reduce rank by 1 with PCA option.)

If the number of channels are different, you can't apply AMICA weight
matrices.

> Let say, after step 5, I have 66 channels and ASR rejects one channel. I
get an error when I try to apply sphering and weighting matrices on non-ASR
cleaned data because icasphere and icaweights are matrices of size 65 by
65. To avoid this problem, should I remove that bad electrode prior average
reference so that ASR would not reject any electrodes?

I assume you want to load AMICA results to the ASR-cleaned data. So no
problem. It's not that clean_rawdata() channel rejection confuses the
number of channels. It just reject bad channels.

Makoto

On Wed, Jul 29, 2015 at 8:47 AM, Srinivas Kota <svkota at gmail.com> wrote:

> Hello
>
> My EEG data consists of 71 channel and of 15 minutes duration with a
> sampling rate of 1000 Hz. The preprocessing pipeline include
> 1.  high pass filter (1Hz)
> 2.  line noise filter
> 3.  bad channel rejection
> 4. common average reference
> 5. Artifact subspace reconstruction
> 6. AMICA
> 7. Apply ICA sphering and weighting matrices to data
>
> Should I consider ASR cleaned data or average referenced data (prior ASR)
> for applying ICA sphering and weighting matrices? Any explanation would be
> helpful.
>
> Let say, after step 5, I have 66 channels and ASR rejects one channel. I
> get an error when I try to apply sphering and weighting matrices on non-ASR
> cleaned data because icasphere and icaweights are matrices of size 65 by
> 65. To avoid this problem, should I remove that bad electrode prior average
> reference so that ASR would not reject any electrodes?
>
> Best
> Srini
>
> --
>
> ***********************************************************
> Srinivas Kota, Ph.D
> Research Scientist
> Movement and Neurosciences Center
> Institute for Rehabilitation Science and Engineering
> Madonna Rehabilitation Hospital
> 5401 South St, Lincoln, NE 68506
> Email: svkota at gmail.com
> Ph:  (618) 319-0471 (cell)
> www.madonna.org/research_institute/index.html
> <https://owa.madonna.org/owa/redir.aspx?C=RNnR5lrQvEmYU7lVtl6kLHIjwe3PiNAI8ouI90lD2Vnn4niuQ5QMBdLYDKmByFhfb525xS5XXT8.&URL=http%3a%2f%2fwww.madonna.org%2fresearch_institute%2findex.html>
> ***********************************************************
>
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-- 
Makoto Miyakoshi
Swartz Center for Computational Neuroscience
Institute for Neural Computation, University of California San Diego
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