[Eeglablist] ICA, re-referencing, interpolation

[Makoto Miyakoshi]

Dear Jumana,

> I am hoping that if I delete the ICA information and then interpolate and
rereference the raw data,that this should be fine?

It is always fine as long as you re-run ICA.

Makoto


On Fri, Jan 13, 2017 at 1:22 AM, Ahmad, Jumana <jumana.ahmad at kcl.ac.uk>
wrote:

>
> Hi Makoto,
> I think your code does, but I am following a mix of your pipeline when
> appropriate but also reordering this it to keep in line with what my
> colleagues in the same project are doing, and they interpolate after. So I
> am trying to follow those steps. I am hoping that if I delete the ICA
> information and then interpolate and rereference the raw data,that this
> should be fine? I will check carefully but when I view the raw data after
> rereferencing, the blinks are still removed.
> Best wishes,
> Jumana
> ------------------------------------------
> Jumana Ahmad
> Post-Doctoral Research Worker in Cognitive Neuroscience
> EU-AIMS Longitudinal European Autism Project (LEAP) & SynaG Study
> Room M1.26.Department of Forensic and Neurodevelopmental Sciences (PO 23)
> | Institute of Psychiatry, Psychology & Neuroscience | King’s College
> London | 16 De Crespigny Park | London SE5 8AF
>
> Phone: 0207 848 5359| Email: jumana.ahmad at kcl.ac.uk | Website:
> www.eu-aims.eu | Facebook: www.facebook.com/euaims
>
> ------------------------------
> *From:* Makoto Miyakoshi <mmiyakoshi at ucsd.edu>
> *Sent:* 13 January 2017 10:02:59
>
> *To:* Ahmad, Jumana
> *Cc:* eeglablist at sccn.ucsd.edu
> *Subject:* Re: [Eeglablist] ICA, re-referencing, interpolation
>
> Dear Jumana,
>
> > I am trying to replicate a pipeline very precisely and this pipeline
> interpolates after ICA.
>
> Oops, is that true? But when I checked the latest description now, I found
> that they do NOT change channels after AMICA. Press 'refresh' button to
> update the page if you haven't done so.
>
> > If possible I would like to interpolate after, as I only need to work
> with the channel data after the ICA.
>
> If that's the goal, then I think it's fine. But test it carefully before
> you press the final button! If you are not confident, I recommend you use
> dead copy of my code and use the channel information in the end (assuming
> that my latest code does NOT interpolate channels after ICA).
>
> Makoto
>
>
>
> On Thu, Jan 12, 2017 at 11:31 PM, Ahmad, Jumana <jumana.ahmad at kcl.ac.uk>
> wrote:
>
>>
>> Hi Makoto,
>> I am trying to replicate a pipeline very precisely and this pipeline
>> interpolates after ICA. I only wanted to remove the artefacts from the data
>> and then convert back to channel data. If I delete the eye blink components
>> and then convert back to raw data, -and then delete all ICA info, such as
>> the weights and activations etc, is it then safe for me to interpolate
>> using the channel data (which now has blinks removed)?
>>
>> If I really have to avoid the situation, then how do you get around rank
>> issues of interpolating before? I know you delete channels but how do you
>> know how many to delete in relation to the number of channels interpolated.
>> If possible I would like to interpolate after, as I only need to work with
>> the channel data after the ICA.
>>
>> Thank you again for your advice! Very much appreciated.
>> Jumana
>> ------------------------------------------
>> Jumana Ahmad
>> Post-Doctoral Research Worker in Cognitive Neuroscience
>> EU-AIMS Longitudinal European Autism Project (LEAP) & SynaG Study
>> Room M1.26.Department of Forensic and Neurodevelopmental Sciences (PO 23)
>> | Institute of Psychiatry, Psychology & Neuroscience | King’s College
>> London | 16 De Crespigny Park | London SE5 8AF
>>
>> Phone: 0207 848 5359| Email: jumana.ahmad at kcl.ac.uk | Website:
>> www.eu-aims.eu
>> <https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.eu-aims.eu&data=01%7C01%7Cjumana.ahmad%40kcl.ac.uk%7C89d274d92ca94825ded208d43b8ab8d2%7C8370cf1416f34c16b83c724071654356%7C0&sdata=b2bm%2BLN%2BqlU%2Ff%2BfqHuP1cDUBtGGS8VSHrYwdKzl5d8A%3D&reserved=0>
>> | Facebook: www.facebook.com/euaims
>> <https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.facebook.com%2Feuaims&data=01%7C01%7Cjumana.ahmad%40kcl.ac.uk%7C89d274d92ca94825ded208d43b8ab8d2%7C8370cf1416f34c16b83c724071654356%7C0&sdata=G%2BWt3IuifCY5wZcspxBMYq1li3tZFcTBhSynPUzpTCc%3D&reserved=0>
>>
>> ------------------------------
>> *From:* Makoto Miyakoshi <mmiyakoshi at ucsd.edu>
>> *Sent:* 13 January 2017 08:05:04
>> *To:* Ahmad, Jumana
>> *Cc:* eeglablist at sccn.ucsd.edu
>> *Subject:* Re: [Eeglablist] ICA, re-referencing, interpolation
>>
>> Dear Jumana,
>>
>> I encountered that kind of situation many times, which is why I thought
>> it would be a nice idea to show the exact steps in the wiki page. Now you
>> see my point!
>>
>> Editing channels after ICA is DANGEROUS. There are even some phenomena
>> that confused me to death which I still don't understand (and do not
>> remember well any more). Some of EEGLAB's check function can detect the
>> change of channel number difference and inconsistency with EEG.ica-items,
>> but not all the operations are not supported, particualy any behavior
>> outside GUI (but the worst mysterious case I experienced was replicated
>> even using GUI, so I guess it was like I was performing bug finding in
>> EEGLAB, as if several test players plays an alpha version of a computer
>> game trying to do the weirdest things to find bugs.)
>>
>> So, my advice is that DO NOT EDIT CHANNELS AFTER ICA. Once the mixing
>> matrix is confused and how it happened, you are done. Just stay away from
>> that situation.
>>
>> I appreciate though you have been doing exploration! I'm glad to see that
>> at least other guys than I experience the same issues.
>>
>> From Lufthansa455 to Frankfurt,
>>
>> Makoto
>>
>>
>>
>> On Wed, Jan 4, 2017 at 9:06 AM, Ahmad, Jumana <jumana.ahmad at kcl.ac.uk>
>> wrote:
>>
>>> Dear EEGLab,
>>>
>>>
>>>
>>> I do not include noisy channels in ICA which I only do to remove eye
>>> related components, and specifically want to interpolate then after ICA for
>>> rank reasons. I have now done this to over 100 datasets.
>>>
>>> However, once I interpolate and then re-reference my data to the
>>> average, I get the error: Error: some channels not used for ICA
>>> decomposition are used for rereferencing
>>>
>>>        the ICA decomposition has been removed
>>>
>>>
>>>
>>> However, I purposefully wanted to interpolate these after ICA, and then
>>> use them for the average.
>>>
>>> Is my eye-blink removal via ICA now affected and undone?
>>>
>>> I would appreciate any advice.
>>>
>>> Best wishes,
>>>
>>> Jumana
>>>
>>>
>>>
>>> *------------------------------------------*
>>>
>>> *Jumana Ahmad*
>>>
>>> Post-Doctoral Research Worker in Cognitive Neuroscience
>>>
>>> *EU-AIMS Longitudinal European Autism Project (LEAP) & SynaG Study*
>>>
>>> Room M1.09. Department of Forensic and Neurodevelopmental Sciences (PO
>>> 23) | Institute of Psychiatry, Psychology & Neuroscience | King’s College
>>> London | 16 De Crespigny Park | London SE5 8AF
>>>
>>>
>>>
>>> *Phone:* 0207848 0260| *Email:* jumana.ahmad at kcl.ac.uk
>>> <antonia.sanjose at kcl.ac.uk> | *Website:* www.eu-aims.eu
>>> <https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.eu-aims.eu%2F&data=01%7C01%7Cjumana.ahmad%40kcl.ac.uk%7C283380d9389643d9653708d43b7a38bc%7C8370cf1416f34c16b83c724071654356%7C0&sdata=NdhNvFWrTx1tn28VuA31t4ZIiyIMuEoGJ2%2FR5XnRKaI%3D&reserved=0>
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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
>



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