[Eeglablist] Channels for ICA

[Giatsidis, Fabio]

Thank you Tarik and Makoto for your precious suggestions!

Actually, I should have clarified that the 2-minutes recordings are
segments from a single 10-minute EEG recording, and the patient was asked
to do different things every 2 minutes (keep eyes open, keep eyes closed,
etc.). I thought that chunking the continuous recording in small,
task-specific sub-recording before start cleaning each sub-recording would
have made better sense. But given your answers, a new question comes to my
mind:
- let's assume I first cut down arbitrarily the number of channels to ~100
or less as per Tarik's suggestion (i.e. excluding those around the ears,
etc. that are of little help anyway). Can I run ICA on the 10-minute
continuous recording (even if different "states" happen every 2 minutes) so
that I have enough data points (sqrt(500 Hz x 600 sec / 30) = 100), and *then
*do my chunking? Or is this approach invalid because of the variance in the
tasks that are asked every 2 min?

Sorry for the confusion, I'm just trying to make the most sense out of what
I have and to not make missteps! Thank you immensely for all your help!
-Fabio

--------------------------------
*Fabio Giatsidis, M.D.*
Resident in Neurology - University of Rome "Tor Vergata" - Rome, Italy
Post-doctoral research fellow - Brown University - Providence, RI, USA


On Wed, Jul 25, 2018 at 3:18 PM, Makoto Miyakoshi <mmiyakoshi at ucsd.edu>
wrote:

> Dear Fabio,
>
> > I have a (probably naive) question regarding ICA.
>
> I'll give you my naive answers, not intentionally but due to my
> limitations. Follow them at your own risk.
>
> > - whether I should or not choose the whole 128 channel set for running
> ICA
>
> Yes, unless your data is too short for that. Remember, (number of
> channels)^2 x 30 data points at 256 Hz sampling rate is a rule of thumb for
> running ICA.
>
> > - consequently, how I should *a priori* decide which channels to
> consider for ICA and which not.
>
> You can determine a priori which anatomical regions you are going to
> analyze. Then, if ICA gives you the '(stationary) effective source
> locations' that overlap /are close enough to those pre-selected regions,
> pick them up for the final analysis.
>
> ICA is a hypothesis-free approach, but that does not mean you cannot have
> a hypothesis.
> You might enjoy reading the classic discussion between ICA pioneers and
> Karl Friston about how ICA could be used in neuroscience data analysis.
> Friston KJ. Modes or models: a critique on independent component analysis
> for fMRI. Trends Cogn Sci.  1998. Oct 01; 2(10) 373-375
>
> > The recordings are ~2 minutes long and the sampling rate is 1000 Hz.
>
> If you have only 2 min, you definitely cannot perform >100ch ICA.
> sqrt(250 Hz x 120 sec / 30) is about 31, so you want to use 'pca' option
> to perform dimension reduction to obtain 31 ICs.
>
> > I would like to keep as many channels as possible during pre-processing,
> and afterwards discard the ones I realize are not useful to my analysis -
> if this approach seems reasonable.
>
> Record longer. 2-min EEG is too short if you want to use ICA.
>
> Makoto
>
> On Thu, Jul 19, 2018 at 3:26 AM Giatsidis, Fabio <
> fabio_giatsidis at brown.edu> wrote:
>
>> Hello EEGLAB list,
>>
>> I have a (probably naive) question regarding ICA.
>> I have been using an EGI 128-channel system to record resting states. I
>> have been reading a bit about ICA, but it is still not clear to me:
>> - whether I should or not choose the whole 128 channel set for running
>> ICA, and
>> - consequently, how I should *a priori* decide which channels to
>> consider for ICA and which not.
>>
>> The recordings are ~2 minutes long and the sampling rate is 1000 Hz. I
>> would like to keep as many channels as possible during pre-processing, and
>> afterwards discard the ones I realize are not useful to my analysis - if
>> this approach seems reasonable.
>>
>> Also:
>> - if as a very first step I delete some clearly bad channels and then
>> interpolate them to repopulate the original channel set, is it legit to
>> include such interpolated channels during ICA?
>>
>> Thank you very much!
>> Best,
>> -Fabio
>>
>> --------------------------------
>> *Fabio Giatsidis, M.D.*
>> Resident in Neurology - University of Rome "Tor Vergata" - Rome, Italy
>> Post-doctoral research fellow - Brown University - Providence, RI, USA
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>
>
>
> --
> Makoto Miyakoshi
> Swartz Center for Computational Neuroscience
> Institute for Neural Computation, University of California San Diego
>
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