[Eeglablist] how to apply ICA methods on pre-clinical electrode configurations

[Scott Makeig]

The spatial (channel) weights would quantify the degree to which a given
dynamic is truly 'population level' or not ...

On Sun, Jan 17, 2021 at 7:07 PM Brian Harvey <brian.harvey at biogen.com>
wrote:

> Thanks again Dr. Makeig,
>
> Honestly, I don't really care about the "where" as the probe is entirely
> (almost) in sensory thalamus ( 16 channels 50um separation distance). Each
> channel is picking up LFP but also spiking activity (sample rate is ~24K).
> I am detecting different spiking activities at channels in response to the
> stimulus but am not so much concerned about the location but isolating the
> population activity that represents the 10Hz afferent input. My goal in
> this attempt is to avoid a biased selection of channels for quantification.
>
> Best,
> Brian
>
>
>
>
>
>
>
>
> ------------------------------
> *From:* Scott Makeig <smakeig at gmail.com>
> *Sent:* Sunday, January 17, 2021 6:55 PM
> *To:* Brian Harvey <brian.harvey at biogen.com>
> *Cc:* eeglablist at sccn.ucsd.edu <eeglablist at sccn.ucsd.edu>
> *Subject:* Re: [Eeglablist] how to apply ICA methods on pre-clinical
> electrode configurations
>
> ------------------------------
> **** EXTERNAL EMAIL:* Use caution before replying, clicking links, and
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> ------------------------------
> Well, you do want to know & see which electrode combination each IC
> projects to, no?  You need to make an EEG (dataset) structure - then all
> the EEGLAB tools will be readily available...
>
> Scott
>
> On Sun, Jan 17, 2021 at 6:48 PM Brian Harvey <brian.harvey at biogen.com>
> wrote:
>
> Thanks Dr Makeig for your response,
>
> What if one only wanted to see the spectra of each component?  ICA doesn't
> require info about channel locations and in this application, I am not
> concerned about topographies (thus topoplot.m is moot)...
>
> I am naive in regards how to manually use the w and s variables from the
> output of ICA to manually generate the PSDs of each component.
>
> More specifically, the experiment is aimed at evaluating thalamic activity
> in response to whisker deflection (10Hz)... I am hoping to find a component
> that can isolate the driven neural activity... I can do this in the channel
> space using FFT but was thinking to apply ICA and ignore channels....
>
> Cheers,
> Brian
>
>
>
>
>
>
> ------------------------------
> *From:* Scott Makeig <smakeig at gmail.com>
> *Sent:* Sunday, January 17, 2021 6:27 PM
> *To:* Brian Harvey <brian.harvey at biogen.com>
> *Cc:* eeglablist at sccn.ucsd.edu <eeglablist at sccn.ucsd.edu>
> *Subject:* Re: [Eeglablist] how to apply ICA methods on pre-clinical
> electrode configurations
>
> ------------------------------
> **** EXTERNAL EMAIL:* Use caution before replying, clicking links, and
> opening attachments *****
> ------------------------------
> Brian -
>
> The commandline function topoplot.m has a mode in which you can plot
> interpolated electrode positions specified in a rectangular grid (with
> arbitrary 'missing nodes', allowing any grid shape). This can be used to
> plot the IC 'maps'.
>
> As for your main question, read the EEGLAB wiki on building an EEG dataset.
>
> Scott
>
>
> On Sat, Jan 16, 2021 at 11:30 PM Brian Harvey <brian.harvey at biogen.com>
> wrote:
>
> Hi all,
>
> A bit of a hack attempt here... I have LFP data using a 16 channel linear
> probe in VPL/VPM thalamus (in mouse)... I can successfully run ICA using
> CUDAICA
>
> [w,s] = cudaica(LFP,'extended', 1, 'maxsteps', 2048);
>
>
> If I am only interested in the spectral properties of the components (not
> scalp topographies etc) how can I manually plot them for rejection or
> selection? EEGlab functions require channel locations to proceed further
> and I am uncertain how to hack.
>
> Thanks for any insight/assistance
>
> Brian
>
>
>
>
>
>
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> --
> Scott Makeig, Research Scientist and Director, Swartz Center for
> Computational Neuroscience, Institute for Neural Computation, University of
> California San Diego, La Jolla CA 92093-0559, http://sccn.ucsd.edu/~scott
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>
> --
> Scott Makeig, Research Scientist and Director, Swartz Center for
> Computational Neuroscience, Institute for Neural Computation, University of
> California San Diego, La Jolla CA 92093-0559, http://sccn.ucsd.edu/~scott
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-- 
Scott Makeig, Research Scientist and Director, Swartz Center for
Computational Neuroscience, Institute for Neural Computation, University of
California San Diego, La Jolla CA 92093-0559, http://sccn.ucsd.edu/~scott