[Eeglablist] NFT plugin and RELICA to reproduce Acar and Makeig 2020 (BIBE)

[Scott Makeig]

Enea -

RELICA with SCS distributed source localization on the cortical surface
really in practice requires use of SCALE to estimate skull conductivity in
the head model, since using a mis-estimate (e.g., some template value) to
build the head model can mean the equivalent dipole is drawn inward or
outward in error by up to 1 cm in either direction -- making the SCS (or
any high-resolution) cortical surface solution poor-fitting and unreliable.
I know Zeynep is working to make SCALE head modeling freely runnable on HPC
resources via the Neuroscience Gateway (nsgportal.org) and will announce
its availability when it is ready to use.

Scott

On Wed, Sep 22, 2021 at 3:29 PM Ceolini, E. (Enea) via eeglablist <
eeglablist at sccn.ucsd.edu> wrote:

> Dear Zeynep,
>
> Thanks for your response, I had already found that repo but I was
> wondering if there is some public code available to reproduce the pipeline
> that uses RELICA with the SCS localisation method, it seems the repo you
> point to has no mention of this RELICA integration.
>
> Thanks in advance for your help and time.
>
> +Enea
> On 21 Sep 2021, 21:44 +0200, Zeynep Akalin Acar <zeynep at sccn.ucsd.edu>,
> wrote:
> Here is the link:
>
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_sccn_NFT-5Ftest&d=DwIGaQ&c=-35OiAkTchMrZOngvJPOeA&r=kB5f6DjXkuOQpM1bq5OFA9kKiQyNm1p6x6e36h3EglE&m=UgnNOq3qo2xV0m3DtktxVEW8nPnO1Wy31zHzsRdx4B8&s=9M2fpC-8tTHJUWPjI8Ds5z7ii9mY5Hx4bbWCbHFzHao&e=
>
> Thanks,
> Zeynep
>
> On Tue, Sep 21, 2021 at 10:53 AM Clement Lee via eeglablist <
> eeglablist at sccn.ucsd.edu<mailto:eeglablist at sccn.ucsd.edu>> wrote:
> Hi Zeynep,
>
> Is there a permalink to your NFT demo data, or could you please share a new
> link with Ceolini here who is interested in replicating your pipeline?
>
> Thanks,
> Clement Lee
> Applications Programmer
> Swartz Center for Computational Neuroscience
> Institute for Neural Computation, UC San Diego
> 858-822-7535
>
>
> On Tue, Sep 21, 2021 at 7:57 AM Ceolini, E. (Enea) via eeglablist <
> eeglablist at sccn.ucsd.edu<mailto:eeglablist at sccn.ucsd.edu>> wrote:
>
> > Dear all
> >
> > I am very interested in reproducing the pipeline for source localisation
> > that was proposed in this BIBE 2020 paper (
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__ieeexplore.ieee.org_document_9288020&d=DwIGaQ&c=-35OiAkTchMrZOngvJPOeA&r=kB5f6DjXkuOQpM1bq5OFA9kKiQyNm1p6x6e36h3EglE&m=wu9jYMcDx7y_who5XJ1_eUR2KnOXEiNP-qtcb6Dgd5c&s=xJkMBjxKxr7Bn6F_d_Rn9vQoPuk66k06Eu8HUfApYN0&e=
> > ) by Acar and Makeig.
> >
> > In particular I am interested in reproducing the step described in
> Section
> > II paragraph C were the authors used RELICA to estimate the noise
> > covariance matrix for the subsequent SCS: “When we used the variance of
> ICs
> > across the bootstrap clusters as the noise covariance matrix in SCS,..."
> >
> > I am following the paper and the associated slides from the EEGLAB
> > workshop (
> >
> https://sccn.ucsd.edu/githubwiki/files/eeglab2021_high_resolution_source_imaging.pdf
> )
> > and I have located (almost) all of the components except for the demo
> > folders that is cited at the end of the presentation. I think they are
> > supposed to be available at this link (
> > https://rdl-share.ucsd.edu/message/U7F0uMivgbGZJur64TXDac) but the link
> > appears to be broken.
> >
> > I believe the demo could really help me understand how to interface the
> > RELICA output with the NFT plugin and in particular with the SCS method.
> > Could anyone help me locate these demo?
> >
> > Thank you in advance for your time and your help,
> >
> > Best regards,
> >
> > +Enea
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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