[Eeglablist] Get Clean Raw Data to report removed channels

Dr Cyril, Pernet wamcyril at gmail.com
Wed Mar 17 11:40:38 PDT 2021


Hi Paul

here is a generic pipeline (from BIDS import and preprocessing to stats) 
we wrote with Arno: 
https://urldefense.com/v3/__https://github.com/LIMO-EEG-Toolbox/limo_meeg/blob/master/resources/from_bids2stats.m__;!!Mih3wA!VFCANPoZqK4Lwd9DtLUZvSGCLnLYMjswYaqcIe0qq8EqzkjSuoHkmsv_acfHH9DcGfIK-Q$  
<https://urldefense.com/v3/__https://github.com/LIMO-EEG-Toolbox/limo_meeg/blob/master/resources/from_bids2stats.m__;!!Mih3wA!VFCANPoZqK4Lwd9DtLUZvSGCLnLYMjswYaqcIe0qq8EqzkjSuoHkmsv_acfHH9DcGfIK-Q$ >

CRD - ICA - IClabel - that's it, data ready :-)

published as 
https://urldefense.com/v3/__https://www.frontiersin.org/articles/10.3389/fnins.2020.610388/full__;!!Mih3wA!VFCANPoZqK4Lwd9DtLUZvSGCLnLYMjswYaqcIe0qq8EqzkjSuoHkmsv_acfHH9BQhMHt0g$  
<https://urldefense.com/v3/__https://www.frontiersin.org/articles/10.3389/fnins.2020.610388/full__;!!Mih3wA!VFCANPoZqK4Lwd9DtLUZvSGCLnLYMjswYaqcIe0qq8EqzkjSuoHkmsv_acfHH9BQhMHt0g$ >


cyril


On 17/03/2021 17:44, Beach, Paul Anthony via eeglablist wrote:
> Thank you Clement! I will check this out.
> To confirm - I would run this after running CRD, correct?
>
> On Mar 17, 2021, at 1:42 PM, Clement Lee <cll008 at eng.ucsd.edu<mailto:cll008 at eng.ucsd.edu>> wrote:
>
> Hi Paul,
>
> Here's a line I just wrote that hopefully helps:
> rmChanIdx = find(~ismember({EEG.chanlocs.labels}, {cleanedEEG.chanlocs.labels}));
> IIRC CRD changes the chanlocs structure when removing channels. If this is the case, we can compare the chanlocs structure before and after clean raw data. `rmChanIdx` stands for removed channel indices. You can access the channel labels with `EEG.chanlocs(rmChanIdx).labels` to see the labels of the removed channels.
>
> Best,
> Clement Lee
> Applications Programmer
> Swartz Center for Computational Neuroscience
> Institute for Neural Computation, UC San Diego
> 858-822-7535
>
>
> On Wed, Mar 17, 2021 at 8:47 AM Beach, Paul Anthony via eeglablist <eeglablist at sccn.ucsd.edu<mailto:eeglablist at sccn.ucsd.edu>> wrote:
> Hello EEGLAB community,
>
> Does anyone have a quick script that could be added to the clean_raw_data (CRD) function (or separately on command line) to spit out exactly what channels (number and name) are removed as part of the CRD function?
>
> The latter would help for quickly interpolating the removed channels.
> As it is I have to stare at a list of original channels/numbers and compare it to the subsequent one leftover after CRD. It’s painful.
>
> Thanks!
> --
> Paul Beach DO, PhD
> PGY5, Movement Disorder Fellow
> Department of Neurology
> Emory University School of Medicine
>
>
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-- 
Dr Cyril Pernet,
Neurobiology Research Unit
Copenhagen University Hospital, Rigshospitalet
Building 8057, Blegdamsvej 9
DK-2100 Copenhagen, Denmark

wamcyril at gmail.com
https://urldefense.com/v3/__https://cpernet.github.io/__;!!Mih3wA!VFCANPoZqK4Lwd9DtLUZvSGCLnLYMjswYaqcIe0qq8EqzkjSuoHkmsv_acfHH9A0XYmf7A$ 
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