[Eeglablist] online reference

[Roy Cox]

hi all,

(apologies for possibly sending this twice)

saw this discussion and I'm trying to do something similar from the command
line, but no luck.

I import 63 channel data that I know to be referenced to the forehead. then
I remove 3 EOG and EMG channels (60 remaining).

I've created a 61 channel electrode location file, that I read in and
separate into the first 60 "active" locations and the 61st ref/forehead
location. I assign the 60 channel locations to my EEG, and then want to
rereference to average mastoids, while keeping both mastoid channels and
reconstructing the forehead channel. I've tried a couple of things, calling
both pop_reref and reref. I'm sure there's a simple solution but can't get
it to work. the code to my latest attempt:

%read in electrode locations

allchanlocs=readlocs(electrodeFile,'filetype','custom','format',{'labels'
'X' 'Y' 'Z'});



%split into active and ref locs

chanlocs_active=allchanlocs(1:60);

chanlocs_ref=allchanlocs(61);



%read in 63 channel EDF and remove eyes and emg

EEG=pop_biosig(fullfile(subjectFolder,dataFile),'importevent','off');

EEG=pop_select(EEG,'nochannel',[1 2 63]);

EEG.chanlocs=chanlocs_active;

EEG=eeg_checkset(EEG)  ##STILL OK



%rereference to average mastoids

EEG=pop_reref(EEG,[59 60],'keepref','on','refloc',chanlocs_ref);



this now crashes like this:


Attempt to reference field of non-structure array.


Error in pop_reref (line 215)

         allinds = [allinds strmatch( g.refloc(iElec).labels, {
tmpchaninfo.nodatchans.labels }) ];


thanks for any input,


Roy

On Thu, May 7, 2015 at 2:30 PM, Roy Cox <r.cox at uva.nl> wrote:

> hi all,
>
> saw this discussion and I'm trying to do something similar from the
> command line, but no luck.
>
> I import 63 channel data that I know to be referenced to the forehead.
> then I remove 3 EOG and EMG channels (60 remaining).
>
> I've created a 61 channel electrode location file, that I read in and
> separate into the first 60 "active" locations and the 61st ref/forehead
> location. I assign the 60 channel locations to my EEG, and then want to
> rereference to average mastoids, while keeping both mastoid channels and
> reconstructing the forehead channel. I've tried a couple of things, calling
> both pop_reref and reref. I'm sure there's a simple solution but can't get
> it to work. the code to my latest attempt:
>
> %read in electrode locations
>
> allchanlocs=readlocs(electrodeFile,'filetype','custom','format',{'labels'
> 'X' 'Y' 'Z'});
>
>
>
> %split into active and ref locs
>
> chanlocs_active=allchanlocs(1:60);
>
> chanlocs_ref=allchanlocs(61);
>
>
>
> %read in 63 channel EDF and remove eyes and emg
>
> EEG=pop_biosig(fullfile(subjectFolder,dataFile),'importevent','off');
>
> EEG=pop_select(EEG,'nochannel',[1 2 63]);
>
> EEG.chanlocs=chanlocs_active;
>
> EEG=eeg_checkset(EEG)  ##STILL OK
>
>
>
> %rereference to average mastoids
>
> EEG=pop_reref(EEG,[59 60],'keepref','on','refloc',chanlocs_ref);
>
>
>
> this now crashes like this:
>
>
> Attempt to reference field of non-structure array.
>
>
> Error in pop_reref (line 215)
>
>          allinds = [allinds strmatch( g.refloc(iElec).labels, {
> tmpchaninfo.nodatchans.labels }) ];
>
> On Tue, Apr 28, 2015 at 5:36 AM, Dezhong Yao <dyao at uestc.edu.cn> wrote:
>
>>  Hi, all reference-issue followers;
>>   Physically,  "add current reference channel back to data" actually adds
>> a channel with zero potential to current configuration,
>> then you may re-reference to any other configuration, such average,
>> linked ears reference.
>> The best re-reference is  the  "zero reference" realized  by "REST"
>> (reference electrode standardization technique) at
>> www.neuro.uestc.edu.cn/rest , where free-software is available,
>> and it may interpolate bad channel the same time.
>>     Best wishes
>> ------------------
>> Dezhong Yao  PhD
>> Cheung Kong Professor of Neuroengineering, Neuroimaging
>> E-mail: dyao at uestc.edu.cn
>> Fax: 86-28-83208238; Tel: 86-28-83201018
>> Director, Key Laboratory for NeuroInformation,  Ministry of Education,
>> China
>>               International Joint Research Center for NeuroInformation,
>> Ministry of Science and Technology, China
>> Dean,      School of Life Science and Technology, University of
>> Electronic Science and Technology of China, Sichuan,Chengdu 610054, China
>> Director,  Center for Information in BioMedicine, University of
>> Electronic Science and Technology of China, China
>> http://www.neuro.uestc.edu.cn/bci/member/yao/yao.html
>> 2015-04-28
>> -------------------------------------------------------------
>> 发件人：Brittany Alperin
>> 发送日期：2015-04-28 14:04:07
>> 收件人：Andreas Widmann
>> 抄送：EEGLAB List
>> 主题：Re: [Eeglablist] online reference
>>
>> Hi Andreas
>>
>> You're right. I forgot that compute average reference is automatically
>> checked, so I was looking at the data with the average reference instead
>> of
>> a Cz reference.
>>
>> I think I have this all cleared up now. Thanks for the help!
>>
>> Brittany
>>
>> On Sat, Apr 25, 2015 at 9:17 AM, Andreas Widmann <widmann at uni-leipzig.de>
>> wrote:
>>
>> > > To clarify, I have 31 channels + ref (Cz) + ground. So 33 in total.
>> > Good!
>> >
>> > > I added Cz to my channel locations and selected "add current reference
>> > channel back to data" without re-referencing to anything else.
>> > Sorry, could you please clarify how you use the "add current reference
>> > channel back to data“-option *without* actually re-referencing? To my
>> > understanding this should be impossible. Either the „Compute average
>> > reference“ or the „Re-reference data to channel(s)“-option is always
>> > selected in the pop_reref GUI. In case „Compute average reference“ was
>> > selected, the data were re-referenced to the mean of all channels.
>> >
>> > > I can now see Cz, but it isn't a flat line. Am I incorrect in thinking
>> > that it should be totally flat?
>> > Without re-referencing the implicit reference should indeed be a flat
>> > line/zero.
>> >
>> > Hope this helps!
>> > Andreas
>> >
>> > > Thanks,
>> > > Brittany
>> > >
>> > > On Thu, Apr 23, 2015 at 5:29 AM, Andreas Widmann <
>> widmann at uni-leipzig.de>
>> > wrote:
>> > > Hi Brittany,
>> > >
>> > > this sounds like two different problems:
>> > > If you record from 32 channels + Ref + Ground the imported file should
>> > have 32 channels (but not your Cz Ref channel). Please reconfirm that
>> your
>> > Pycorder setup really records from 32 data channels (34 electrodes). In
>> > case there is really a channel missing, please, submit a bug report to
>> the
>> > bugtracker including a short sample file.
>> > >
>> > > If you want to keep the implicit online reference (Cz) as a new
>> channel
>> > after re-referencing the data to another channel you have to use the
>> „Add
>> > current reference channel back to the data“-option (GUI; 'refloc‘ on
>> > command line). To use this option you have to first append a (Cz-)
>> channel
>> > in the GUI channel editor (appearing in EEG.chaninfo.nodatchans) which
>> you
>> > can subsequently select during re-referencing. The „new“ Cz-channel is
>> the
>> > inverse of the channel the data were re-referenced to (now missing in
>> the
>> > data or being flat if "Retain old reference channels in data“ was
>> selected).
>> > >
>> > > Please note that the „Add current reference channel back to the
>> > data“-option should not be used for systems where common mode rejection
>> is
>> > applied offline (e.g. Biosemi).
>> > >
>> > > Hope this helps,
>> > > Andreas
>> > >
>> > > > Am 22.04.2015 um 21:59 schrieb Brittany Alperin <
>> balperin07 at gmail.com
>> > >:
>> > > >
>> > > > Hello
>> > > >
>> > > > I'm using a 32 channel brain vision system and am recording with
>> > PyCorder. When I import my data using the brain vision recorder plugin,
>> > only 31 channels are present. I'm recording with Cz as an online
>> reference
>> > and Cz is the channel that is missing. I can re-reference, but Cz is
>> still
>> > absent.
>> > > >
>> > > > Has anyone had an issue with recording with an online reference and
>> > not having that data import into EEGlab? Or does anyone have a different
>> > way to import brain vision data?
>> > > >
>> > > > Thanks,
>> > > > Brittany
>> > > >
>> > > >
>> > > > _______________________________________________
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>> > >
>> >
>> >
>>
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