[Eeglablist] online reference
Roy Cox
roycox.roycox at gmail.com
Mon May 11 11:48:18 PDT 2015
Andreas,
thanks for your continuing support.
your first suggestion does not work:
EEG = pop_chanedit(EEG, 'append‘, 60, 'changefield‘, {61 'labels‘
'ref.abel'});
EEG=pop_reref(EEG,[59 60],'keepref','on','refloc',ref);
*Reference to non-existent field 'ref'.*
*Error in getfield (line 36)*
* f = s.(deblank(strField)); % deblank field name*
*Error in reref (line 155)*
* g.elocs(end) = setfield(g.elocs(end), fieldloc{ind},
getfield(g.refloc(iLocs), fieldloc{ind}));*
*Error in pop_reref (line 189)*
*[EEG.data EEG.chanlocs refchan ] = reref(EEG.data, ref, optionscall{:});*
line 155 of reref is expecting a "ref" field that doesn't exist.
so I went for your alternative:
EEG.data(EEG.nbchan + 1, :) = zeros(1, EEG.pnts); % Append implicit
reference
EEG.nbchan = EEG.nbchan + 1;
EEG.data = EEG.data - repmat(mean(EEG.data(59:60, :), 1), [EEG.nbchan 1]);
% Re-reference
EEG.chanlocs=allchanlocs; %61 channel location struct;
but if I then call:
EEG=eeg_checkset(EEG);
I still get:
*Warning: the size of the channel location structure does not match with*
* number of channels. Channel information have been removed.*
looks like EEG.chaninfo and EEG.chanlocs must match on certain aspects to
get everything going.
almost there? :)
Roy
On Sat, May 9, 2015 at 2:36 AM, Andreas Widmann <widmann at uni-leipzig.de>
wrote:
> > (I might submit a bug report later on, but I'm hoping for a faster
> solution.)
> Ok, fastest solution is to manually re-reference on the command line:
>
> EEG.data(EEG.nbchan + 1, :) = zeros(1, EEG.pnts); % Append implicit
> reference
> EEG.nbchan = EEG.nbchan + 1;
> EEG.data = EEG.data - repmat(mean(EEG.data(59:60, :), 1), [EEG.nbchan 1]);
> % Re-reference
>
> And adjust the EEG.chanlocs structure.
> Please file a bug report anyway as also others might tap into that problem.
> Andreas
>
> > Am 08.05.2015 um 19:23 schrieb Roy Cox <roycox.roycox at gmail.com>:
> >
> > Thanks for the clear explanation Andreas.
> >
> > Unfortunately, pop_chanedit only gets me into deeper trouble.
> >
> > %split into active and ref locs
> >
> > chanlocs_active=allchanlocs(1:60);
> >
> > 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]); #60 chans now
> >
> >
> >
> >
> > EEG.chanlocs=chanlocs_active;
> >
> >
> >
> > I crash when I now call:
> >
> >
> EEG=pop_chanedit(EEG,'append',{60,ref.labels,ref.theta,ref.radius,ref.X,ref.Y,ref.Z,ref.sph_theta,ref.sph_phi,ref.sph_radius});
> >
> >
> >
> > Error using pop_chanedit (line 601)
> >
> > pop_chanedit: not enough arguments to change all field values
> >
> >
> >
> > the reason seems to be that the ref structure (with 10 fields) ends up
> as a 10 element cell in pop_chanedit, where the allfields variable has 13
> elements, including 'datachan', 'ref', and 'urchan'. But I never set these
> other fields for the other channels.
> >
> >
> >
> > I also tried:
> >
> > EEG=pop_chanedit(EEG,'append',60,'changefield',{61,'labels',
> ref.labels,'theta', ref.theta, 'radius',ref.radius,...
> >
> >
> >
> 'X',ref.X,'Y',ref.Y,'Z',ref.Z,'sph_theta',ref.sph_theta,'sph_phi',ref.sph_phi,'sph_radius',ref.sph_radius});
> >
> >
> >
> > but: Wrong channel structure size, changes ignored
> >
> >
> >
> > Finally, I also tried:
> >
> > EEG.chaninfo.nodatchans=ref;
> >
> >
> > EEG=pop_reref(EEG,[59 60],'keepref','on','refloc',ref);
> >
> >
> >
> > which actually results in a 61 channel EEG struct, but I get a warning:
> >
> > Warning: the size of the channel location structure does not match with
> >
> > number of channels. Channel information have been removed.
> >
> >
> >
> > Now, EEG.chanlocs is empty so I don't want to assume everything went
> according to plan and I can just re-attach my 61-channel location struct.
> If someone knows what chaninfo.nodatachans is supposed to look like that
> might help.
> >
> >
> >
> > (I might submit a bug report later on, but I'm hoping for a faster
> solution.)
> >
> >
> >
> > Thanks
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > On Fri, May 8, 2015 at 6:37 AM, Andreas Widmann <widmann at uni-leipzig.de>
> wrote:
> > Hi Roy,
> >
> > this is presumably a bug. I suggest reporting to the bugtracker. From
> GUI perspective it might be considered as unintended use of the function
> but it should actually work.
> >
> > In the GUI you can only select a channel for the 'refloc'-option if it
> was appended before in the channel editor and appears in the
> EEG.chaninfo.nodatchans structure. pop_reref tries to remove the channel
> from this structure after re-referencing (as it is a data channel now). In
> your case there is no such structure and pop_reref crashes.
> >
> > Temporary workaround is to append the channel first from the command
> line before re-referencing:
> > EEG = pop_chanedit(EEG, 'append‘, 60, 'changefield‘, {61 'labels‘
> 'YourLabel'});
> >
> > Hope this helps,
> > Andreas
> >
> > > Am 07.05.2015 um 20:32 schrieb Roy Cox <roycox.roycox at gmail.com>:
> > >
> > > 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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