<div dir="ltr">Thanks for the clear explanation Andreas.<div><br></div><div>Unfortunately, pop_chanedit only gets me into deeper trouble.</div><div><br></div><div>
<p><i>%split into active and ref locs</i></p>
<p><i>chanlocs_active=allchanlocs(1:60);</i></p>
<p><i>ref=allchanlocs(61);</i></p><p><br></p><p><i>%read in 63 channel EDF and remove eyes and emg</i></p><p><i>EEG=pop_biosig(fullfile(subjectFolder,dataFile),<span>'importevent'</span>,<span>'off'</span>);</i></p><p><i>EEG=pop_select(EEG,<span>'nochannel'</span>,[1 2 63]); #60 chans now</i></p><p><i> </i></p><p>
</p><p><i>EEG.chanlocs=chanlocs_active;</i></p><p><br></p><p>I crash when I now call:</p><div>
<p><i>EEG=pop_chanedit(EEG,<span>'append'</span>,{60,ref.labels,ref.theta,ref.radius,ref.X,ref.Y,ref.Z,ref.sph_theta,ref.sph_phi,ref.sph_radius});</i></p><p><i><br></i></p><p><i>Error using pop_chanedit (line 601)</i></p><p><i>pop_chanedit: not enough arguments to change all field values</i></p><p><i><br></i></p><p>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.</p><p><br></p><p>I also tried:</p><p class=""><i>EEG=pop_chanedit(EEG,<span class="">'append'</span>,60,<span class="">'changefield'</span>,{61,<span class="">'labels'</span>, ref.labels,<span class="">'theta'</span>, ref.theta, <span class="">'radius'</span>,ref.radius,<span class="">...</span></i></p><p>
</p><p class=""><i> <span class="">'X'</span>,ref.X,<span class="">'Y'</span>,ref.Y,<span class="">'Z'</span>,ref.Z,<span class="">'sph_theta'</span>,ref.sph_theta,<span class="">'sph_phi'</span>,ref.sph_phi,<span class="">'sph_radius'</span>,ref.sph_radius});</i></p><p><br></p>
<p>but: <i>Wrong channel structure size, changes ignored</i></p><p><i><br></i></p><p>Finally, I also tried:</p><p><i>EEG.chaninfo.nodatchans=ref;</i></p><p>
</p><p class=""><i>EEG=pop_reref(EEG,[59 60],<span class="">'keepref'</span>,<span class="">'on'</span>,<span class="">'refloc'</span>,ref);</i></p><p class=""><i><br></i></p><p class="">which actually results in a 61 channel EEG struct, but I get a warning:</p><p class=""><i>Warning: the size of the channel location structure does not match with</i></p><p class=""><i> number of channels. Channel information have been removed.</i></p><p class=""><i><br></i></p><p class="">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.</p><p class=""><br></p><p class="">(I might submit a bug report later on, but I'm hoping for a faster solution.)</p><p class=""><br></p><p class="">Thanks</p><p><i><br></i></p>
<p class=""><br></p><p><i><br></i></p></div><div> </div></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, May 8, 2015 at 6:37 AM, Andreas Widmann <span dir="ltr"><<a href="mailto:widmann@uni-leipzig.de" target="_blank">widmann@uni-leipzig.de</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Roy,<br>
<br>
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.<br>
<br>
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.<br>
<br>
Temporary workaround is to append the channel first from the command line before re-referencing:<br>
EEG = pop_chanedit(EEG, 'append‘, 60, 'changefield‘, {61 'labels‘ 'YourLabel'});<br>
<br>
Hope this helps,<br>
Andreas<br>
<div class="HOEnZb"><div class="h5"><br>
> Am 07.05.2015 um 20:32 schrieb Roy Cox <<a href="mailto:roycox.roycox@gmail.com">roycox.roycox@gmail.com</a>>:<br>
><br>
> hi all,<br>
><br>
> (apologies for possibly sending this twice)<br>
><br>
> saw this discussion and I'm trying to do something similar from the command line, but no luck.<br>
><br>
> I import 63 channel data that I know to be referenced to the forehead. then I remove 3 EOG and EMG channels (60 remaining).<br>
><br>
> 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:<br>
><br>
> %read in electrode locations<br>
> allchanlocs=readlocs(electrodeFile,'filetype','custom','format',{'labels' 'X' 'Y' 'Z'});<br>
><br>
><br>
> %split into active and ref locs<br>
><br>
> chanlocs_active=allchanlocs(1:60);<br>
><br>
> chanlocs_ref=allchanlocs(61);<br>
><br>
><br>
> %read in 63 channel EDF and remove eyes and emg<br>
><br>
> EEG=pop_biosig(fullfile(subjectFolder,dataFile),'importevent','off');<br>
><br>
> EEG=pop_select(EEG,'nochannel',[1 2 63]);<br>
><br>
> EEG.chanlocs=chanlocs_active;<br>
><br>
> EEG=eeg_checkset(EEG) ##STILL OK<br>
><br>
><br>
> %rereference to average mastoids<br>
><br>
> EEG=pop_reref(EEG,[59 60],'keepref','on','refloc',chanlocs_ref);<br>
><br>
><br>
><br>
><br>
><br>
> this now crashes like this:<br>
><br>
><br>
><br>
> Attempt to reference field of non-structure array.<br>
><br>
><br>
><br>
> Error in pop_reref (line 215)<br>
><br>
> allinds = [allinds strmatch( g.refloc(iElec).labels, { tmpchaninfo.nodatchans.labels }) ];<br>
><br>
><br>
><br>
> thanks for any input,<br>
><br>
><br>
><br>
> Roy<br>
><br>
><br>
> On Thu, May 7, 2015 at 2:30 PM, Roy Cox <<a href="mailto:r.cox@uva.nl">r.cox@uva.nl</a>> wrote:<br>
> hi all,<br>
><br>
> saw this discussion and I'm trying to do something similar from the command line, but no luck.<br>
><br>
> I import 63 channel data that I know to be referenced to the forehead. then I remove 3 EOG and EMG channels (60 remaining).<br>
><br>
> 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:<br>
><br>
> %read in electrode locations<br>
> allchanlocs=readlocs(electrodeFile,'filetype','custom','format',{'labels' 'X' 'Y' 'Z'});<br>
><br>
><br>
> %split into active and ref locs<br>
><br>
> chanlocs_active=allchanlocs(1:60);<br>
><br>
> chanlocs_ref=allchanlocs(61);<br>
><br>
><br>
> %read in 63 channel EDF and remove eyes and emg<br>
><br>
> EEG=pop_biosig(fullfile(subjectFolder,dataFile),'importevent','off');<br>
><br>
> EEG=pop_select(EEG,'nochannel',[1 2 63]);<br>
><br>
> EEG.chanlocs=chanlocs_active;<br>
><br>
> EEG=eeg_checkset(EEG) ##STILL OK<br>
><br>
><br>
> %rereference to average mastoids<br>
><br>
> EEG=pop_reref(EEG,[59 60],'keepref','on','refloc',chanlocs_ref);<br>
><br>
><br>
><br>
><br>
><br>
> this now crashes like this:<br>
><br>
><br>
><br>
> Attempt to reference field of non-structure array.<br>
><br>
><br>
><br>
> Error in pop_reref (line 215)<br>
><br>
> allinds = [allinds strmatch( g.refloc(iElec).labels, { tmpchaninfo.nodatchans.labels }) ];<br>
><br>
><br>
> On Tue, Apr 28, 2015 at 5:36 AM, Dezhong Yao <<a href="mailto:dyao@uestc.edu.cn">dyao@uestc.edu.cn</a>> wrote:<br>
> Hi, all reference-issue followers;<br>
> Physically, "add current reference channel back to data" actually adds a channel with zero potential to current configuration,<br>
> then you may re-reference to any other configuration, such average, linked ears reference.<br>
> The best re-reference is the "zero reference" realized by "REST" (reference electrode standardization technique) at <a href="http://www.neuro.uestc.edu.cn/rest" target="_blank">www.neuro.uestc.edu.cn/rest</a> , where free-software is available,<br>
> and it may interpolate bad channel the same time.<br>
> Best wishes<br>
> ------------------<br>
> Dezhong Yao PhD<br>
> Cheung Kong Professor of Neuroengineering, Neuroimaging<br>
> E-mail: <a href="mailto:dyao@uestc.edu.cn">dyao@uestc.edu.cn</a><br>
> Fax: 86-28-83208238; Tel: 86-28-83201018<br>
> Director, Key Laboratory for NeuroInformation, Ministry of Education, China<br>
> International Joint Research Center for NeuroInformation, Ministry of Science and Technology, China<br>
> Dean, School of Life Science and Technology, University of Electronic Science and Technology of China, Sichuan,Chengdu 610054, China<br>
> Director, Center for Information in BioMedicine, University of Electronic Science and Technology of China, China<br>
> <a href="http://www.neuro.uestc.edu.cn/bci/member/yao/yao.html" target="_blank">http://www.neuro.uestc.edu.cn/bci/member/yao/yao.html</a><br>
> 2015-04-28<br>
> -------------------------------------------------------------<br>
> 发件人：Brittany Alperin<br>
> 发送日期：2015-04-28 14:04:07<br>
> 收件人：Andreas Widmann<br>
> 抄送：EEGLAB List<br>
> 主题：Re: [Eeglablist] online reference<br>
><br>
> Hi Andreas<br>
><br>
> You're right. I forgot that compute average reference is automatically<br>
> checked, so I was looking at the data with the average reference instead of<br>
> a Cz reference.<br>
><br>
> I think I have this all cleared up now. Thanks for the help!<br>
><br>
> Brittany<br>
><br>
> On Sat, Apr 25, 2015 at 9:17 AM, Andreas Widmann <<a href="mailto:widmann@uni-leipzig.de">widmann@uni-leipzig.de</a>><br>
> wrote:<br>
><br>
> > > To clarify, I have 31 channels + ref (Cz) + ground. So 33 in total.<br>
> > Good!<br>
> ><br>
> > > I added Cz to my channel locations and selected "add current reference<br>
> > channel back to data" without re-referencing to anything else.<br>
> > Sorry, could you please clarify how you use the "add current reference<br>
> > channel back to data“-option *without* actually re-referencing? To my<br>
> > understanding this should be impossible. Either the „Compute average<br>
> > reference“ or the „Re-reference data to channel(s)“-option is always<br>
> > selected in the pop_reref GUI. In case „Compute average reference“ was<br>
> > selected, the data were re-referenced to the mean of all channels.<br>
> ><br>
> > > I can now see Cz, but it isn't a flat line. Am I incorrect in thinking<br>
> > that it should be totally flat?<br>
> > Without re-referencing the implicit reference should indeed be a flat<br>
> > line/zero.<br>
> ><br>
> > Hope this helps!<br>
> > Andreas<br>
> ><br>
> > > Thanks,<br>
> > > Brittany<br>
> > ><br>
> > > On Thu, Apr 23, 2015 at 5:29 AM, Andreas Widmann <<a href="mailto:widmann@uni-leipzig.de">widmann@uni-leipzig.de</a>><br>
> > wrote:<br>
> > > Hi Brittany,<br>
> > ><br>
> > > this sounds like two different problems:<br>
> > > If you record from 32 channels + Ref + Ground the imported file should<br>
> > have 32 channels (but not your Cz Ref channel). Please reconfirm that your<br>
> > Pycorder setup really records from 32 data channels (34 electrodes). In<br>
> > case there is really a channel missing, please, submit a bug report to the<br>
> > bugtracker including a short sample file.<br>
> > ><br>
> > > If you want to keep the implicit online reference (Cz) as a new channel<br>
> > after re-referencing the data to another channel you have to use the „Add<br>
> > current reference channel back to the data“-option (GUI; 'refloc‘ on<br>
> > command line). To use this option you have to first append a (Cz-) channel<br>
> > in the GUI channel editor (appearing in EEG.chaninfo.nodatchans) which you<br>
> > can subsequently select during re-referencing. The „new“ Cz-channel is the<br>
> > inverse of the channel the data were re-referenced to (now missing in the<br>
> > data or being flat if "Retain old reference channels in data“ was selected).<br>
> > ><br>
> > > Please note that the „Add current reference channel back to the<br>
> > data“-option should not be used for systems where common mode rejection is<br>
> > applied offline (e.g. Biosemi).<br>
> > ><br>
> > > Hope this helps,<br>
> > > Andreas<br>
> > ><br>
> > > > Am 22.04.2015 um 21:59 schrieb Brittany Alperin <<a href="mailto:balperin07@gmail.com">balperin07@gmail.com</a><br>
> > >:<br>
> > > ><br>
> > > > Hello<br>
> > > ><br>
> > > > I'm using a 32 channel brain vision system and am recording with<br>
> > PyCorder. When I import my data using the brain vision recorder plugin,<br>
> > only 31 channels are present. I'm recording with Cz as an online reference<br>
> > and Cz is the channel that is missing. I can re-reference, but Cz is still<br>
> > absent.<br>
> > > ><br>
> > > > Has anyone had an issue with recording with an online reference and<br>
> > not having that data import into EEGlab? Or does anyone have a different<br>
> > way to import brain vision data?<br>
> > > ><br>
> > > > Thanks,<br>
> > > > Brittany<br>
> > > ><br>
> > > ><br>
> > > > _______________________________________________<br>
> > > > Eeglablist page: <a href="http://sccn.ucsd.edu/eeglab/eeglabmail.html" target="_blank">http://sccn.ucsd.edu/eeglab/eeglabmail.html</a><br>
> > > > To unsubscribe, send an empty email to<br>
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> > ><br>
> > ><br>
> ><br>
> ><br>
><br>
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><br>
><br>
<br>
</div></div></blockquote></div><br></div>