[Eeglablist] Shifted rejection boundaries in continuous data
Maria Teresa Wijaya
a0089301 at nus.edu.sg
Fri Nov 23 00:18:36 PST 2012
Hi James,
I have run your script:
1. On the files which have gone through the artifact rejection and had
the rejection boundaries shifted: I did not get the 50µV ERP in the ERP
image. I thought the ERP may be added at the wrong time point (not
coinciding with the events) but I also did not see it in the channel
data scroll at all. I am not sure if this is relevant but I got these
error messages:
>> EEG.data(EEG.nbchan,[EEG.event.latency])=50;
??? Subscript indices must either be real positive integers or logicals.
>> pop_erpimage(EEG,1, [EEG.nbchan],[[]],'trig',1,1,{},[],'' , ...
'yerplabel','\muV', ...
'erp','on', ...
'cbar','on', ...
'topo', { [EEG.nbchan] EEG.chanlocs EEG.chaninfo } );
Command executed by pop_erpimage:
erpimage( mean(EEG.data([72], :),1), ones(1,
EEG.trials)*EEG.xmax*1000, linspace(EEG.xmin*1000, EEG.xmax*1000,
EEG.pnts), 'trig', 1, 1 , 'yerplabel', '\muV', 'erp', 'on', 'cbar',
'on', 'topo', { [72]' EEG.chanlocs EEG.chaninfo });
Plotting input data as 683 epochs of 204 frames sampled at 256.0 Hz.
Sorting data on input sortvar.
100.00% of the trials (i.e., 683 out of 683) have the same sortvar
value as at least one other trial.
Distribution of number ties per unique value of sortvar:
Min: 683, 25th ptile: 683, Median: 683, 75th ptile: 683, Max: 683
The caxis range will be the sym. abs. data range -> [-0,0].
Data will be plotted between -398.438 and 394.531 ms.
??? Error using ==> set
Bad property value found.
Object Name : axes
Property Name : 'CLim'
Values must be increasing and non-NaN.
Error in ==> imagesc at 47
set(cax,'CLim',clim)
Error in ==> erpimage at 2042
h_eim=imagesc(times,outtrials,data',[mindat,maxdat]);%
plot time on x-axis
Error in ==> pop_erpimage at 668
eval(com)
2. On the files from the same subjects which I re-did the the artifact
rejection and now they have the correct boundaries: I got the 50µV ERP
and the vertical stripe (though it's black) in the ERP image. I also got
a slightly different message when running the pop_erpimage command on
these files:
>> pop_erpimage(EEG,1, [EEG.nbchan],[[]],'trig',1,1,{},[],'' , ...
'yerplabel','\muV', ...
'erp','on', ...
'cbar','on', ...
'topo', { [EEG.nbchan] EEG.chanlocs EEG.chaninfo } );
Command executed by pop_erpimage:
erpimage( mean(EEG.data([72], :),1), ones(1,
EEG.trials)*EEG.xmax*1000, linspace(EEG.xmin*1000, EEG.xmax*1000,
EEG.pnts), 'trig', 1, 1 , 'yerplabel', '\muV', 'erp', 'on', 'cbar',
'on', 'topo', { [72]' EEG.chanlocs EEG.chaninfo });
Plotting input data as 791 epochs of 204 frames sampled at 256.0 Hz.
Sorting data on input sortvar.
100.00% of the trials (i.e., 791 out of 791) have the same sortvar
value as at least one other trial.
Distribution of number ties per unique value of sortvar:
Min: 791, 25th ptile: 791, Median: 791, 75th ptile: 791, Max: 791
The caxis range will be the sym. abs. data range -> [-50,50].
Data will be plotted between -398.438 and 394.531 ms.
Output data will be 204 frames by 791 smoothed trials.
Outtrials: 1.00 to 791.00
Overplotting sorted sortvar on data.
Plotting the ERP trace below the ERP image
??? Undefined function or variable "l1".
Error in ==> erpimage>plot1trace at 3566
plot_handle=[plot_handle l1 l2];
Error in ==> erpimage at 2878
tmph =
plot1trace(ax2,times,erp,limit,erpsig,[],[],erp_grid,erp_vltg_ticks); %
plot ERP and 0+/-alpha threshold
Error in ==> pop_erpimage at 668
eval(com)
I also got similar message when running the scripts on data from
subjects which never have any boundary problem.
Do you have any advice as to what I should look at next?
Thank you for your help.
Regards,
Maria
On Thursday 22,November,2012 10:37 PM, James Desjardins wrote:
>
> Hi Maria,
>
> We can check to see if your shift is affecting the event markers other
> than the "boundary" events.
>
> Load a file like you normally do and copy the following code to the
> command line to create a "trig" channel in the EEG.data array (and
> save a test file named "trig_test.set" in the current directory):
>
> EEG.nbchan=EEG.nbchan+1;
> EEG.data(EEG.nbchan,:)=zeros(size(EEG.data(1,:)));
> EEG.chanlocs(EEG.nbchan).labels='trig';
> EEG.data(EEG.nbchan,[EEG.event.latency])=50;
>
> EEG=eeg_checkset(EEG);
> eeglab redraw
>
> pop_eegplot( EEG, 1, 0, 1);
>
> EEG = pop_saveset( EEG, 'filename','trig_test.set', ... 'filepath',cd);
>
>
> At this point you can remove a data interval the way that you normally
> do (perhaps remove an approximately 1 second data portion following
> the 10th event marker).
>
> Now copy the following code to the command line in order to segment
> +/-400ms intervals around all event types and plot an ERPimage figure.
>
>
> EEG = pop_epoch( EEG, unique({EEG.event.type}), [-0.4 0.4], ...
> 'newname', 'trigLock', ...
> 'epochinfo', 'yes');
> EEG = eeg_checkset( EEG );
> figure;
> pop_erpimage(EEG,1, [EEG.nbchan],[[]],'trig',1,1,{},[],'' , ...
> 'yerplabel','\muV', ...
> 'erp','on', ...
> 'cbar','on', ...
> 'topo', { [EEG.nbchan] EEG.chanlocs EEG.chaninfo } );
>
>
> If everything is OK there should be a red vertical stripe in the
> surface plot at 0 ms and a 50 µV ERP at 0 ms in the bottom waveform.
>
> If there is not a vertical stripe at 0 ms we can use the trig_test.set
> file to explore the cause of the shift.
>
> This will also let us know if the "boundary" shift is a separate issue.
>
> James
> ________________________________________
> From: Maria Teresa Wijaya [a0089301 at nus.edu.sg]
> Sent: November-22-12 1:53 AM
> To: James Desjardins
> Cc: mmiyakoshi at ucsd.edu; eeglablist at sccn.ucsd.edu
> Subject: Re: [Eeglablist] Shifted rejection boundaries in continuous data
>
> Hi James,
>
> I did everything using the GUI: plot > channel data (scroll) > drag and
> click to specify the boundaries > reject button > save it as file . In
> my case, my events seem to still be in the right place when I tried
> using eeg_eegrej function with overlapping boundaries.
>
> Maria
>
>
> On Wednesday 21,November,2012 11:41 AM, James Desjardins wrote:
> > Hi Maria,
> >
> > What were the exact functions or menu items that you used to select
> the periods for rejection?
> >
> > Similarly, what exactly did you use to remove the periods?
> >
> > I am interested in this problem because I have caused such things to
> happen while tinkering with the EEG structure from the command line.
> The shifting of events from their true position relative to the data
> can occur if there is overlap among the latency boundaries specified
> for removal in a call to the eeg_eegrej function, but I have never
> seen it happen while building latency boundaries or removing
> continuous data periods using the EEGLab GUI.
> >
> > For example, If I specify overlapping latency boundaries:
> >
> > rejarr=[10000 11000;10900 11900];
> >
> > Then try to remove both of them with one call to eeg_eegrej:
> >
> > EEG = eeg_eegrej(EEG, rejarr);
> >
> > I find that all of the events following the rejection period are
> shifted to the left (relative to their true position) in the data
> scroll (with the shift distance being equal to the duration of the
> overlap across the rejarr latency boundaries).
> >
> > If you are building latency boundaries outside of the EEGLab GUI and
> using eeg_eegrej to purge them it is crucial that you merge the
> overlapping latency boundaries.
> >
> > Again, I am very interested in this topic. I look forward to
> exploring this further if you have more to add.
> >
> >
> > James
> >
> > ________________________________________
> > From: eeglablist-bounces at sccn.ucsd.edu
> [eeglablist-bounces at sccn.ucsd.edu] on behalf of Maria Teresa Wijaya
> [a0089301 at nus.edu.sg]
> > Sent: November-18-12 11:07 PM
> > To: mmiyakoshi at ucsd.edu
> > Cc: eeglablist at sccn.ucsd.edu
> > Subject: Re: [Eeglablist] Shifted rejection boundaries in continuous
> data
> >
> > Dear Makoto,
> >
> > I recorded my data using Biosemi Active two system with 64 electrodes at
> > 256Hz. Data were band pass filtered at 0.1-20 Hz and re-referenced
> > offline first to nose reference to remove bad channels. Removed channels
> > were interpolated and the data were re-referenced to average reference.
> > I then checked the continuous data for non-typical artifacts, removed
> > them, and saved the data with a new name. The shifted rejection
> > boundaries problem appeared in this new data set.
> >
> > Kindly let me know if I need to provide any other information.
> >
> > Thank you.
> >
> > Regards,
> > Maria
> >
> >
> >
> > On Saturday 17,November,2012 01:33 PM, Makoto Miyakoshi wrote:
> >
> >> Dear Maria,
> >>
> >> We need more information to identify what caused this.
> >> Could you tell me more detail?
> >>
> >> Makoto
> >>
> >> 2012/11/12 Maria Teresa Wijaya<a0089301 at nus.edu.sg>:
> >>
> >>
> >>> Dear list,
> >>>
> >>> I did rejection on continuous data and noticed that the rejection
> >>> boundaries shifted from where they are supposed to be (picture here:
> >>> http://www.flickr.com/photos/89964745@N02/8178303896/in/photostream).
> >>> This happened to several of my subjects, and it also happened to
> someone
> >>> else in our lab before. My questions are:
> >>>
> >>> - What are the possible reasons of this shift?
> >>> - Is there any way I can know if any of my event triggers have
> also been
> >>> shifted or if only the rejection boundaries are shifted?
> >>>
> >>> Thank you for your help.
> >>>
> >>> Regards,
> >>> Maria
> >>> _______________________________________________
> >>> Eeglablist page: http://sccn.ucsd.edu/eeglab/eeglabmail.html
> >>> To unsubscribe, send an empty email to
> eeglablist-unsubscribe at sccn.ucsd.edu
> >>> For digest mode, send an email with the subject "set digest mime"
> to eeglablist-request at sccn.ucsd.edu
> >>>
> >>>
> >>
> >>
> >>
> > _______________________________________________
> > Eeglablist page: http://sccn.ucsd.edu/eeglab/eeglabmail.html
> > To unsubscribe, send an empty email to
> eeglablist-unsubscribe at sccn.ucsd.edu
> > For digest mode, send an email with the subject "set digest mime" to
> eeglablist-request at sccn.ucsd.edu
> >
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://sccn.ucsd.edu/pipermail/eeglablist/attachments/20121123/1aa41e56/attachment.html>
More information about the eeglablist
mailing list