[Eeglablist] Coherence connection lines in 2d (Arnaud Delorme)

Thu Dec 13 00:27:57 PST 2012

http://www.mathworks.com/matlabcentral/fileexchange/32563-connected-topoplot

On Wed, Dec 12, 2012 at 10:43 PM, <eeglablist-request at sccn.ucsd.edu> wrote:

> Send eeglablist mailing list submissions to
>         eeglablist at sccn.ucsd.edu
>
> To subscribe or unsubscribe via the World Wide Web, visit
>         http://sccn.ucsd.edu/mailman/listinfo/eeglablist
> or, via email, send a message with subject or body 'help' to
>         eeglablist-request at sccn.ucsd.edu
>
> You can reach the person managing the list at
>         eeglablist-owner at sccn.ucsd.edu
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of eeglablist digest..."
>
> Today's Topics:
>
>    1. Re: Scroll Plot Marked Trial / Channel Identification
>       (Arnaud Delorme)
>    2. Re: talaraich coordinate question (Arnaud Delorme)
>    3. Re: STUDY design: spectrum negative power values (Arnaud Delorme)
>    4. Re: Coherence connection lines in 2d (Arnaud Delorme)
>
>
> ---------- Forwarded message ----------
> From: Arnaud Delorme <arno at ucsd.edu>
> To: Frank Preston <ffpresto at uwaterloo.ca>
> Cc: "EEGLab List \(eeglablist at sccn.ucsd.edu\)" <eeglablist at sccn.ucsd.edu>
> Date: Wed, 12 Dec 2012 20:24:32 -0800
> Subject: Re: [Eeglablist] Scroll Plot Marked Trial / Channel Identification
> Dear Frank,
>
> one option is to increase the scale. This way, each channel data is
> horizontally aligned with its label.
> Not ideal but should help in the short range.
> Thanks,
>
> Arno
>
> On 28 Nov 2012, at 07:41, Frank Preston wrote:
>
> Hi,****
> ** **
> If Scroll Plot is opened after trials have been marked by EEGLab, the
> channel which caused the trial to be marked is highlighted in red. We would
> like to know which channel is marked and it is often very difficult to tell
> because the plotted signal is outside of range by quite a bit. Is there an
> easy way to tell this, perhaps by highlighting the channel on the y-axis?*
> ***
> ** **
> We are viewing results from a BioSemi Active 2 system. We record 72
> electrodes, 66 of which are on the cap.****
> ** **
> Thank you,****
>   .. Frank****
> ** **
> ** **
> --
> *Frank Preston*
> Psychophysiology Lab Technician          University of Waterloo
> PAS 2270, Psychology Department        200 University Ave. W.
> Phone: 519-888-4567 x 38976               Waterloo, Ontario, N2L 3G1****
> ** **
> _______________________________________________
> 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
>
>
>
>
> ---------- Forwarded message ----------
> From: Arnaud Delorme <arno at ucsd.edu>
> To: Julia Kline <jekline at umich.edu>
> Cc: eeglablist <eeglablist at sccn.ucsd.edu>, Alejandro Ojeda <
> alejo.ojeda83 at gmail.com>, Nima Bigdely <nima at sccn.ucsd.edu>
> Date: Wed, 12 Dec 2012 20:30:39 -0800
> Subject: Re: [Eeglablist] talaraich coordinate question
> Dear Julia,
>
> yes there are tools. I think Nima in our lab interfaced from Matlab a tool
> to indicate which brain region a coordinate in dipplot correspond to. Or
> maybe it was Alejandro? Both copied just in case.
>
> Best wishes,
>
> Arno
>
> On 30 Nov 2012, at 14:27, Julia Kline wrote:
>
> > Tarik, thanks for the help. Although I must admit I am a little
> > confused. You said that:
> >
> > The question of which software that is best for determining closest
> > BA or region for a specific set of coordinates is different from the
> > question of which software or algorithm is best
> > for your needs in  determining source estimates to begin with.
> >
> > In that case, can I pose both questions to the list? I would like to
> > localize my independent components to their nearest brodmann areas.
> > What software do you feel is best to determine source estimates and
> > also what software do you feel is best for determining BA or region of
> > interest from a specific set of talairach coordinates returned by
> > eeglab?
> >
> > Thanks!
> >
> > -Julia
> >
> >
> >
> >
> >
> > On Thu, Nov 29, 2012 at 3:32 PM, Tarik S Bel-Bahar
> > <tarikbelbahar at gmail.com> wrote:
> >> Hi Julia,
> >>
> >> I use the Tailarch client too to get a rough idea
> >> of nearest BAs for a particular "estimated" dipole.
> >>
> >> The dipfit estimations of dipoles that account for particular ICs
> >> "in or near" a particular brain area or region should be taken with some
> >> caution.
> >> There are issues with not easily constraining results to cortex,
> >> and with interpreting/coordinating results with other source estimation
> >> techniques or software.
> >>
> >> Last, the question of which software is best for determining closest
> >> BA or region for a specific set of coordinates...
> >>
> >> is different from the question of what software or algorithm is best
> >> for your needs in  determining source estimates to begin with.
> >>
> >>
> >> Respectfully,
> >> Tarik
> >>
> >>
> >>
> >> On Wed, Nov 28, 2012 at 12:28 PM, Julia Kline <jekline at umich.edu>
> wrote:
> >>>
> >>> Hi all. I had a question regarding working with the talaraich
> >>> coordinate output of pop_dipfit.
> >>> It is my understanding that pop_dipfit returns the talaraich
> >>> coordinates of the equivalent current dipoles and plots them inside a
> >>> standard MNI brain.
> >>> Our lab has been using talaraich client to find the equivalent
> >>> brodmann areas for these coordinates.
> >>>
> >>> In your experience, is this the best software for identifying brodmann
> >>> areas? I had heard that there were other better methods and I wanted
> >>> to ask what you have found to be the most method of identifying
> >>> brodmann areas. Thanks.
> >>>
> >>> -Julia
> >>> _______________________________________________
> >>> 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
>
>
>
>
>
> ---------- Forwarded message ----------
> From: Arnaud Delorme <arno at ucsd.edu>
> To: Andrew Hill <andrewhill at ucla.edu>
> Cc: eeglablist at sccn.ucsd.edu
> Date: Wed, 12 Dec 2012 20:32:43 -0800
> Subject: Re: [Eeglablist] STUDY design: spectrum negative power values
> Dear Andrew,
>
> yes, there was a typo, it should be 10.^(specdata{index}/10) and not 10^
> (specdata{index}/10).
> Sorry about that,
>
> Arno
>
> On 29 Nov 2012, at 23:28, Andrew Hill wrote:
>
> Arno or any other helpful soul - I'm replying in Christian's thread as I'm
> trying to do something similar.
>
> Using the code snippets Arno provided, to convert specdata from log back
> into amplitude produces this error:
>
> [STUDY specdata specfreqs] = std_specplot(STUDY, ALLEEG,'channels', ('C3'}
> , 'plotsubjects','off', 'freqrange', [0.5 40]);
>
>  for index = 1:length(specdata(:));
> specdata{index} = sqrt(10^(specdata{index}/10));
> end;
>
> ??? Error using ==> mpower
> Inputs must be a scalar and a square matrix.
>
>
> My specdata is in a 4x2 cell array of 159 x 25 doubles (holding 159
> quarter-hz bins for 25 subjects).
> Is there a different way to call the math against the cell array so that
> it converts back to amplitude?
>
> Thanks,
> Andrew
>
>
>
> On Jul 5, 2012, at 9:55 PM, Arnaud Delorme wrote:
>
> Dear Christian,
>
> yes, you are getting 10*log10(power) in these plots which is the usual way
> of visualizing EEG data.
> You may recuperate the data values on the command line
>
> *[STUDY specdata freqs] = std_specplot(STUDY, ALLEEG, 'channels', { 'Cz'
> });*
>
> and convert the data back to absolute power values and visualize the data
>
> *for index = 1:length(specdata(:))*
> * specdata{index} = 10^(specdata{index}/10);*
> *end;*
> *std_plotcurve(freqs, specdata);*
>
> Note, if you want amplitude not power, use instead *specdata{index} =
> 10^(specdata{index}/20);** *or *specdata{index} =
> sqrt(10^(specdata{index}/10)); *which is equivalent.
> Best,
>
> Arno
>
> On May 7, 2012, at 12:56 AM, Christian Scharinger wrote:
>
> Dear eeglab users,
>
> I use the following code for calculating the spectrum in a STUDY design:
>
> [STUDY ALLEEG] = std_precomp(STUDY, ALLEEG, 'channels', 'design', [1],
> 'erp', 'off', 'spec', 'on', 'ersp', 'off', 'specparams', { 'specmode',
> 'psd', 'recompute', 'on', 'timerange', [1300 1800], 'freqfac', [4] },
> 'savetrials', 'off');
>
> STUDY = pop_specparams(STUDY, 'groupstats','on', 'mcorrect','fdr',
> 'threshold',0.05,'plotgroups','together','freqrange',[1 30],
> 'rmsubjmean', 'off');
>
> With this code, I'm getting negative power values when I use the
> std_specplot function for plotting (or when I do the plotting via GUI).
>
> So I guess I'm not getting absolute power values (what I would like to
> have) but power values in relation to some kind of baseline.
>
> Is it possible to get absolute power values for a spectrum in a STUDY
> design?
> Where can I see/change what baseline eeglab uses for calculating power
> values?
>
> Many thanks in advance,
>
> Christian
>
>
>
> --
> Christian Scharinger, M.A.
>
> Knowledge Media Research Center (KMRC)
> Schleichstraße 6 | 72076 Tuebingen
>
> Phone: +49 (0)7071 979-360
> Internet: http://www.iwm-kmrc.de/c.scharinger
> E-Mail: c.scharinger at iwm-kmrc.de
>
> _______________________________________________
> 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
>
>
>
>
>
> ---------- Forwarded message ----------
> From: Arnaud Delorme <arno at ucsd.edu>
> To: "Iman M.Rezazadeh" <irezazadeh at ucdavis.edu>
> Cc: eeglablist <eeglablist at sccn.ucsd.edu>
> Date: Wed, 12 Dec 2012 20:42:53 -0800
> Subject: Re: [Eeglablist] Coherence connection lines in 2d
> Dear Iman,
>
> erpwavelab, an EEGLAB associated toolbox can do that. We usually do not
> recommend computing coherence on channel arrays (for obvious reasons since
> a common source projecting to 2 channels will increase 0-lag or 180-degree
> lab coherence at a given frequency). However, Morten Mørup, the principal
> developer of erpwavelab, has a math background and the proper checks are in
> place to make sure that you are looking at actual source coherence
> (although you still do not know where the sources unless you do source
> localization - in that case the SIFT toolbox is a better choice).
>
> http://www.erpwavelab.org/
>
> Best,
>
> Arno
>
> On 30 Nov 2012, at 15:08, Iman M.Rezazadeh wrote:
>
> Hi EEGLABers,****
> ** **
> I want to plot a line as  connection strength between two electrodes based
> on their cross-coherence / correlation value on the 2D electrode plot . Do
> you know how to do that and if there is a function or toolbox for that?***
> *
> Best,****
> Iman****
> ** **
> Iman M.Rezazadeh, PhD****
> Postdoctoral Research Fellow****
> Center for Mind and Brain****
> University of California, Davis****
> irezazadeh at ucdavis.edu****
> Cell:310-490-1808****
> Skype: Imanmr****
> ** **
> _______________________________________________
> 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 mailing list eeglablist at sccn.ucsd.edu
> Eeglablist page: http://www.sccn.ucsd.edu/eeglab/eeglabmail.html
> To unsubscribe, send an empty email to eeglablist-unsub at sccn.ucsd.edu
> To switch to non-digest mode, send an empty email to
> eeglablist-nodigest at sccn.ucsd.edu
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://sccn.ucsd.edu/pipermail/eeglablist/attachments/20121213/9ff5c40d/attachment.html>