<div dir="ltr"><a href="http://www.mathworks.com/matlabcentral/fileexchange/32563-connected-topoplot">http://www.mathworks.com/matlabcentral/fileexchange/32563-connected-topoplot</a><br><div class="gmail_extra"><br><br><div class="gmail_quote">
On Wed, Dec 12, 2012 at 10:43 PM, <span dir="ltr"><<a href="mailto:eeglablist-request@sccn.ucsd.edu" target="_blank">eeglablist-request@sccn.ucsd.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
Send eeglablist mailing list submissions to<br>
<a href="mailto:eeglablist@sccn.ucsd.edu">eeglablist@sccn.ucsd.edu</a><br>
<br>
To subscribe or unsubscribe via the World Wide Web, visit<br>
<a href="http://sccn.ucsd.edu/mailman/listinfo/eeglablist" target="_blank">http://sccn.ucsd.edu/mailman/listinfo/eeglablist</a><br>
or, via email, send a message with subject or body 'help' to<br>
<a href="mailto:eeglablist-request@sccn.ucsd.edu">eeglablist-request@sccn.ucsd.edu</a><br>
<br>
You can reach the person managing the list at<br>
<a href="mailto:eeglablist-owner@sccn.ucsd.edu">eeglablist-owner@sccn.ucsd.edu</a><br>
<br>
When replying, please edit your Subject line so it is more specific<br>
than "Re: Contents of eeglablist digest..."<br>
<br>Today's Topics:<br>
<br>
1. Re: Scroll Plot Marked Trial / Channel Identification<br>
(Arnaud Delorme)<br>
2. Re: talaraich coordinate question (Arnaud Delorme)<br>
3. Re: STUDY design: spectrum negative power values (Arnaud Delorme)<br>
4. Re: Coherence connection lines in 2d (Arnaud Delorme)<br>
<br><br>---------- Forwarded message ----------<br>From: Arnaud Delorme <<a href="mailto:arno@ucsd.edu">arno@ucsd.edu</a>><br>To: Frank Preston <<a href="mailto:ffpresto@uwaterloo.ca">ffpresto@uwaterloo.ca</a>><br>
Cc: "EEGLab List \(<a href="mailto:eeglablist@sccn.ucsd.edu">eeglablist@sccn.ucsd.edu</a>\)" <<a href="mailto:eeglablist@sccn.ucsd.edu">eeglablist@sccn.ucsd.edu</a>><br>Date: Wed, 12 Dec 2012 20:24:32 -0800<br>
Subject: Re: [Eeglablist] Scroll Plot Marked Trial / Channel Identification<br><div style="word-wrap:break-word">Dear Frank,<div><br></div><div>one option is to increase the scale. This way, each channel data is horizontally aligned with its label.</div>
<div>Not ideal but should help in the short range.</div><div>Thanks,</div><div><br></div><div>Arno</div><div><br><div><div>On 28 Nov 2012, at 07:41, Frank Preston wrote:</div><br><blockquote type="cite"><span style="border-collapse:separate;font-family:Helvetica;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;font-size:medium"><div lang="EN-US" link="blue" vlink="purple">
<div><div style="margin:0in 0in 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">Hi,<u></u><u></u></div><div style="margin:0in 0in 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif"><u></u> <u></u></div><div style="margin:0in 0in 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">
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?<u></u><u></u></div>
<div style="margin:0in 0in 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif"><u></u> <u></u></div><div style="margin:0in 0in 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">We are viewing results from a BioSemi Active 2 system. We record 72 electrodes, 66 of which are on the cap.<u></u><u></u></div>
<div style="margin:0in 0in 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif"><u></u> <u></u></div><div style="margin:0in 0in 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">Thank you,<u></u><u></u></div><div style="margin:0in 0in 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">
.. Frank<u></u><u></u></div><div style="margin:0in 0in 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif"><u></u> <u></u></div><div style="margin:0in 0in 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif"><u></u> <u></u></div>
<div style="margin:0in 0in 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:12pt">--<span> </span><br><b><span style="color:rgb(192,0,0)">Frank Preston</span></b><br>Psychophysiology Lab Technician University of Waterloo<br>
PAS 2270, Psychology Department 200 University Ave. W.<br>Phone: <a href="tel:519-888-4567%20x%2038976" value="+15198884567" target="_blank">519-888-4567 x 38976</a> Waterloo, Ontario, N2L 3G1<u></u><u></u></span></div>
<div style="margin:0in 0in 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif"><u></u> <u></u></div></div>_______________________________________________<br>Eeglablist page:<span> </span><a href="http://sccn.ucsd.edu/eeglab/eeglabmail.html" style="color:blue;text-decoration:underline" target="_blank">http://sccn.ucsd.edu/eeglab/eeglabmail.html</a><br>
To unsubscribe, send an empty email to<span> </span><a href="mailto:eeglablist-unsubscribe@sccn.ucsd.edu" style="color:blue;text-decoration:underline" target="_blank">eeglablist-unsubscribe@sccn.ucsd.edu</a><br>For digest mode, send an email with the subject "set digest mime" to<a href="mailto:eeglablist-request@sccn.ucsd.edu" style="color:blue;text-decoration:underline" target="_blank">eeglablist-request@sccn.ucsd.edu</a></div>
</span></blockquote></div><br></div></div><br><br>---------- Forwarded message ----------<br>From: Arnaud Delorme <<a href="mailto:arno@ucsd.edu">arno@ucsd.edu</a>><br>To: Julia Kline <<a href="mailto:jekline@umich.edu">jekline@umich.edu</a>><br>
Cc: eeglablist <<a href="mailto:eeglablist@sccn.ucsd.edu">eeglablist@sccn.ucsd.edu</a>>, Alejandro Ojeda <<a href="mailto:alejo.ojeda83@gmail.com">alejo.ojeda83@gmail.com</a>>, Nima Bigdely <<a href="mailto:nima@sccn.ucsd.edu">nima@sccn.ucsd.edu</a>><br>
Date: Wed, 12 Dec 2012 20:30:39 -0800<br>Subject: Re: [Eeglablist] talaraich coordinate question<br>Dear Julia,<br>
<br>
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.<br>
<br>
Best wishes,<br>
<br>
Arno<br>
<br>
On 30 Nov 2012, at 14:27, Julia Kline wrote:<br>
<br>
> Tarik, thanks for the help. Although I must admit I am a little<br>
> confused. You said that:<br>
><br>
> The question of which software that is best for determining closest<br>
> BA or region for a specific set of coordinates is different from the<br>
> question of which software or algorithm is best<br>
> for your needs in determining source estimates to begin with.<br>
><br>
> In that case, can I pose both questions to the list? I would like to<br>
> localize my independent components to their nearest brodmann areas.<br>
> What software do you feel is best to determine source estimates and<br>
> also what software do you feel is best for determining BA or region of<br>
> interest from a specific set of talairach coordinates returned by<br>
> eeglab?<br>
><br>
> Thanks!<br>
><br>
> -Julia<br>
><br>
><br>
><br>
><br>
><br>
> On Thu, Nov 29, 2012 at 3:32 PM, Tarik S Bel-Bahar<br>
> <<a href="mailto:tarikbelbahar@gmail.com">tarikbelbahar@gmail.com</a>> wrote:<br>
>> Hi Julia,<br>
>><br>
>> I use the Tailarch client too to get a rough idea<br>
>> of nearest BAs for a particular "estimated" dipole.<br>
>><br>
>> The dipfit estimations of dipoles that account for particular ICs<br>
>> "in or near" a particular brain area or region should be taken with some<br>
>> caution.<br>
>> There are issues with not easily constraining results to cortex,<br>
>> and with interpreting/coordinating results with other source estimation<br>
>> techniques or software.<br>
>><br>
>> Last, the question of which software is best for determining closest<br>
>> BA or region for a specific set of coordinates...<br>
>><br>
>> is different from the question of what software or algorithm is best<br>
>> for your needs in determining source estimates to begin with.<br>
>><br>
>><br>
>> Respectfully,<br>
>> Tarik<br>
>><br>
>><br>
>><br>
>> On Wed, Nov 28, 2012 at 12:28 PM, Julia Kline <<a href="mailto:jekline@umich.edu">jekline@umich.edu</a>> wrote:<br>
>>><br>
>>> Hi all. I had a question regarding working with the talaraich<br>
>>> coordinate output of pop_dipfit.<br>
>>> It is my understanding that pop_dipfit returns the talaraich<br>
>>> coordinates of the equivalent current dipoles and plots them inside a<br>
>>> standard MNI brain.<br>
>>> Our lab has been using talaraich client to find the equivalent<br>
>>> brodmann areas for these coordinates.<br>
>>><br>
>>> In your experience, is this the best software for identifying brodmann<br>
>>> areas? I had heard that there were other better methods and I wanted<br>
>>> to ask what you have found to be the most method of identifying<br>
>>> brodmann areas. Thanks.<br>
>>><br>
>>> -Julia<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>
>>> <a href="mailto:eeglablist-unsubscribe@sccn.ucsd.edu">eeglablist-unsubscribe@sccn.ucsd.edu</a><br>
>>> For digest mode, send an email with the subject "set digest mime" to<br>
>>> <a href="mailto:eeglablist-request@sccn.ucsd.edu">eeglablist-request@sccn.ucsd.edu</a><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 <a href="mailto:eeglablist-unsubscribe@sccn.ucsd.edu">eeglablist-unsubscribe@sccn.ucsd.edu</a><br>
> For digest mode, send an email with the subject "set digest mime" to <a href="mailto:eeglablist-request@sccn.ucsd.edu">eeglablist-request@sccn.ucsd.edu</a><br>
<br>
<br>
<br>
<br><br>---------- Forwarded message ----------<br>From: Arnaud Delorme <<a href="mailto:arno@ucsd.edu">arno@ucsd.edu</a>><br>To: Andrew Hill <<a href="mailto:andrewhill@ucla.edu">andrewhill@ucla.edu</a>><br>
Cc: <a href="mailto:eeglablist@sccn.ucsd.edu">eeglablist@sccn.ucsd.edu</a><br>Date: Wed, 12 Dec 2012 20:32:43 -0800<br>Subject: Re: [Eeglablist] STUDY design: spectrum negative power values<br><div style="word-wrap:break-word">
Dear Andrew,<div><br></div><div>yes, there was a typo, it should be 10.^<span style="font-family:Arial">(specdata{index}/10) and not </span>10^<span style="font-family:Arial">(specdata{index}/10).</span></div><div><span style="font-family:Arial">Sorry about that,</span></div>
<div><span style="font-family:Arial"><br></span></div><div><span style="font-family:Arial">Arno</span></div><div><br><div><div>On 29 Nov 2012, at 23:28, Andrew Hill wrote:</div><br><blockquote type="cite">
<div style="word-wrap:break-word">Arno or any other helpful soul - I'm replying in Christian's thread as I'm trying to do something similar.<div><br></div><div>Using the code snippets Arno provided, to convert specdata from log back into amplitude produces this error:</div>
<div><br></div><div>
<span style="font-family:Arial">[STUDY specdata specfreqs] = std_specplot(STUDY, ALLEEG,'channels', ('C3'} , 'plotsubjects','off', 'freqrange', [0.5 40]</span><span style="font-family:Arial">);</span></div>
<div><span style="font-family:Arial"><br></span></div><div>
<div style="font-family:Arial">
<div>for index = 1:length(specdata(:));</div><div>specdata{index} = sqrt(10^(specdata{index}/10));</div><div>end;</div><div><br></div></div></div><div><div>??? Error using ==> mpower</div><div>Inputs must be a scalar and a square matrix.</div>
<div> </div><div><br></div><div>My specdata is in a 4x2 cell array of 159 x 25 doubles (holding 159 quarter-hz bins for 25 subjects).</div><div>Is there a different way to call the math against the cell array so that it converts back to amplitude?</div>
<div><br></div><div>Thanks,</div><div>Andrew</div><div><br></div><div><br></div><div><br></div><div><div>On Jul 5, 2012, at 9:55 PM, Arnaud Delorme wrote:</div><br><blockquote type="cite"><div style="word-wrap:break-word">
Dear Christian,<div><br></div><div>yes, you are getting 10*log10(power) in these plots which is the usual way of visualizing EEG data.</div><div>You may recuperate the data values on the command line</div><div><br></div>
<div>
<i>[STUDY specdata freqs] = std_specplot(STUDY, ALLEEG, 'channels', { 'Cz' });</i></div><div><br></div><div>and convert the data back to absolute power values and visualize the data</div><div><br></div><div>
<i>for index = 1:length(specdata(:))</i></div><div><i><span style="white-space:pre-wrap"> </span>specdata{index} = 10^(specdata{index}/10);</i></div><div><i>end;</i></div><div><i>std_plotcurve(freqs, specdata);</i></div>
<div>
<br></div><div>Note, if you want amplitude not power, use instead <i>specdata{index} = 10^(specdata{index}/20);</i><i> </i>or <i>specdata{index} = sqrt(10^(specdata{index}/10)); </i>which is equivalent.</div><div>Best,</div>
<div><br></div><div>Arno</div><div><br><div><div>On May 7, 2012, at 12:56 AM, Christian Scharinger wrote:</div><br><blockquote type="cite"><div>Dear eeglab users,<br><br>I use the following code for calculating the spectrum in a STUDY design:<br>
<br>[STUDY ALLEEG] = std_precomp(STUDY, ALLEEG, 'channels', 'design', [1], <br>'erp', 'off', 'spec', 'on', 'ersp', 'off', 'specparams', { 'specmode', <br>
'psd', 'recompute', 'on', 'timerange', [1300 1800], 'freqfac', [4] }, <br>'savetrials', 'off');<br><br>STUDY = pop_specparams(STUDY, 'groupstats','on', 'mcorrect','fdr', <br>
'threshold',0.05,'plotgroups','together','freqrange',[1 30], <br>'rmsubjmean', 'off');<br><br>With this code, I'm getting negative power values when I use the <br>std_specplot function for plotting (or when I do the plotting via GUI).<br>
<br>So I guess I'm not getting absolute power values (what I would like to <br>have) but power values in relation to some kind of baseline.<br><br>Is it possible to get absolute power values for a spectrum in a STUDY <br>
design?<br>Where can I see/change what baseline eeglab uses for calculating power <br>values?<br><br>Many thanks in advance,<br><br>Christian<br><br><br><br>-- <br>Christian Scharinger, M.A.<br><br>Knowledge Media Research Center (KMRC)<br>
Schleichstraße 6 | 72076 Tuebingen<br><br>Phone: <a href="tel:%2B49%20%280%297071%20979-360" value="+497071979360" target="_blank">+49 (0)7071 979-360</a><br>Internet: <a href="http://www.iwm-kmrc.de/c.scharinger" target="_blank">http://www.iwm-kmrc.de/c.scharinger</a><br>
E-Mail: <a href="mailto:c.scharinger@iwm-kmrc.de" target="_blank">c.scharinger@iwm-kmrc.de</a><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 <a href="mailto:eeglablist-unsubscribe@sccn.ucsd.edu" target="_blank">eeglablist-unsubscribe@sccn.ucsd.edu</a><br>For digest mode, send an email with the subject "set digest mime" to <a href="mailto:eeglablist-request@sccn.ucsd.edu" target="_blank">eeglablist-request@sccn.ucsd.edu</a><br>
</div></blockquote></div><br></div></div>_______________________________________________<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 <a href="mailto:eeglablist-unsubscribe@sccn.ucsd.edu" target="_blank">eeglablist-unsubscribe@sccn.ucsd.edu</a><br>For digest mode, send an email with the subject "set digest mime" to <a href="mailto:eeglablist-request@sccn.ucsd.edu" target="_blank">eeglablist-request@sccn.ucsd.edu</a></blockquote>
</div><br></div></div></blockquote></div><br></div></div><br><br>---------- Forwarded message ----------<br>From: Arnaud Delorme <<a href="mailto:arno@ucsd.edu">arno@ucsd.edu</a>><br>To: "Iman M.Rezazadeh" <<a href="mailto:irezazadeh@ucdavis.edu">irezazadeh@ucdavis.edu</a>><br>
Cc: eeglablist <<a href="mailto:eeglablist@sccn.ucsd.edu">eeglablist@sccn.ucsd.edu</a>><br>Date: Wed, 12 Dec 2012 20:42:53 -0800<br>Subject: Re: [Eeglablist] Coherence connection lines in 2d<br><div style="word-wrap:break-word">
Dear Iman,<div><br></div><div>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).</div>
<div><br></div><div><a href="http://www.erpwavelab.org/" target="_blank">http://www.erpwavelab.org/</a></div><div><br></div><div>Best,</div><div><br></div><div>Arno</div><div><br><div><div>On 30 Nov 2012, at 15:08, Iman M.Rezazadeh wrote:</div>
<br><blockquote type="cite"><div lang="EN-US" link="blue" vlink="purple"><div><div style="margin:0in 0in 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">Hi EEGLABers,<u></u><u></u></div><div style="margin:0in 0in 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">
<u></u> <u></u></div><div style="margin:0in 0in 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">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?<u></u><u></u></div>
<div style="margin:0in 0in 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">Best,<u></u><u></u></div><div style="margin:0in 0in 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">Iman<u></u><u></u></div><div style="margin:0in 0in 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">
<u></u> <u></u></div><div style="margin:0in 0in 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-family:Arial,sans-serif">Iman M.Rezazadeh, PhD<u></u><u></u></span></div><div style="margin:0in 0in 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">
<span style="font-family:Arial,sans-serif">Postdoctoral Research Fellow<u></u><u></u></span></div><div style="margin:0in 0in 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-family:Arial,sans-serif">Center for Mind and Brain<u></u><u></u></span></div>
<div style="margin:0in 0in 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-family:Arial,sans-serif">University of California, Davis<u></u><u></u></span></div><div style="margin:0in 0in 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">
<span style="font-family:Arial,sans-serif"><a href="mailto:irezazadeh@ucdavis.edu" style="color:blue;text-decoration:underline" target="_blank">irezazadeh@ucdavis.edu</a><u></u><u></u></span></div><div style="margin:0in 0in 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">
<span style="font-family:Arial,sans-serif">Cell:<a href="tel:310-490-1808" value="+13104901808" target="_blank">310-490-1808</a><u></u><u></u></span></div><div style="margin:0in 0in 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">
<span style="font-family:Arial,sans-serif">Skype: Imanmr<u></u><u></u></span></div><div style="margin:0in 0in 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif"><u></u> <u></u></div></div>_______________________________________________<br>
Eeglablist page:<span> </span><a href="http://sccn.ucsd.edu/eeglab/eeglabmail.html" style="color:blue;text-decoration:underline" target="_blank">http://sccn.ucsd.edu/eeglab/eeglabmail.html</a><br>To unsubscribe, send an empty email to<span> </span><a href="mailto:eeglablist-unsubscribe@sccn.ucsd.edu" style="color:blue;text-decoration:underline" target="_blank">eeglablist-unsubscribe@sccn.ucsd.edu</a><br>
For digest mode, send an email with the subject "set digest mime" to<span> </span><a href="mailto:eeglablist-request@sccn.ucsd.edu" style="color:blue;text-decoration:underline" target="_blank">eeglablist-request@sccn.ucsd.edu</a></div>
</blockquote></div><br></div></div><br>_______________________________________________<br>
eeglablist mailing list <a href="mailto:eeglablist@sccn.ucsd.edu">eeglablist@sccn.ucsd.edu</a><br>
Eeglablist page: <a href="http://www.sccn.ucsd.edu/eeglab/eeglabmail.html" target="_blank">http://www.sccn.ucsd.edu/eeglab/eeglabmail.html</a><br>
To unsubscribe, send an empty email to <a href="mailto:eeglablist-unsub@sccn.ucsd.edu">eeglablist-unsub@sccn.ucsd.edu</a><br>
To switch to non-digest mode, send an empty email to <a href="mailto:eeglablist-nodigest@sccn.ucsd.edu">eeglablist-nodigest@sccn.ucsd.edu</a><br></blockquote></div><br></div></div>