<div dir="ltr"><div><div><div>Dear Arjen, <br></div>thanks for your quick reply. <br></div>With the version of sunday (yesterdays version the file was invalid, my windows couldn't open it and there is not yet a version of today) the misplotting still occurs. <br>
<br></div>I dont know if attachments work in this email list, but attached there is the surface and the orthoplot of exactly the same interploated data. <br><br></div><div class="gmail_extra"><br><br><div class="gmail_quote">
2014-04-08 12:00 GMT+02:00 <span dir="ltr"><<a href="mailto:fieldtrip-request@science.ru.nl" target="_blank">fieldtrip-request@science.ru.nl</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<br>
Today's Topics:<br>
<br>
1. Re: denoising data (Todorovic, A.)<br>
2. surfaceplot made by ft_sourceplot sparing the frontal lobes<br>
(Marlene B?nstrup)<br>
3. Re: surfaceplot made by ft_sourceplot sparing the frontal<br>
lobes (Arjen Stolk)<br>
4. fieldtrip2eeglab (Tyler Grummett)<br>
5. fieldtrip2eeglab (Julian Keil)<br>
6. Re: denoising data (<a href="mailto:s.rombetto@cib.na.cnr.it">s.rombetto@cib.na.cnr.it</a>)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Tue, 8 Apr 2014 07:25:18 +0200 (CEST)<br>
From: "Todorovic, A." <<a href="mailto:a.todorovic@fcdonders.ru.nl">a.todorovic@fcdonders.ru.nl</a>><br>
To: FieldTrip List <<a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a>><br>
Subject: Re: [FieldTrip] denoising data<br>
Message-ID:<br>
<<a href="mailto:818248357.305942.1396934718615.JavaMail.root@monoceros.zimbra.ru.nl">818248357.305942.1396934718615.JavaMail.root@monoceros.zimbra.ru.nl</a>><br>
Content-Type: text/plain; charset=utf-8<br>
<br>
Hi Haiteng,<br>
<br>
Thanks for your reply.<br>
<br>
Just to be sure if I understand you correctly - do you use BOTH denoise_pca and denoise_synthetic on the same data?<br>
<br>
If not, how do you choose which one to use?<br>
<br>
Cheers,<br>
Ana<br>
<br>
><br>
> Dear Ana,<br>
><br>
><br>
> If I understand correctly , we use ft_denoise_synthetic and<br>
> ft_denoise_pca to reduce noise due to recording (e.g. environment noise ,<br>
> thermal noise... ) not the brain signal artefact (e.g eye blink). Normally<br>
> ,I use these two functions in the very early stage .<br>
><br>
> Best,<br>
> Haiteng<br>
<br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Tue, 8 Apr 2014 09:07:46 +0200<br>
From: Marlene B?nstrup <<a href="mailto:marlene.boenstrup@googlemail.com">marlene.boenstrup@googlemail.com</a>><br>
To: <a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a><br>
Subject: [FieldTrip] surfaceplot made by ft_sourceplot sparing the<br>
frontal lobes<br>
Message-ID:<br>
<CAG0LeN=<a href="mailto:hQuwNwyu2qf-GFmF84qzVje7ENjq86MSsrpE31_J2vQ@mail.gmail.com">hQuwNwyu2qf-GFmF84qzVje7ENjq86MSsrpE31_J2vQ@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Dear fieldtrip-experts,<br>
<br>
The plot I generated by ft_sourceplot using cfg.method = 'surface' with<br>
either projectionemthod 'nearest' or 'project' looks funny. The frontal<br>
lobes don't show any activation, they are just left grey. And also specific<br>
activations on the cortex are shifted towards the back (y-axis). I compared<br>
the same 3-D- sourceactivation data (interpolated on the standard T1 output<br>
of ft_interpolate with ft_interpolate) in an orthoplot and there the<br>
sourceactivation is neatly arranged in the whole brain volume, including<br>
the frontal lobes. So that the mistake must origin in the ft_sourceplot<br>
function.<br>
I use the version of the 18th of December 2013.<br>
<br>
Do you know this problem and can help me with it?<br>
If not, do you have an idea to solve it or cirumvent it?<br>
<br>
Thanks in advance,<br>
Marlene<br>
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<br>
Message: 3<br>
Date: Tue, 8 Apr 2014 10:59:00 +0200<br>
From: Arjen Stolk <<a href="mailto:a.stolk8@gmail.com">a.stolk8@gmail.com</a>><br>
To: FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>><br>
Subject: Re: [FieldTrip] surfaceplot made by ft_sourceplot sparing the<br>
frontal lobes<br>
Message-ID:<br>
<CAAiwptRCAm4xwLyyLAK4gAgP-B4A1QyLzanOyUkAay=<a href="mailto:nRhoRBQ@mail.gmail.com">nRhoRBQ@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hi Marlene,<br>
<br>
Could you download today's version of FieldTrip, and let us know whether<br>
this problem still occurs? I'm saying because we just made an update to<br>
surface plotting, potentially solving your issue.<br>
<br>
Best,<br>
Arjen<br>
<br>
<br>
2014-04-08 9:07 GMT+02:00 Marlene B?nstrup <<a href="mailto:marlene.boenstrup@googlemail.com">marlene.boenstrup@googlemail.com</a><br>
>:<br>
<br>
> Dear fieldtrip-experts,<br>
><br>
> The plot I generated by ft_sourceplot using cfg.method = 'surface' with<br>
> either projectionemthod 'nearest' or 'project' looks funny. The frontal<br>
> lobes don't show any activation, they are just left grey. And also specific<br>
> activations on the cortex are shifted towards the back (y-axis). I compared<br>
> the same 3-D- sourceactivation data (interpolated on the standard T1 output<br>
> of ft_interpolate with ft_interpolate) in an orthoplot and there the<br>
> sourceactivation is neatly arranged in the whole brain volume, including<br>
> the frontal lobes. So that the mistake must origin in the ft_sourceplot<br>
> function.<br>
> I use the version of the 18th of December 2013.<br>
><br>
> Do you know this problem and can help me with it?<br>
> If not, do you have an idea to solve it or cirumvent it?<br>
><br>
> Thanks in advance,<br>
> Marlene<br>
><br>
> _______________________________________________<br>
> fieldtrip mailing list<br>
> <a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br>
> <a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip" target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
><br>
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<br>
------------------------------<br>
<br>
Message: 4<br>
Date: Tue, 8 Apr 2014 09:01:47 +0000<br>
From: Tyler Grummett <<a href="mailto:tyler.grummett@flinders.edu.au">tyler.grummett@flinders.edu.au</a>><br>
To: FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>><br>
Subject: [FieldTrip] fieldtrip2eeglab<br>
Message-ID:<br>
<<a href="mailto:36a06a30eef54304859a734a2deb7153@SIXPR03MB368.apcprd03.prod.outlook.com">36a06a30eef54304859a734a2deb7153@SIXPR03MB368.apcprd03.prod.outlook.com</a>><br>
<br>
Content-Type: text/plain; charset="us-ascii"<br>
<br>
?Hey fieldtrip,<br>
<br>
<br>
Is there a fieldtrip2eeglab function somewhere?<br>
<br>
<br>
It says in the documentation of 'integrating with eeglab', and I was wondering whether there already was one.<br>
<br>
<br>
Tyler<br>
<br>
<br>
*************************<br>
<br>
Tyler Grummett ( BBSc, BSc(Hons I))<br>
PhD Candidate<br>
Brain Signals Laboratory<br>
Flinders University<br>
Rm 5A301<br>
Ext 66124<br>
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------------------------------<br>
<br>
Message: 5<br>
Date: Tue, 8 Apr 2014 11:19:34 +0200<br>
From: Julian Keil <<a href="mailto:julian.keil@gmail.com">julian.keil@gmail.com</a>><br>
To: Tyler Grummett <<a href="mailto:tyler.grummett@flinders.edu.au">tyler.grummett@flinders.edu.au</a>>, FieldTrip<br>
discussion list <<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>><br>
Subject: [FieldTrip] fieldtrip2eeglab<br>
Message-ID: <<a href="mailto:60EC99B5-A742-420D-84A2-3B86336EB37A@gmail.com">60EC99B5-A742-420D-84A2-3B86336EB37A@gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hi Tyler,<br>
<br>
there was a mail by Arno Delorme last year containing the function.<br>
<br>
See below.<br>
<br>
Best,<br>
<br>
Julian<br>
********************<br>
Dr. Julian Keil<br>
<br>
AG Multisensorische Integration<br>
Psychiatrische Universit?tsklinik<br>
der Charit? im St. Hedwig-Krankenhaus<br>
Gro?e Hamburger Stra?e 5-11, Raum E 307<br>
10115 Berlin<br>
<br>
Telefon: <a href="tel:%2B49-30-2311-1879" value="+493023111879">+49-30-2311-1879</a><br>
Fax: <a href="tel:%2B49-30-2311-2209" value="+493023112209">+49-30-2311-2209</a><br>
<a href="http://psy-ccm.charite.de/forschung/bildgebung/ag_multisensorische_integration" target="_blank">http://psy-ccm.charite.de/forschung/bildgebung/ag_multisensorische_integration</a><br>
<br>
Anfang der weitergeleiteten E-Mail:<br>
<br>
> Von: Arnaud Delorme <<a href="mailto:arno@cerco.ups-tlse.fr">arno@cerco.ups-tlse.fr</a>><br>
> Betreff: Re: [FieldTrip] Channel layout FT to EEGLAB<br>
> Datum: 29. Oktober 2013 01:27:53 MEZ<br>
> An: FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>><br>
> Antwort an: FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>><br>
><br>
> Dear Rajat,<br>
><br>
> this old function transforms EEG data contained in the Fieldtrip structure into an EEGLAB structure.<br>
> After you have done that, to transform a channel location file, simply type in<br>
><br>
> EEG.chanlocs = struct('labels', cfg.elec.label, 'X', mattocell(cfg.elec.pnt(1,:)), 'Y', mattocell(cfg.elec.pnt(2,:)),'Z', mattocell(cfg.elec.pnt(3,:)));<br>
> EEG.chanlocs = convertlocs(EEG.chanlocs, 'cart2all');<br>
><br>
> This code is untested. You might have to switch X, Y and Z to obtain the correct orientation for the electrode cap.<br>
> Best,<br>
><br>
> Arno<br>
><br>
><br>
><br>
> On Oct 28, 2013, at 7:36 AM, Raquel Bibi <<a href="mailto:bibi.raquel@gmail.com">bibi.raquel@gmail.com</a>> wrote:<br>
><br>
>> Hi Rajat,<br>
>> I don't know EEGLAB, but I use the "ordered" option in Fieldtrip to display my time-locked ICA components.<br>
>><br>
>> Best,<br>
>><br>
>> Raquel<br>
>><br>
>><br>
>> On Mon, Oct 28, 2013 at 9:39 AM, Rajat Thomas <<a href="mailto:rajatthomas@gmail.com">rajatthomas@gmail.com</a>> wrote:<br>
>> Dear all,<br>
>><br>
>> I made a layout file using the image of the ecog array I had, just like described in the<br>
>> tutorial.<br>
>><br>
>> I would like to port this to EEGLAB, so that I can use the various ICA options to plot<br>
>> the components at the channel locations and so on.<br>
>><br>
>> Could anyone either point me to a file that does this conversion? or<br>
>> Any way of using ICA within fieldtrip to plot the various components on the different<br>
>> channels using the layout file?<br>
>><br>
>> I know it is used for channel rejection and so on but any help on plotting the components<br>
>> back on the ICA would be appreciated.<br>
>><br>
>> Thanks a lot in advance.<br>
>><br>
>> Rajat<br>
>><br>
>> --<br>
>> Rajat Mani Thomas<br>
>> Netherlands Institute for Neuroscience<br>
>> Amsterdam, The Netherlands<br>
>> <a href="http://www.cita.utoronto.ca/~thomas" target="_blank">http://www.cita.utoronto.ca/~thomas</a><br>
>><br>
>> _______________________________________________<br>
>> fieldtrip mailing list<br>
>> <a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br>
>> <a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip" target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
>><br>
>> _______________________________________________<br>
>> fieldtrip mailing list<br>
>> <a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br>
>> <a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip" target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
><br>
> _______________________________________________<br>
> fieldtrip mailing list<br>
> <a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br>
> <a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip" target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
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<br>
Message: 6<br>
Date: Tue, 8 Apr 2014 11:51:12 +0200<br>
From: <a href="mailto:s.rombetto@cib.na.cnr.it">s.rombetto@cib.na.cnr.it</a><br>
To: <a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a><br>
Subject: Re: [FieldTrip] denoising data<br>
Message-ID: <<a href="mailto:20140408115112.cn1ddeuo840s8s84@arco.cib.na.cnr.it">20140408115112.cn1ddeuo840s8s84@arco.cib.na.cnr.it</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";<br>
format="flowed"<br>
<br>
Hi<br>
I am interested in this topic too.<br>
As I have mainly environmental noise I use denoise_pca but I would<br>
like to understand if with a different code I couold improve my S/N<br>
ratio. Moreover I would ask if there is any difference if you apply<br>
first one denoising procedure or the other.<br>
<br>
Regards<br>
Sara Rombetto, PhD<br>
<br>
> Hi Haiteng,<br>
><br>
> Thanks for your reply.<br>
><br>
> Just to be sure if I understand you correctly - do you use BOTH<br>
> denoise_pca and denoise_synthetic on the same data?<br>
><br>
> If not, how do you choose which one to use?<br>
><br>
> Cheers,<br>
> Ana<br>
><br>
>><br>
>> Dear Ana,<br>
>><br>
>><br>
>> If I understand correctly , we use ft_denoise_synthetic and<br>
>> ft_denoise_pca to reduce noise due to recording (e.g. environment noise ,<br>
>> thermal noise... ) not the brain signal artefact (e.g eye blink). Normally<br>
>> ,I use these two functions in the very early stage .<br>
>><br>
>> Best,<br>
>> Haiteng<br>
> _______________________________________________<br>
> fieldtrip mailing list<br>
> <a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br>
> <a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip" target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
><br>
<br>
<br>
<br>
-------------------------<br>
Dott.ssa Sara Rombetto<br>
Istituto di Cibernetica<br>
"E. Caianiello"<br>
Via Campi Flegrei, 34<br>
80078 Pozzuoli (NA)<br>
Italy<br>
mob <a href="tel:%2B39%203401689815" value="+393401689815">+39 3401689815</a><br>
tel <a href="tel:%2B39%200818675361" value="+390818675361">+39 0818675361</a><br>
fax <a href="tel:%2B39%200818675128" value="+390818675128">+39 0818675128</a><br>
Lab MEG <a href="tel:0817483511" value="+49817483511">0817483511</a><br>
--------------------------<br>
"I disapprove of what you say, but I will defend to the death your<br>
right to say<br>
it." [Evelyn Beatrice Hall, The Friends Of Voltaire]<br>
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End of fieldtrip Digest, Vol 41, Issue 16<br>
*****************************************<br>
</blockquote></div><br></div>