<html><head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<style type="text/css" style="display:none;"><!-- P {margin-top:0;margin-bottom:0;} --></style>
</head>
<body dir="ltr">
<div id="divtagdefaultwrapper" style="font-size:12pt;color:#000000;font-family:Calibri,Helvetica,sans-serif;" dir="ltr">
<p style="margin-top:0;margin-bottom:0"><span style="font-size: 12pt;">Hi Mikkel,</span><br>
</p>
<div style="color: rgb(0, 0, 0);">
<div dir="ltr">
<div id="x_divtagdefaultwrapper" dir="ltr" style="font-size:12pt; color:rgb(0,0,0); font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols">
<p style="margin-top:0; margin-bottom:0"><br>
</p>
<p style="margin-top:0; margin-bottom:0">Many thanks for your response on source analysis of EEG data in fieldtrip.</p>
<p style="margin-top:0; margin-bottom:0">Your pipeline is very informative, thank you (<a href="http://natmeg.se/MEEG_course2018/preprocess_MRI_data2.html" class="x_OWAAutoLink" id="LPlnk16407" previewremoved="true">http://natmeg.se/MEEG_course2018/preprocess_MRI_data2.html</a>). </p>
<p style="margin-top:0; margin-bottom:0"><span style="font-size:12pt"><br>
</span></p>
<p style="margin-top:0; margin-bottom:0"><span style="font-size:12pt">I was wondering if you could possibly give some direction on how to do this in data without individual MRI scans?</span></p>
<p style="margin-top:0; margin-bottom:0"><span style="font-size:12pt"><br>
</span></p>
<p style="margin-top:0; margin-bottom:0"><span style="font-size:12pt">Thank you very much again,</span></p>
<p style="margin-top:0; margin-bottom:0"><span style="font-size:12pt"><br>
</span></p>
<p style="margin-top:0; margin-bottom:0"><span style="font-size:12pt">Best wishes,</span></p>
<p style="margin-top:0; margin-bottom:0"><span style="font-size:12pt">Ioanna</span></p>
<br>
<div style="color:rgb(0,0,0)">
<hr tabindex="-1" style="display:inline-block; width:98%">
<div id="x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> fieldtrip <fieldtrip-bounces@science.ru.nl> on behalf of fieldtrip-request@science.ru.nl <fieldtrip-request@science.ru.nl><br>
<b>Sent:</b> 18 April 2019 11:00<br>
<b>To:</b> fieldtrip@science.ru.nl<br>
<b>Subject:</b> fieldtrip Digest, Vol 101, Issue 15</font>
<div> </div>
</div>
<div class="x_BodyFragment"><font size="2"><span style="font-size:11pt">
<div class="x_PlainText">Send fieldtrip mailing list submissions to<br>
fieldtrip@science.ru.nl<br>
<br>
To subscribe or unsubscribe via the World Wide Web, visit<br>
<a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" id="LPlnk139254" class="x_OWAAutoLink" previewremoved="true">
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
or, via email, send a message with subject or body 'help' to<br>
fieldtrip-request@science.ru.nl<br>
<br>
You can reach the person managing the list at<br>
fieldtrip-owner@science.ru.nl<br>
<br>
When replying, please edit your Subject line so it is more specific<br>
than "Re: Contents of fieldtrip digest..."<br>
<br>
<br>
Today's Topics:<br>
<br>
1. Beamforming in FieldTrip and Brainstorm (Ioanna Zioga)<br>
2. Re: Beamforming in FieldTrip and Brainstorm (Vladimir Litvak)<br>
3. Re: Beamforming in FieldTrip and Brainstorm (Mikkel Vinding)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Wed, 17 Apr 2019 10:08:29 +0000<br>
From: Ioanna Zioga <i.zioga@qmul.ac.uk><br>
To: "fieldtrip@science.ru.nl" <fieldtrip@science.ru.nl><br>
Subject: [FieldTrip] Beamforming in FieldTrip and Brainstorm<br>
Message-ID:<br>
<AM0PR07MB480157E4E35F89F21CE27AAFDE250@AM0PR07MB4801.eurprd07.prod.outlook.com><br>
<br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hi All,<br>
<br>
<br>
I'm Ioanna and I'm a PhD student in Queen Mary University of London, doing EEG research on music learning and creativity [:slight_smile:]<br>
<br>
<br>
My question is on using Brainstorm and FieldTrip interchangeably to do beamforming on EEG data recorded by a 64-channel EGI system.<br>
<br>
I haven't found an option to compute the cross-spectral density matrix for the beamforming in Brainstorm. On the other hand, with Brainstorm I could quite easily create a head model for the 64-channel EGI system my data were recorded with.<br>
<br>
<br>
Therefore, I was wondering if I could:<br>
<br>
1. Calculate the cross-spectral density in Fieldtrip (ft_freqanalysis)<br>
2. Create the head model in Brainstorm<br>
3. Run the source analysis in Fieldtrip (ft_sourceanalysis) using the head model from Brainstorm<br>
<br>
Q1: How can I use the head model (as computed in Brainstorm) in FieldTrip to run the ft_sourceanalysis function? What is the format that the head model structure should have?<br>
<br>
Q2: Does anyone have a FieldTrip head model for a 64-channel EGI system?<br>
<br>
<br>
Any help would be very much appreciated!<br>
<br>
<br>
Thanks so much in advance,<br>
Ioanna<br>
<br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <<a href="http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20190417/1df25251/attachment.html" id="LPlnk324465" class="x_OWAAutoLink" previewremoved="true">http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20190417/1df25251/attachment.html</a>><br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Wed, 17 Apr 2019 11:30:12 +0100<br>
From: Vladimir Litvak <litvak.vladimir@gmail.com><br>
To: FieldTrip discussion list <fieldtrip@science.ru.nl><br>
Subject: Re: [FieldTrip] Beamforming in FieldTrip and Brainstorm<br>
Message-ID:<br>
<CACq1BhK3ByL8r=Rt=Qu8LzczLuc1rkJH=QJfB95UXAiLBZEr8g@mail.gmail.com><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear Ioanna,<br>
<br>
I'm not well familiar with Brainstorm but you could use SPM12 (<br>
<a href="https://www.fil.ion.ucl.ac.uk/spm/" id="LPlnk547133" class="x_OWAAutoLink" previewremoved="true">https://www.fil.ion.ucl.ac.uk/spm/</a>) to make a template head model that you<br>
could then easily use in FT (as SPM and FT share the same forward<br>
computation code), See<br>
<a href="http://www.fieldtriptoolbox.org/workshop/meg-uk-2015/fieldtrip-beamformer-demo/" id="LPlnk157844" class="x_OWAAutoLink" previewremoved="true">http://www.fieldtriptoolbox.org/workshop/meg-uk-2015/fieldtrip-beamformer-demo/</a><br>
for<br>
an example of how you get the head model and sensors to FT. To generate the<br>
head model it would be enough to convert an example of your data to SPM,<br>
load it to '3D source reconstruction' interface and go through the sequence<br>
of buttons there as described in the SPM manual (<br>
<a href="https://www.fil.ion.ucl.ac.uk/spm/doc/manual.pdf" id="LPlnk838452" class="x_OWAAutoLink" previewremoved="true">https://www.fil.ion.ucl.ac.uk/spm/doc/manual.pdf</a>, p 121). You only need to<br>
get up to the 'Forward' button, choose EEG BEM, press 'save' and then you<br>
do:<br>
<br>
D = spm_eeg_load('dataset_name.mat');<br>
<br>
% convert sensors and volume conduction model from SPM<br>
volsens = spm_eeg_inv_get_vol_sens(D, 1, 'MNI-aligned', 'inv', 'EEG');<br>
vol1 = volsens.EEG.vol;<br>
sens1 = volsens.EEG.sens;<br>
<br>
Best,<br>
<br>
Vladimir<br>
<br>
On Wed, Apr 17, 2019 at 11:08 AM Ioanna Zioga <i.zioga@qmul.ac.uk> wrote:<br>
<br>
> Hi All,<br>
><br>
><br>
> I'm Ioanna and I'm a PhD student in Queen Mary University of London, doing<br>
> EEG research on music learning and creativity [image: :slight_smile:]<br>
><br>
><br>
> My question is on using Brainstorm and FieldTrip interchangeably to do<br>
> beamforming on EEG data recorded by a 64-channel EGI system.<br>
><br>
> I haven't found an option to compute the cross-spectral density matrix for<br>
> the beamforming in Brainstorm. On the other hand, with Brainstorm I could<br>
> quite easily create a head model for the 64-channel EGI system my data were<br>
> recorded with.<br>
><br>
><br>
> Therefore, I was wondering if I could:<br>
><br>
> 1. Calculate the cross-spectral density in Fieldtrip (ft_freqanalysis)<br>
> 2. Create the head model in Brainstorm<br>
> 3. Run the source analysis in Fieldtrip (ft_sourceanalysis) using the<br>
> head model from Brainstorm<br>
><br>
> Q1: How can I use the head model (as computed in Brainstorm) in FieldTrip<br>
> to run the ft_sourceanalysis function? What is the format that the head<br>
> model structure should have?<br>
><br>
> Q2: Does anyone have a FieldTrip head model for a 64-channel EGI system?<br>
><br>
><br>
> Any help would be very much appreciated!<br>
><br>
><br>
> Thanks so much in advance,<br>
> Ioanna<br>
><br>
> _______________________________________________<br>
> fieldtrip mailing list<br>
> <a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" id="LPlnk378733" class="x_OWAAutoLink" previewremoved="true">
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
> <a href="https://doi.org/10.1371/journal.pcbi.1002202" id="LPlnk986206" class="x_OWAAutoLink" previewremoved="true">
https://doi.org/10.1371/journal.pcbi.1002202</a><br>
><br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <<a href="http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20190417/5cf15216/attachment.html" id="LPlnk779826" class="x_OWAAutoLink" previewremoved="true">http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20190417/5cf15216/attachment.html</a>><br>
<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Thu, 18 Apr 2019 09:47:39 +0200<br>
From: Mikkel Vinding <mikkel@cnru.dk><br>
To: FieldTrip discussion list <fieldtrip@science.ru.nl><br>
Subject: Re: [FieldTrip] Beamforming in FieldTrip and Brainstorm<br>
Message-ID:<br>
<CAOQsbuZMenR0YtFy3XTZr22+vVYc2m2eDwWpzacFiyHBExpx2g@mail.gmail.com><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear all<br>
<br>
You can also call SPMs function from FieldTrip to make head models and<br>
source models. Here is a quick overview of a standard pipeline:<br>
<a href="http://natmeg.se/MEEG_course2018/preprocess_MRI_data2.html" id="LPlnk418027" class="x_OWAAutoLink" previewremoved="true">http://natmeg.se/MEEG_course2018/preprocess_MRI_data2.html</a><br>
<br>
Best regards<br>
Mikkel<br>
<br>
<br>
Mikkel C. Vinding<br>
NatMEG, Karolinska Institutet<br>
Nobels väg 9<br>
171 77 Stockholm, Sweden<br>
Email: mikkel.vinding@ki.se<br>
<br>
<br>
On Wed, Apr 17, 2019 at 1:12 PM Vladimir Litvak <litvak.vladimir@gmail.com><br>
wrote:<br>
<br>
> Dear Ioanna,<br>
><br>
> I'm not well familiar with Brainstorm but you could use SPM12 (<br>
> <a href="https://www.fil.ion.ucl.ac.uk/spm/" id="LPlnk260593" class="x_OWAAutoLink" previewremoved="true">
https://www.fil.ion.ucl.ac.uk/spm/</a>) to make a template head model that<br>
> you could then easily use in FT (as SPM and FT share the same forward<br>
> computation code), See<br>
> <a href="http://www.fieldtriptoolbox.org/workshop/meg-uk-2015/fieldtrip-beamformer-demo/" id="LPlnk224783" class="x_OWAAutoLink" previewremoved="true">
http://www.fieldtriptoolbox.org/workshop/meg-uk-2015/fieldtrip-beamformer-demo/</a> for<br>
> an example of how you get the head model and sensors to FT. To generate the<br>
> head model it would be enough to convert an example of your data to SPM,<br>
> load it to '3D source reconstruction' interface and go through the sequence<br>
> of buttons there as described in the SPM manual (<br>
> <a href="https://www.fil.ion.ucl.ac.uk/spm/doc/manual.pdf" id="LPlnk90218" class="x_OWAAutoLink" previewremoved="true">
https://www.fil.ion.ucl.ac.uk/spm/doc/manual.pdf</a>, p 121). You only need<br>
> to get up to the 'Forward' button, choose EEG BEM, press 'save' and then<br>
> you do:<br>
><br>
> D = spm_eeg_load('dataset_name.mat');<br>
><br>
> % convert sensors and volume conduction model from SPM<br>
> volsens = spm_eeg_inv_get_vol_sens(D, 1, 'MNI-aligned', 'inv', 'EEG');<br>
> vol1 = volsens.EEG.vol;<br>
> sens1 = volsens.EEG.sens;<br>
><br>
> Best,<br>
><br>
> Vladimir<br>
><br>
> On Wed, Apr 17, 2019 at 11:08 AM Ioanna Zioga <i.zioga@qmul.ac.uk> wrote:<br>
><br>
>> Hi All,<br>
>><br>
>><br>
>> I'm Ioanna and I'm a PhD student in Queen Mary University of London,<br>
>> doing EEG research on music learning and creativity [image:<br>
>> :slight_smile:]<br>
>><br>
>><br>
>> My question is on using Brainstorm and FieldTrip interchangeably to do<br>
>> beamforming on EEG data recorded by a 64-channel EGI system.<br>
>><br>
>> I haven't found an option to compute the cross-spectral density matrix<br>
>> for the beamforming in Brainstorm. On the other hand, with Brainstorm I<br>
>> could quite easily create a head model for the 64-channel EGI system my<br>
>> data were recorded with.<br>
>><br>
>><br>
>> Therefore, I was wondering if I could:<br>
>><br>
>> 1. Calculate the cross-spectral density in Fieldtrip (ft_freqanalysis)<br>
>> 2. Create the head model in Brainstorm<br>
>> 3. Run the source analysis in Fieldtrip (ft_sourceanalysis) using the<br>
>> head model from Brainstorm<br>
>><br>
>> Q1: How can I use the head model (as computed in Brainstorm) in FieldTrip<br>
>> to run the ft_sourceanalysis function? What is the format that the head<br>
>> model structure should have?<br>
>><br>
>> Q2: Does anyone have a FieldTrip head model for a 64-channel EGI system?<br>
>><br>
>><br>
>> Any help would be very much appreciated!<br>
>><br>
>><br>
>> Thanks so much in advance,<br>
>> Ioanna<br>
>><br>
>> _______________________________________________<br>
>> fieldtrip mailing list<br>
>> <a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" id="LPlnk291520" class="x_OWAAutoLink" previewremoved="true">
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
>> <a href="https://doi.org/10.1371/journal.pcbi.1002202" id="LPlnk563559" class="x_OWAAutoLink" previewremoved="true">
https://doi.org/10.1371/journal.pcbi.1002202</a><br>
>><br>
> _______________________________________________<br>
> fieldtrip mailing list<br>
> <a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" id="LPlnk673220" class="x_OWAAutoLink" previewremoved="true">
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
> <a href="https://doi.org/10.1371/journal.pcbi.1002202" id="LPlnk917842" class="x_OWAAutoLink" previewremoved="true">
https://doi.org/10.1371/journal.pcbi.1002202</a><br>
><br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <<a href="http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20190418/3922d22c/attachment.html" id="LPlnk350922" class="x_OWAAutoLink" previewremoved="true">http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20190418/3922d22c/attachment.html</a>><br>
<br>
------------------------------<br>
<br>
Subject: Digest Footer<br>
<br>
_______________________________________________<br>
fieldtrip mailing list<br>
<a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" id="LPlnk847910" class="x_OWAAutoLink" previewremoved="true">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
_______________________________________________<br>
fieldtrip mailing list<br>
<a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" id="LPlnk185023" class="x_OWAAutoLink" previewremoved="true">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
<a href="https://doi.org/10.1371/journal.pcbi.1002202" id="LPlnk530509" class="x_OWAAutoLink" previewremoved="true">https://doi.org/10.1371/journal.pcbi.1002202</a><br>
<br>
<br>
------------------------------<br>
<br>
End of fieldtrip Digest, Vol 101, Issue 15<br>
******************************************<br>
</div>
</span></font></div>
</div>
</div>
</div>
</div>
</div>
</body>
</html>