[FieldTrip] Fw: Re:Re: Beamforming in FieldTrip and Brainstorm
Ioanna Zioga
i.zioga at qmul.ac.uk
Mon Apr 29 21:57:09 CEST 2019
Hi Mikkel,
Many thanks for your response on source analysis of EEG data in fieldtrip.
Your pipeline is very informative, thank you (http://natmeg.se/MEEG_course2018/preprocess_MRI_data2.html).
I was wondering if you could possibly give some direction on how to do this in data without individual MRI scans?
Thank you very much again,
Best wishes,
Ioanna
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Today's Topics:
1. Beamforming in FieldTrip and Brainstorm (Ioanna Zioga)
2. Re: Beamforming in FieldTrip and Brainstorm (Vladimir Litvak)
3. Re: Beamforming in FieldTrip and Brainstorm (Mikkel Vinding)
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Message: 1
Date: Wed, 17 Apr 2019 10:08:29 +0000
From: Ioanna Zioga <i.zioga at qmul.ac.uk>
To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
Subject: [FieldTrip] Beamforming in FieldTrip and Brainstorm
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<AM0PR07MB480157E4E35F89F21CE27AAFDE250 at AM0PR07MB4801.eurprd07.prod.outlook.com>
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Hi All,
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:]
My question is on using Brainstorm and FieldTrip interchangeably to do beamforming on EEG data recorded by a 64-channel EGI system.
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.
Therefore, I was wondering if I could:
1. Calculate the cross-spectral density in Fieldtrip (ft_freqanalysis)
2. Create the head model in Brainstorm
3. Run the source analysis in Fieldtrip (ft_sourceanalysis) using the head model from Brainstorm
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?
Q2: Does anyone have a FieldTrip head model for a 64-channel EGI system?
Any help would be very much appreciated!
Thanks so much in advance,
Ioanna
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Message: 2
Date: Wed, 17 Apr 2019 11:30:12 +0100
From: Vladimir Litvak <litvak.vladimir at gmail.com>
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] Beamforming in FieldTrip and Brainstorm
Message-ID:
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Dear Ioanna,
I'm not well familiar with Brainstorm but you could use SPM12 (
https://www.fil.ion.ucl.ac.uk/spm/) to make a template head model that you
could then easily use in FT (as SPM and FT share the same forward
computation code), See
http://www.fieldtriptoolbox.org/workshop/meg-uk-2015/fieldtrip-beamformer-demo/
for
an example of how you get the head model and sensors to FT. To generate the
head model it would be enough to convert an example of your data to SPM,
load it to '3D source reconstruction' interface and go through the sequence
of buttons there as described in the SPM manual (
https://www.fil.ion.ucl.ac.uk/spm/doc/manual.pdf, p 121). You only need to
get up to the 'Forward' button, choose EEG BEM, press 'save' and then you
do:
D = spm_eeg_load('dataset_name.mat');
% convert sensors and volume conduction model from SPM
volsens = spm_eeg_inv_get_vol_sens(D, 1, 'MNI-aligned', 'inv', 'EEG');
vol1 = volsens.EEG.vol;
sens1 = volsens.EEG.sens;
Best,
Vladimir
On Wed, Apr 17, 2019 at 11:08 AM Ioanna Zioga <i.zioga at qmul.ac.uk> wrote:
> Hi All,
>
>
> I'm Ioanna and I'm a PhD student in Queen Mary University of London, doing
> EEG research on music learning and creativity [image: :slight_smile:]
>
>
> My question is on using Brainstorm and FieldTrip interchangeably to do
> beamforming on EEG data recorded by a 64-channel EGI system.
>
> 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.
>
>
> Therefore, I was wondering if I could:
>
> 1. Calculate the cross-spectral density in Fieldtrip (ft_freqanalysis)
> 2. Create the head model in Brainstorm
> 3. Run the source analysis in Fieldtrip (ft_sourceanalysis) using the
> head model from Brainstorm
>
> 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?
>
> Q2: Does anyone have a FieldTrip head model for a 64-channel EGI system?
>
>
> Any help would be very much appreciated!
>
>
> Thanks so much in advance,
> Ioanna
>
> _______________________________________________
> fieldtrip mailing list
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> https://doi.org/10.1371/journal.pcbi.1002202
>
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Message: 3
Date: Thu, 18 Apr 2019 09:47:39 +0200
From: Mikkel Vinding <mikkel at cnru.dk>
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] Beamforming in FieldTrip and Brainstorm
Message-ID:
<CAOQsbuZMenR0YtFy3XTZr22+vVYc2m2eDwWpzacFiyHBExpx2g at mail.gmail.com>
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Dear all
You can also call SPMs function from FieldTrip to make head models and
source models. Here is a quick overview of a standard pipeline:
http://natmeg.se/MEEG_course2018/preprocess_MRI_data2.html
Best regards
Mikkel
Mikkel C. Vinding
NatMEG, Karolinska Institutet
Nobels väg 9
171 77 Stockholm, Sweden
Email: mikkel.vinding at ki.se
On Wed, Apr 17, 2019 at 1:12 PM Vladimir Litvak <litvak.vladimir at gmail.com>
wrote:
> Dear Ioanna,
>
> I'm not well familiar with Brainstorm but you could use SPM12 (
> https://www.fil.ion.ucl.ac.uk/spm/) to make a template head model that
> you could then easily use in FT (as SPM and FT share the same forward
> computation code), See
> http://www.fieldtriptoolbox.org/workshop/meg-uk-2015/fieldtrip-beamformer-demo/ for
> an example of how you get the head model and sensors to FT. To generate the
> head model it would be enough to convert an example of your data to SPM,
> load it to '3D source reconstruction' interface and go through the sequence
> of buttons there as described in the SPM manual (
> https://www.fil.ion.ucl.ac.uk/spm/doc/manual.pdf, p 121). You only need
> to get up to the 'Forward' button, choose EEG BEM, press 'save' and then
> you do:
>
> D = spm_eeg_load('dataset_name.mat');
>
> % convert sensors and volume conduction model from SPM
> volsens = spm_eeg_inv_get_vol_sens(D, 1, 'MNI-aligned', 'inv', 'EEG');
> vol1 = volsens.EEG.vol;
> sens1 = volsens.EEG.sens;
>
> Best,
>
> Vladimir
>
> On Wed, Apr 17, 2019 at 11:08 AM Ioanna Zioga <i.zioga at qmul.ac.uk> wrote:
>
>> Hi All,
>>
>>
>> I'm Ioanna and I'm a PhD student in Queen Mary University of London,
>> doing EEG research on music learning and creativity [image:
>> :slight_smile:]
>>
>>
>> My question is on using Brainstorm and FieldTrip interchangeably to do
>> beamforming on EEG data recorded by a 64-channel EGI system.
>>
>> 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.
>>
>>
>> Therefore, I was wondering if I could:
>>
>> 1. Calculate the cross-spectral density in Fieldtrip (ft_freqanalysis)
>> 2. Create the head model in Brainstorm
>> 3. Run the source analysis in Fieldtrip (ft_sourceanalysis) using the
>> head model from Brainstorm
>>
>> 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?
>>
>> Q2: Does anyone have a FieldTrip head model for a 64-channel EGI system?
>>
>>
>> Any help would be very much appreciated!
>>
>>
>> Thanks so much in advance,
>> Ioanna
>>
>> _______________________________________________
>> fieldtrip mailing list
>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>> https://doi.org/10.1371/journal.pcbi.1002202
>>
> _______________________________________________
> fieldtrip mailing list
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> https://doi.org/10.1371/journal.pcbi.1002202
>
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