[FieldTrip] Beamforming in FieldTrip and Brainstorm

[Mikkel Vinding]

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
>>
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>> https://doi.org/10.1371/journal.pcbi.1002202
>>
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