[FieldTrip] Beamforming in FieldTrip and Brainstorm

[Mikkel Vinding]

Dear Vladimir

Thank you--that is an important note. We had that exact error in another
tutorial for EEG because of a bad MRI. Moving the mesh surfaces could not
fix the issue. We ended up using a sphere model instead. That still gave
reasonable fits for single dipoles. That might also be an option?

Best regards
Mikkel

Mikkel C. Vinding
NatMEG, Karolinska Institutet
Nobels väg 9
171 77 Stockholm, Sweden
Email: mikkel.vinding at ki.se


On Thu, Apr 18, 2019 at 1:19 PM Vladimir Litvak <litvak.vladimir at gmail.com>
wrote:

> Dear Mikkel,
>
> Your pipeline looks good. Just one point you and everyone else should be
> acutely aware of is that bemcp completely fails if your sources are too
> close to the inner skull surface. That means closer than half the length of
> the triangle side in the inner skull mesh. At some point we tested this
> extensively with Robert and in SPM there is a correction code that pushes
> the mesh inwards to make sure there is no problem. It looks like this (for
> a coordinate system expressed in meters). The distance of 6mm was found
> empirically by looking at correlations between the lead fields computed
> with bemcp vs. the spherical model and finding a value for which they are
> all above 0.9. For shorter distances, you can clearly see how the
> computation completely breaks down and gives nonsense lead-fields so it's
> not that they are slightly wrong, they are completely off.
>
> cfg = [];
> cfg.headmodel = vol;
> cfg.grid.pos = mesh.tess_ctx.vert;
> cfg.moveinward = 6e-3; %move to empirically determined BEM safe zone
> gridcorrect = ft_prepare_sourcemodel(cfg);
>
> mesh.tess_ctx.vert = gridcorrect.pos;
>
>
> I saw someone not being happy with bemcp on the list some time ago and
> that was the reason. If you make sure you stay in the safe zone, bemcp is
> great so I suggest you add something along these lines to your pipeline to
> save your users some misery.
>
> Best,
>
> Vladimir
>
>
>
>
> On Thu, Apr 18, 2019 at 9:35 AM Mikkel Vinding <mikkel at cnru.dk> wrote:
>
>> 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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>>>
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