[Mne_analysis] Using a BEM model with Xfit

Marijn van Vliet marijn.vanvliet at aalto.fi
Sun Jan 10 11:35:36 EST 2021
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Dear Jamit,

thanks, that works like a charm!

Because of data management policies, we could not just place all BEM 
models into a single /neuro/database/bem folder. However, the Xfit 
manual mentioned that you can set the BEM_MODEL_DIR environment variable 
to the dir in which the BEM models can be found.

best,
Marijn.

On 09/01/2021 23:41, amit kumar Jaiswal wrote:
>
>         External Email - Use Caution
>
> Hi Marijn,
> Yes, I've used it earlier quite often. The original workflow utilizes 
> /*Seglab *for MRI segmentation and meshes preparation /and /*Xfit *for 
> the actual BEM preparation (Menu > Estimates > Prepare a new BEM 
> model)/. The native workflow is a bit of time taking because of the 
> manual segmentation in Seglab. But there are several ways to bypass 
> this issue, e.g, using the freesurfer segmented brain in Seglab, etc.
> We can also bypass the whole BEM preparation process by using MNE 
> prepared BEM, importantly remember to chose the file name ending with 
> '/-bem-sol.fif' /while writing the BEM solution to 
> //neuro/database/bem/ / directory, as below:
> /model = mne.make_bem_model(subject=subject, subjects_dir=sub_dir, 
> conductivity=[0.3])
> bem = mne.make_bem_solution(model)
> /
>
> /mne.write_bem_solution('/neuro/database/bem/subjectname_1L-bem-sol.fif', 
> bem)/
>
>
> /For using it,/ change the conductor model from Sphere to BEM and 
> select the written file from /neuro/database/bem/.
>
> The below is showing an example, where I've used the single layer BEM 
> prepared in MNE-Python. You can also use a 3-layered similarly if needed.
>
> image.png
>
> Regards,
>
>
> On Thu, Jan 7, 2021 at 8:40 PM Marijn van Vliet 
> <w.m.vanvliet at gmail.com <mailto:w.m.vanvliet at gmail.com>> wrote:
>
>             External Email - Use Caution
>
>     Hi MNE users,
>
>     did any of you ever manage to use a BEM model with Xfit for dipole
>     fitting? I
>     only ever used the default sphere model. If one of you knows how
>     to do it, can
>     you show me?
>
>     best,
>     Marijn.
>
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> -- 
> /Thanks & Regards....../
> /Amit Jaiswal/
> /@ //MEGIN, Helsinki (Finland)/
> /+358-405222805//
> /
> /
> /
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-- 
Marijn van Vliet
Research Software Engineer
Aalto University

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