[Mne_analysis] How to create a sphere file to compute source space?

Andrea Brovelli andrea.brovelli at univ-amu.fr
Mon May 2 14:22:19 EDT 2016
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Dear Alexandre,
thanks for your feedback. What we are trying to do with Alexandre 
(Fabre), who posted the first email, is to create a source space using 
the cortical meshes from Brainvisa.
Today, we managed to create a .sphere file in Brainvisa that maps each 
node of the Lwhite mesh onto the sphere. This seems equivalent to the 
procedure done in Freesurfer. Both have approximately 50k nodes per 
hemisphere. What we are tying to deal now is to create the source space by :
1) downsample the mesh to 10k or 5k nodes
2) avoid some nodes which are not on the cortical sheet. For example, in 
Brainvisa some nodes are in the cingular pole, where we don't want 
source reconstruction from. We do have a "texture" for each node of the 
mesh that indicates the brain region according to MarsAtlas (the atlas 
we use in Brainvisa).

To do so, we were thinking to use mne.setup_source_space. Any suggestion 
as you said to "hack" this functiona are welcome.
If it is not possible, I guess we will have to modify the function.
Thanks a lot,
Andrea

On 5/2/2016 5:33 PM, Alexandre Gramfort wrote:
> hi,
>
>> I would like to create a forward solution using source space
>> (mne.setup_source_space).
>>
>> I’ve created the surface mesh from Brainvisa but I don’t have the sphere
>> file (.sphere) to compute a source space.
> you cannot generate a source space with MNE for a surface not produced
> by freesurfer.
> at least not easily without hacking the MNE data structures.
>
>> How can I create it in MNE ? I’m thinking to use mne.make_sphere_model but
>> I’m not sure how it works.
> the make_sphere_model is for the forward model and is unrelated with
> the freesurfer .sphere files that are used for source space
> subsampling.
>
> I really recommend you use freesurfer to generate your cortical
> surfaces. Unless it does not work it will make your life much easier
> with MNE.
>
> HTH
> Alex
>
>> Any help or suggestion would be appreciated!
>>
>>
>> Thanks.
>>
>>
>> Alexandre F
>>
>>
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