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

[Alexandre Gramfort]

hi Andrea,

thinking about it what you can do is to setup a discrete source space
using the locations and normals for your cortical mesh.

See setup_volume_source_space and the pos parameter.
You'll have a source space that you can then use for forward/inverse modeling.

Let me know it this works.

Alex

On Mon, May 2, 2016 at 8:22 PM, Andrea Brovelli
<andrea.brovelli at univ-amu.fr> wrote:
> 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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