[Mne_analysis] volume source space

[Alexandre Gramfort]

hi,

> I am interested in reconstructing volume source spaces as opposed to
> surface source spaces. So, I was running the tutorial below.
> http://martinos.org/mne/stable/auto_examples/inverse/plot_lcmv_beamformer_volume.html
>
> Moreover, I would like to eventually run my own inversion algorithm
> (Based on Fokas work).

great initiative :)

> Can you kindly help me with the following questions:
> a) I need to have the volume coordinates of the points used by the
> MNE-built in inversion routines.

see

https://github.com/mne-tools/mne-python/blob/master/mne/source_estimate.py#L2620

> b)  The coordinates of the sensors after all the necessary
> transformations and corrections.

you'll need to have a look at the forward code and how we handle the
trans files.

I think that just using the forward solution at first is the easiest.

> c) I would like to also display the neuronal current after it has been
> reconstructed.

the example you point out uses nilearn to make nice 3d slices.

you can also save a nifti file and use your favorite interactive
viewer (freeview, fslview etc.)

> I do not use dipoles. I assume that the current is a continous function.
> However, for the sake of displaying it, I can sample the current at the
> volume source points for example in the LMCV routine.

yes that's the way

let us know if you have more questions.

A

> If you kindly point me to how to extract the volume source points and
> the sensor points, that would be great start.
> Many Many thanks
> Parham hashemzadeh
> --
> best regards
> Parham Hashemzadeh
> Research Associate
> Department of Applied Mathematics and Theoretical Physics
> University of Cambridge, UK.
> email: hashemzadeh at damtp.cam.ac.uk
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