[FieldTrip] plotting freesurfer mesh on the mri_aligned.

Schoffelen, J.M. (Jan Mathijs) jan.schoffelen at donders.ru.nl
Tue Oct 4 17:29:49 CEST 2016

Hi Parham,

It is possible, but certainly not pain free, nor straightforward.
I think this is not really a fieldtrip question, but more a general matlab related issue.

It should be possible to plot a slice through an MRI volume as a MATLAB patch, where the coordinates of the voxels are expressed in some coordinate system. Then, it is possible to generate and intersection of the freesurfer mesh through the plane of visualization.


> On 04 Oct 2016, at 16:41, parham hashemzadeh <ph442 at cam.ac.uk> wrote:
> Dear Fieldtrippers
> Is there a straightforward pain free method ( I appreciate if you can give me the command)
> to plot arbitrary points such as the vertices of the freesurfer output (mesh) onto the MRI image?
> The reason that I ask is that I would like to plot my solution on the MRI image.
> Unfortunately I do not use dipoles. In EEG, I model the irrotational component of the current as a scalar function and therefore I am doing function estimation.
>  IF you use dipoles, it is straightforward because you follow one of the tutorials.
>  But if you do not use dipoles and model the current as the gradient of the irrotational component of the current in EEG then one can get lost.
> Any help would be appreciated.
> Many thanks
> -- 
> 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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