[FieldTrip] plotting freesurfer mesh on the mri_aligned.

[Darren Price]

Hi Parham 

For a non-linear interpolation onto a regular grid, spm_mesh_to_grid might be ideal (from the spm package of course). I don't have  a working example to hand, but I may be able to dig one out if you can't get it working. 

Darren


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-----Original Message-----
From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of parham hashemzadeh
Sent: 04 October 2016 16:59
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] plotting freesurfer mesh on the mri_aligned.

Hi Jan
  Thank you, my functional data are the function values of some function (irrotational component of the current). From my limited experience of Fieldtrip, your explanation feels (to myself) a bit cryptic at the moment.

      You see if my inversion strategy was one of the classical ones such as the ones provided by "ft_sourceanalysis" lcmv,sam,..., eloreta
           then the available fieldtrip tutorials are great in showing how to plot functional values on the top of anatomical values.
  But, since, I work on inversion methods, then I need a hacking strategy to be able to plot functional values of "some function"(estimated) on top of anatomical data MRI.

  I would appreciate if you would kindly let me know, if there is hack to it such that
  ft_sourceplot can accept the input.
best regards parham





On 2016-10-04 16:29, Schoffelen, J.M. (Jan Mathijs) wrote:
> 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.
> 
> Best,
> Jan-Mathijs
> 
> 
> 
>> 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
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> 
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
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-- 
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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