[FieldTrip] plotting freesurfer mesh on the mri_aligned.

parham hashemzadeh ph442 at cam.ac.uk
Tue Oct 4 19:08:29 CEST 2016


Dear Darren
  Thank you very much, and I will try to give it a go.
  In the event that I can not. You are a life saver if you can help me 
out. Everything is in place except this incredibly important item. I 
have noticed that you are in Cambridge, maybe we can meet at some point. 
I am close by at the mathematics department.
  Many many thanks
best regards parham

On 2016-10-04 17:45, Darren Price wrote:
> 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
> 
> 
> -------------------------------------------------------
> Dr. Darren Price
> Investigator Scientist and Cam-CAN Data Manager
> MRC Cognition & Brain Sciences Unit
> 15 Chaucer Road
> Cambridge, CB2 7EF
> England
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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
>> 
>> 
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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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> 
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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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