[FieldTrip] plotting freesurfer mesh on the mri_aligned.
A. Donda
a.donda at hotmail.com
Wed Oct 5 00:47:27 CEST 2016
Hi Parham,
if you wanna plot it in FieldTrip, these commands worked well for me, but in my case (MEG data) I had to make sure first that these data were on the same coordinate system (co-registration of MRI and MEG sensor-data). If you do not have this issue, then you can simply plot an MRI and a mesh obtained from freesurfer the following way (make sure that both MRI and the mesh are in the same units, e.g. cm or mm):
ft_determine_coordsys(mricor_cm, 'interactive', 'no')
hold on
ft_plot_mesh(sourcespace);
Alternatively, if you want to plot the vertices of the mesh as dots, you can use
ft_plot_mesh(sourcespace.pnt,'vertexcolor','b');
sourcespace has the following structure (in case this is helpful for you):
pnt: [8196x3 double]
tri: [16384x3 double]
area: [16384x1 double]
orig: [1x1 struct]
unit: 'm'
I obtained sourcespace by loading the boundary element model (bem) surface, created with the watershed algorthim of Freesurfer:
sourcespace = ft_read_headshape([subjectname/bem/subjectname-oct-6-src.fif'], 'format', 'mne_source'); %in meters
Note that I had to transform the sourcespace dataset to the right coordinate system and units.
Finally I plotted the mri and mesh in cm
To convert units in Fieldtrip, as you know, use X_cm = ft_convert_units(X,'cm');
I hope this is helpful.
Best
A.Donda
________________________________
From: fieldtrip-bounces at science.ru.nl <fieldtrip-bounces at science.ru.nl> on behalf of parham hashemzadeh <ph442 at cam.ac.uk>
Sent: Tuesday, October 4, 2016 6:08 PM
To: FieldTrip discussion list
Subject: Re: [FieldTrip] plotting freesurfer mesh on the mri_aligned.
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
> EMAIL: darren.price at mrc-cbu.cam.ac.uk
> URL: http://www.mrc-cbu.cam.ac.uk/people/darren.price
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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
>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
> --
> 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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