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<p>Hi Parham, </p>
<p><br>
</p>
<p>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):</p>
<p><br>
</p>
<p></p>
<div> ft_determine_coordsys(mricor_cm, 'interactive', 'no')</div>
<div>
<div> hold on</div>
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ft_plot_mesh(sourcespace);</div>
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<div><br>
</div>
<div><br>
</div>
<div>Alternatively, if you want to plot the vertices of the mesh as dots, you can use</div>
<div><br>
</div>
<div><span>ft_plot_mesh(sourcespace.pnt,'vertexcolor','b');</span><br>
</div>
<div><span><br>
</span></div>
<div><span>sourcespace has the following structure<span> (in case this is helpful for you)</span>:</span></div>
<div><span><br>
</span></div>
<div><span>
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pnt: [8196x3 double]</div>
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tri: [16384x3 double]</div>
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area: [16384x1 double]</div>
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orig: [1x1 struct]</div>
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unit: 'm'</div>
<br>
</span></div>
<div><br>
</div>
I obtained sourcespace by loading the <span style="font-size: 12pt;">boundary element model (bem) surface, created with the watershed algorthim of Freesurfer: </span>
<p></p>
<p><br>
</p>
<p></p>
<div> <span style="font-size: 12pt;">sourcespace = ft_read_headshape([subjectname/bem/</span><span style="font-size: 12pt;">subjectname</span><span style="font-size: 12pt;">-oct-6-src.fif'], 'format', 'mne_source'); %in meters</span></div>
<div><br>
</div>
<div><br>
</div>
<div>
<div><span style="font-size: 12pt;">Note that I had to </span><span style="font-size: 12pt;">transform the sourcespace dataset to the right coordinate system and units. </span><br>
</div>
</div>
<div><br>
</div>
<div>Finally I plotted the mri and mesh in cm</div>
<div><br>
</div>
<div>To convert units in Fieldtrip, as you know, use <span>X_cm = ft_convert_units(X,'cm');</span></div>
<div></div>
<div>
<div><br>
</div>
<div>I hope this is helpful.</div>
</div>
<div><br>
</div>
<p></p>
<p><br>
</p>
<p><br>
</p>
<p>Best</p>
<p><br>
</p>
<p>A.Donda</p>
<br>
<br>
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<div id="x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> fieldtrip-bounces@science.ru.nl <fieldtrip-bounces@science.ru.nl> on behalf of parham hashemzadeh <ph442@cam.ac.uk><br>
<b>Sent:</b> Tuesday, October 4, 2016 6:08 PM<br>
<b>To:</b> FieldTrip discussion list<br>
<b>Subject:</b> Re: [FieldTrip] plotting freesurfer mesh on the mri_aligned.</font>
<div> </div>
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<font size="2"><span style="font-size:10pt;">
<div class="PlainText">Dear Darren<br>
Thank you very much, and I will try to give it a go.<br>
In the event that I can not. You are a life saver if you can help me <br>
out. Everything is in place except this incredibly important item. I <br>
have noticed that you are in Cambridge, maybe we can meet at some point. <br>
I am close by at the mathematics department.<br>
Many many thanks<br>
best regards parham<br>
<br>
On 2016-10-04 17:45, Darren Price wrote:<br>
> Hi Parham<br>
> <br>
> For a non-linear interpolation onto a regular grid, spm_mesh_to_grid<br>
> might be ideal (from the spm package of course). I don't have a<br>
> working example to hand, but I may be able to dig one out if you can't<br>
> get it working.<br>
> <br>
> Darren<br>
> <br>
> <br>
> -------------------------------------------------------<br>
> Dr. Darren Price<br>
> Investigator Scientist and Cam-CAN Data Manager<br>
> MRC Cognition & Brain Sciences Unit<br>
> 15 Chaucer Road<br>
> Cambridge, CB2 7EF<br>
> England<br>
> EMAIL: darren.price@mrc-cbu.cam.ac.uk<br>
> URL: <a href="http://www.mrc-cbu.cam.ac.uk/people/darren.price" id="LPlnk457978" previewremoved="true">
http://www.mrc-cbu.cam.ac.uk/people/darren.price</a><br>
> TEL +44 (0)1223 355 294 x202<br>
> FAX +44 (0)1223 359 062<br>
> MOB +44 (0)7717822431<br>
> -------------------------------------------------------<br>
> <br>
> <br>
> -----Original Message-----<br>
> From: fieldtrip-bounces@science.ru.nl<br>
> [<a href="mailto:fieldtrip-bounces@science.ru.nl">mailto:fieldtrip-bounces@science.ru.nl</a>] On Behalf Of parham<br>
> hashemzadeh<br>
> Sent: 04 October 2016 16:59<br>
> To: FieldTrip discussion list <fieldtrip@science.ru.nl><br>
> Subject: Re: [FieldTrip] plotting freesurfer mesh on the mri_aligned.<br>
> <br>
> Hi Jan<br>
> Thank you, my functional data are the function values of some<br>
> function (irrotational component of the current). From my limited<br>
> experience of Fieldtrip, your explanation feels (to myself) a bit<br>
> cryptic at the moment.<br>
> <br>
> You see if my inversion strategy was one of the classical ones<br>
> such as the ones provided by "ft_sourceanalysis" lcmv,sam,..., eloreta<br>
> then the available fieldtrip tutorials are great in showing<br>
> how to plot functional values on the top of anatomical values.<br>
> But, since, I work on inversion methods, then I need a hacking<br>
> strategy to be able to plot functional values of "some<br>
> function"(estimated) on top of anatomical data MRI.<br>
> <br>
> I would appreciate if you would kindly let me know, if there is hack<br>
> to it such that<br>
> ft_sourceplot can accept the input.<br>
> best regards parham<br>
> <br>
> <br>
> <br>
> <br>
> <br>
> On 2016-10-04 16:29, Schoffelen, J.M. (Jan Mathijs) wrote:<br>
>> Hi Parham,<br>
>> <br>
>> It is possible, but certainly not pain free, nor straightforward.<br>
>> I think this is not really a fieldtrip question, but more a general<br>
>> matlab related issue.<br>
>> <br>
>> It should be possible to plot a slice through an MRI volume as a<br>
>> MATLAB patch, where the coordinates of the voxels are expressed in<br>
>> some coordinate system. Then, it is possible to generate and<br>
>> intersection of the freesurfer mesh through the plane of<br>
>> visualization.<br>
>> <br>
>> Best,<br>
>> Jan-Mathijs<br>
>> <br>
>> <br>
>> <br>
>>> On 04 Oct 2016, at 16:41, parham hashemzadeh <ph442@cam.ac.uk> wrote:<br>
>>> <br>
>>> Dear Fieldtrippers<br>
>>> Is there a straightforward pain free method ( I appreciate if you can<br>
>>> give me the command)<br>
>>> to plot arbitrary points such as the vertices of the freesurfer <br>
>>> output<br>
>>> (mesh) onto the MRI image?<br>
>>> The reason that I ask is that I would like to plot my solution on the<br>
>>> MRI image.<br>
>>> Unfortunately I do not use dipoles. In EEG, I model the irrotational<br>
>>> component of the current as a scalar function and therefore I am <br>
>>> doing<br>
>>> function estimation.<br>
>>> IF you use dipoles, it is straightforward because you follow one of<br>
>>> the tutorials.<br>
>>> But if you do not use dipoles and model the current as the gradient<br>
>>> of the irrotational component of the current in EEG then one can get<br>
>>> lost.<br>
>>> Any help would be appreciated.<br>
>>> Many thanks<br>
>>> <br>
>>> --<br>
>>> best regards<br>
>>> Parham Hashemzadeh<br>
>>> Research Associate<br>
>>> Department of Applied Mathematics and Theoretical Physics<br>
>>> University of Cambridge, UK.<br>
>>> email: hashemzadeh@damtp.cam.ac.uk<br>
>>> _______________________________________________<br>
>>> fieldtrip mailing list<br>
>>> fieldtrip@donders.ru.nl<br>
>>> <a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
>> <br>
>> <br>
>> _______________________________________________<br>
>> fieldtrip mailing list<br>
>> fieldtrip@donders.ru.nl<br>
>> <a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
> <br>
> --<br>
> best regards<br>
> Parham Hashemzadeh<br>
> Research Associate<br>
> Department of Applied Mathematics and Theoretical Physics<br>
> University of Cambridge, UK.<br>
> email: hashemzadeh@damtp.cam.ac.uk<br>
> _______________________________________________<br>
> fieldtrip mailing list<br>
> fieldtrip@donders.ru.nl<br>
> <a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
> <br>
> _______________________________________________<br>
> fieldtrip mailing list<br>
> fieldtrip@donders.ru.nl<br>
> <a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
<br>
-- <br>
best regards<br>
Parham Hashemzadeh<br>
Research Associate<br>
Department of Applied Mathematics and Theoretical Physics<br>
University of Cambridge, UK.<br>
email: hashemzadeh@damtp.cam.ac.uk<br>
<br>
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