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<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hi Jan-Mathijs,
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">You can download my best result from this link:
<a href="https://surfdrive.surf.nl/files/public.php?service=files&t=6d591406015bcb7715ffaebd18fd7d03">
https://surfdrive.surf.nl/files/public.php?service=files&t=6d591406015bcb7715ffaebd18fd7d03</a><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I don’t think is optimal.
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Some of the frontal electrodes are placed inside the head and some of the back ones are floating.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">In my case the automatic alignment with the fiducials didn’t work well, do you have any suggestions on how to make this in a better way?<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">After reading posts on the discussion list, I  defined left ear as what seems the right ear.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">But are there some other tricks that I should apply on the fiducials identification  or at the ft_warp_apply?<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I agree that it will never be optimal because of the issues you described.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">But I was wondering when is it satisfying in order not to influence my inverse solution.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">One more question,  is there a function that I should I use that will optimize my electrodes locations after doing the alignment?<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Thank you for your help.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Best,
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Nadia<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">
<a href="mailto:fieldtrip-bounces@science.ru.nl">fieldtrip-bounces@science.ru.nl</a> [<a href="mailto:fieldtrip-bounces@science.ru.nl">mailto:fieldtrip-bounces@science.ru.nl</a>]
<b>On Behalf Of </b>Schoffelen, J.M. (Jan Mathijs)<br>
<b>Sent:</b> dinsdag 21 juli 2015 20:55<br>
<b>To:</b> FieldTrip discussion list<br>
<b>Subject:</b> Re: [FieldTrip] align MRI- headmodel- EEG electrodes problem<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hi Nadia, <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">From the code I cannot see any obvious flaws, but it’s hard to tell, without some pictorial feedback. It could be that all went well, but that the end result is just the best that can be achieved. Note that there will always be some discrepancy
 between the head surface reconstructed from the anatomical image (image distortion, thresholding issues etc), and the electrode positions (having the cap in between, some slight inacurracy between the recorded fiducial positions, and the positions obtained
 by clicking in the MR-image). Do you have an image of your ‘best result’? <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Best,<o:p></o:p></p>
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<p class="MsoNormal">Jan-Mathijs<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="color:black">Jan-Mathijs Schoffelen, MD PhD, Senior researcher
<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black"><br>
Max Planck Institute for Psycholinguistics<br>
Donders Centre for Cognitive Neuroimaging<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black"><br>
E-mail: <a href="mailto:j.schoffelen@donders.ru.nl">j.schoffelen@donders.ru.nl</a><br>
Telephone: +31-24-3614793<br>
<br>
<a href="http://www.hettaligebrein.nl">http://www.hettaligebrein.nl</a><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black"><a href="http://www.fieldtriptoolbox.org">http://www.fieldtriptoolbox.org</a><o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Jul 21, 2015, at 4:56 PM, Konstantina Kalogianni <<a href="mailto:K.Kalogianni@tudelft.nl">K.Kalogianni@tudelft.nl</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">Dear fieldtrippers,</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">I am struggling with aligning the individual MRI, the headmodel and electrode positions(EEG) for some days now, without any success.</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">I would appreciate some help.</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">To begin with,  as an input I have the subject specific MRI which was segmented with the use of freesurfer and MNE software.</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">I load first the MRI ,the triangulated meshes for brain skull and skin, and the electrodes positions of 65-channel EEG.</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">I am then computing the bem headmodel from the brain skull skin (computed with the use of MNE software)</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">Afterwards I am aligning the MRI to my headmodel (ft_volumerealign) and then I identify the fiducials with the interactive mode (ft_volumerealign).</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">I do the transformation of the fiducial points  with ft_warp_apply to the coordinates specified at the alignment.</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">Then I call the  ft_electroderealign to align my electrodes to the mri’s fiducial points.</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">And then I realign  my electrodes manually.</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">The problem is that no matter how much rotation translation scaling I do, it’s IMPOSSIBLE TO FIT THE ELECTRODES TO THE HEADMODEL!</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">I tried the volume_realign with ctf coordinates as well and I tried the ft_electroderalign with the interactive mode only(without matching the fiducials), it
 doesn’t work.</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">Below you can find the code that I used.</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">Any ideas on this issue would be of great help!</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">%% READ</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">% read mri</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">mri=ft_read_mri([freesurferDir 'mri\orig.mgz']);</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">mri.coordsys='neuromag';</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">% read surfaces</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">brain=ft_read_headshape([freesurferDir 'bem\brain.surf\Pilot08_brain_surface']);</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">skull=ft_read_headshape([freesurferDir 'bem\brain.surf\Pilot08_inner_skull_surface' ]);</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">skin=ft_read_headshape([freesurferDir 'bem\brain.surfilot08_outer_skin_surface' ]);</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">% read electrodes positions</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">elec_file=[datadir '\raw\M10.elc'];</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">elec=ft_read_sens(elec_file );</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">elec.coordsys='neuromag';</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">elec.label=upper(elec.label);</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">%% HEADMODEL</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">%assign values of segmented surfaces</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">geom(1).tri=brain.tri;</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">geom(2).tri=skull.tri;</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">geom(3).tri=skin.tri;</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">geom(1).pnt=brain.pnt;</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">geom(2).pnt=skull.pnt;</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">geom(3).pnt=skin.pnt;</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">% compute headmodel<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">vol=ft_headmodel_bemcp(geom);<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">vol=ft_convert_units(vol, 'mm');<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">vol.coordsys='neuromag';</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">%% ALIGNMENTS</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">%align mri and headshape</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">mri_coord=ft_determine_coordsys(mri, 'interactive', 'yes');</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">vol_coord=ft_determine_coordsys(vol, 'interactive', 'yes');</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">cfg=[];</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">cfg.method = 'headshape';</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">cfg.headshape=vol_coord.bnd(3);</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">mri_headshape=ft_volumerealign(cfg,mri_coord);</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">%find fiducials</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">cfg=[];</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">cfg.method='interactive';</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">cfg.coordsys='neuromag';</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">mri_fid=ft_volumerealign(cfg,mri_headshape);</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">%% APPLY TRANSFORMATIONS ON FIDUCIALS</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">transm=mri_fid.transform;</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">nas=ft_warp_apply(transm,mri_fid.cfg.fiducial.nas, 'homogenous');</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">lpa=ft_warp_apply(transm,mri_fid.cfg.fiducial.rpa, 'homogenous');</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">rpa=ft_warp_apply(transm,mri_fid.cfg.fiducial.lpa, 'homogenous');</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="FR" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">fid.chanpos       = [nas;  rpa; lpa];</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">fid.elecpos       =fid.chanpos;</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">fid.label         = {'NASION',  'RIGHTEAR','LEFTEAR'}; % same labels as in elec</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">fid.unit          = 'mm';            % same units as mri</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">% Automatic electrode alignment using the fiducials </span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">cfg               = [];</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">cfg.method        = 'fiducial';           </span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">cfg.template      = fid;                 </span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">cfg.elec          = elec;</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">cfg.fiducial      = {'NASION',  'RIGHTEAR','LEFTEAR'};  % labels of fiducials in fid and in sens</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">cfg.headshape=vol_coord.bnd(3); % use the scalp as headshape</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">elec_aligned_fid      = ft_electroderealign(cfg);</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">%% Interactive alignment of electrodes to fix some misalignment</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">cfg=[];</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">cfg.method='interactive';</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">cfg.elec=elec_aligned_fid;</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">cfg.headshape=vol_coord.bnd(3); % use the scalp as headshape</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">elec_aligned=ft_electroderealign(cfg);</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">Best Regards,</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
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<p class="MsoNormal"><b><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">K. (Nadia) Kalogianni</span></b><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">PhD candidate</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Tahoma","sans-serif""> </span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">T<span style="color:#2298FF">U </span>Delft /Department of Biomechanical Engneering</span></b><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">Neuromuscular Control Laboratory</span></b><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""><br>
</span></b><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">Mekelweg 2<br>
2628 CD Delft<br>
</span><span lang="EN-GB" style="font-size:11.0pt;font-family:"Tahoma","sans-serif";color:#00B0F0">Room: F-1-320</span><span lang="DE" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#2298FF"><br>
T </span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";background:white">+31 15-27 84230</span><span lang="DE" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""><br>
<span style="color:#2298FF">E</span> </span><span lang="EN-GB" style="font-size:8.5pt;font-family:"Tahoma","sans-serif";background:white"> </span><span lang="EN-GB" style="font-size:11.0pt;font-family:"Tahoma","sans-serif""><a href="mailto:k.kalogianni@tudelft.nl"><span style="color:purple">k.kalogianni@tudelft.nl</span></a></span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
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<p class="MsoNormal">_______________________________________________<br>
fieldtrip mailing list<br>
<a href="mailto:fieldtrip@donders.ru.nl"><span style="color:purple">fieldtrip@donders.ru.nl</span></a><br>
<a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip"><span style="color:purple">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</span></a><o:p></o:p></p>
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