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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Dear Nadia,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Looking at your images the registration seems to be quite fine. Having some electrodes in/outside of the head due to the issues JM addressed is not a problem
as electrode positions are projected onto the scalp surface anyway when creating the leadfield.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Best,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Jim<o:p></o:p></span></p>
<p class="MsoNormal"><span 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 style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> fieldtrip-bounces@science.ru.nl [mailto:fieldtrip-bounces@science.ru.nl]
<b>On Behalf Of </b>Konstantina Kalogianni<br>
<b>Sent:</b> woensdag 22 juli 2015 15:53<br>
<b>To:</b> FieldTrip discussion list<br>
<b>Subject:</b> [FieldTrip] FW: 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"><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 style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span 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"><span lang="NL"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="NL">Hi Nadia, <o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="NL"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="NL">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></span></p>
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<p class="MsoNormal"><span lang="NL"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="NL">Best,<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="NL">Jan-Mathijs<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="NL"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="NL"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="NL" style="color:black">Jan-Mathijs Schoffelen, MD PhD, Senior researcher
<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="NL" 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 lang="NL" 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 lang="NL" 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"><span lang="NL"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="NL"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="NL"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="NL"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="NL"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="NL">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></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span lang="NL"><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"">Dear fieldtrippers,</span><span lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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"">skull=ft_read_headshape([freesurferDir 'bem\brain.surf\Pilot08_inner_skull_surface' ]);</span><span lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="NL" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">% compute headmodel<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><b><span lang="EN-GB" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">K. (Nadia) Kalogianni</span></b><span lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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 lang="NL" 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="NL">_______________________________________________<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></span></p>
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<p class="MsoNormal"><span lang="NL"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="NL"><o:p> </o:p></span></p>
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