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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hi Debora,<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 lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I tried to do so before, but I ended up with the following error:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Do you want to change the anatomical labels for the axes [Y, n]? Y<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">What is the anatomical label for the positive X-axis [r, l, a, p, s, i]? r<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">What is the anatomical label for the positive Y-axis [r, l, a, p, s, i]? a<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">What is the anatomical label for the positive Z-axis [r, l, a, p, s, i]? s<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Is the origin of the coordinate system at the a(nterior commissure), i(nterauricular), n(ot a landmark)? n<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Undefined function or variable 'template'.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Error in ft_electroderealign (line 244)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> for j=1:length(template)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Error in eeg_beamforming (line 107)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> elec_aligned = ft_electroderealign(cfg);<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I prepared now a template following this instruction:
<a href="http://www.fieldtriptoolbox.org/example/align_eeg_electrode_positions_to_bem_headmodel">
http://www.fieldtriptoolbox.org/example/align_eeg_electrode_positions_to_bem_headmodel</a><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">In this example the template is only used for the cfg.method = ‘fiducial’ but not for the ‘interactiv’ option.
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Anyhow I additionally specified the template together with the ‘interactiv’ method like this:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New"">cfg = [];<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New"">cfg.method = 'interactive';<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New"">cfg.elec = elec;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New"">cfg.headshape = vol.bnd(1);<o:p></o:p></span></p>
<pre>cfg.template = elec_mni;<o:p></o:p></pre>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New"">elec_new = ft_electroderealign(cfg);<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">now it works!
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Thanks!<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Iris<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<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""> fieldtrip-bounces@science.ru.nl [mailto:fieldtrip-bounces@science.ru.nl]
<b>On Behalf Of </b>Debora Desideri<br>
<b>Sent:</b> Mittwoch, 17. Februar 2016 11:20<br>
<b>To:</b> FieldTrip discussion list<br>
<b>Subject:</b> Re: [FieldTrip] Align electrods to headmodel with method 'interactiv'<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-family:"Verdana","sans-serif"">Dear Iris,<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-family:"Verdana","sans-serif"">you should press Y and specify the coordinate system following the questions that will appear on the command window (you will be asked to specify whether your
coordinate sytsem is ras or lps and so on and where the origin of the coordinate system is located). afterwards, the GUI will display the electrodes and the head of the subject as well. You should then be able to align the electrode by simply applying translation/rotation
or whatever you need make the electrode fit on the head surface.<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-family:"Verdana","sans-serif"">In case you want to use the methiod 'fiducials', you should have recorded together with the elctrode positions some anatomical landmarks that you can easily find
in the MRI of the subject. If you did not record such landmarks during the acquisition of the electrode positions, than I guess your only option is to use the method 'interactive'<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Verdana","sans-serif"">Hope this helps!<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Verdana","sans-serif"">Best,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Verdana","sans-serif"">Debora<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">On Tue, Feb 16, 2016 at 6:07 PM, Steinmann, Iris <<a href="mailto:iris.steinmann@med.uni-goettingen.de" target="_blank">iris.steinmann@med.uni-goettingen.de</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">Hi FieldTripper,</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">I want to do source reconstruction with my EEG data and try to align my electrodes to the headmodel (calculated with my own MR data)</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">(following this description:
<a href="http://www.fieldtriptoolbox.org/example/align_eeg_electrode_positions_to_bem_headmodel" target="_blank">
http://www.fieldtriptoolbox.org/example/align_eeg_electrode_positions_to_bem_headmodel</a>)
</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">I run the ft_electroderealign function with the following options:</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">cfg = [];</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">cfg.method = 'interactive';</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">cfg.elec = elec;</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">cfg.headshape = vol.bnd(1);</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">elec_new = ft_electroderealign(cfg);</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">But all I get is a figure showing a coordinate system with my electrodepositions. The scull saved in vol.bnd(1) is not plotted.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">(I attached a jpg of the figure).
</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">The MATLAB panel asked me: "Do you want to change the anatomical labels for the axes [Y, n]? "</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">If I say 'no', I get the following error:
</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">Undefined function or variable 'template'.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">Error in ft_electroderealign (line 244)</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> for j=1:length(template)
</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">I tried the ft_electroderealign function with the cfg.method = 'fiducials', but ended up with the same figure and the same question in
</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">the MATLAB panel.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">Would be great if someone could help me to figure out what's going wrong here and how I can align my electrodes to the headmodel.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Thanks!<o:p></o:p></p>
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<p class="MsoNormal"><br>
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-- <o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Verdana","sans-serif""><br>
Debora Desideri, PhD Student</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Verdana","sans-serif"">BNP Lab - Neurology Department</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Verdana","sans-serif"">University Hospital Tübingen</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Verdana","sans-serif"">Eberhard Karls University Tübingen</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Verdana","sans-serif"">Hoppe-Seyler Str. 3</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Verdana","sans-serif"">D-72076 Tübingen</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Verdana","sans-serif"">Tel: +49 7071/29 80478</span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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