<html><head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body dir="auto"><div dir="ltr"></div><div dir="ltr">Dear Irene,</div><div dir="ltr">This is not going to work.</div><div dir="ltr">1. The headmodel is expressed in units of ‘m’ and aligned to the 4D/bti MEG coordinates. This has nothing to do with your EEG electrode positions.</div><div dir="ltr">2. As you already anticipated the type of headmodel is not appropriate for EEG source analysis.</div><div dir="ltr"><br></div><div dir="ltr">I recommend the following:</div><div dir="ltr">1. Work out the tutorial with the provided data. </div><div dir="ltr">2. Go thru it again and try to internalize the order of the analysis steps.</div><div dir="ltr">3. Switch to an EEG source analysis tutorial. Use the provided data there and try to understand the key differences. For example here: <a href="http://www.fieldtriptoolbox.org/workshop/natmeg/dipolefitting/">http://www.fieldtriptoolbox.org/workshop/natmeg/dipolefitting/</a></div><div dir="ltr">Or also here <a href="http://www.fieldtriptoolbox.org/workshop/aarhus/beamformingerf/">http://www.fieldtriptoolbox.org/workshop/aarhus/beamformingerf/</a></div><div dir="ltr">4. Go back and try to merge the two tutorials to reflect your needs.</div><div dir="ltr"><br></div><div dir="ltr">Good luck</div><div dir="ltr">Tzvetan </div><div dir="ltr"><br>Am 23.05.2019 um 08:55 schrieb Irene Varela Leniz <<a href="mailto:irene.varela@alumni.mondragon.edu">irene.varela@alumni.mondragon.edu</a>>:<br><br></div><blockquote type="cite"><div dir="ltr"><div dir="ltr"><div class="gmail_default" style="font-family:arial,helvetica,sans-serif">Dear both, </div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><br></div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif">You are right. I thought I was working with the latest version but I did not know that another more recent one had been released on April 19th. Anyway, what I could see investigating inside the function is that they have changed the way to configure the cfg in the function, right?<br></div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><br></div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif">The function is not able to understand the cfg that I am configuring. I must mention that in my case, I am working with EEG, so for example the configuration of lcmv.reducerank I had to change it to 3. Anyway I get the following error related to the cfg:<br></div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><br></div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><span style="font-family:Arial,Helvetica,sans-serif"> <i> cfg = [];</i></span><i><br style="font-family:Arial,Helvetica,sans-serif"><span style="font-family:Arial,Helvetica,sans-serif"> cfg.label = data.label;</span><br style="font-family:Arial,Helvetica,sans-serif"><span style="font-family:Arial,Helvetica,sans-serif"> cfg.elec = data.elec;</span><br style="font-family:Arial,Helvetica,sans-serif"><span style="font-family:Arial,Helvetica,sans-serif"> cfg.vol = hdm;</span><br style="font-family:Arial,Helvetica,sans-serif"><span style="font-family:Arial,Helvetica,sans-serif"> cfg.lcmv.reducerank = 3; % I am working with EEG data</span><br style="font-family:Arial,Helvetica,sans-serif"><span style="font-family:Arial,Helvetica,sans-serif"> cfg.normalize = 'yes'</span><br style="font-family:Arial,Helvetica,sans-serif"><span style="font-family:Arial,Helvetica,sans-serif"> cfg.grid = sourcemodel;</span><br style="font-family:Arial,Helvetica,sans-serif"><span style="font-family:Arial,Helvetica,sans-serif"> [grid] = ft_prepare_leadfield(cfg);</span><br style="font-family:Arial,Helvetica,sans-serif"></i><div style="font-family:Arial,Helvetica,sans-serif"><i><br></i></div><div style="font-family:Arial,Helvetica,sans-serif"><i><br></i></div></div><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><div style="font-family:Arial,Helvetica,sans-serif"><font color="#ff0000"><i>Error using ft_prepare_leadfield (line 110)</i></font></div></div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><div style="font-family:Arial,Helvetica,sans-serif"><font color="#ff0000"><i><b>It seems as if the first input argument is a FieldTrip data structure, while a cfg is expected</b></i></font></div></div></blockquote></blockquote><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><br></div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif">I also add information about how the data (EEG), the headmodel and the sourcemodel are:<br></div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><br></div><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><i><b>hdm = </b></i></div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><i> struct with fields:</i></div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><i> bnd: [1×1 struct]</i></div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><i> type: 'singleshell'</i></div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><i> unit: 'm'</i></div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><i> cfg: [1×1 struct]</i></div></blockquote></blockquote><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><br></div><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><i><b>sourcemodel = </b></i></div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><i> struct with fields:</i></div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><i> pos: [6426×3 double]</i></div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><i> dim: [17 21 18]</i></div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><i> unit: 'm'</i></div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><i> inside: [17×21×18 logical]</i></div></blockquote><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><i> cfg: [1×1 struct]</i></div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><i><br></i></div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><i><b>data = <br> </b> struct with fields:<br> hdr: [1×1 struct]<br> trial: {1×69 cell}<br> time: {1×69 cell}<br> elec: [1×1 struct]<br> fsample: 256<br> label: {128×1 cell}<br> sampleinfo: [69×2 double]<br> cfg: [1×1 struct]</i><br></div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><i><br></i></div></blockquote></blockquote><font face="arial, helvetica, sans-serif"><i><span class="gmail_default" style="font-family:arial,helvetica,sans-serif"></span></i></font>On the other hand, if I'm working with EEG, do you think it makes sense to use files <i>standard_singleshell.mat</i>, <i>atlas ROI_MNI_V4.nii</i>, <i>mri.mat </i>and <i>hdm.mat</i> to create the leadfield? Do I need others for EEG?<font face="arial, helvetica, sans-serif"><i><span class="gmail_default" style="font-family:arial,helvetica,sans-serif"></span><br></i></font><div><font face="arial, helvetica, sans-serif"><i><span class="gmail_default" style="font-family:arial,helvetica,sans-serif"><br></span></i></font></div><div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif">Thank you for your attention. </div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><br></div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif">Best wishes, </div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><br></div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif">Irene </div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">El mié., 22 may. 2019 a las 9:51, Schoffelen, J.M. (Jan Mathijs) (<<a href="mailto:jan.schoffelen@donders.ru.nl" target="_blank">jan.schoffelen@donders.ru.nl</a>>) escribió:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<div>You are not using the most recent fieldtrip code. See attached screenshot for a section of ft_checkconfig (which I took from
<a href="https://github.com/fieldtrip/fieldtrip" target="_blank">https://github.com/fieldtrip/fieldtrip</a> (utilities/ft_checkconfig.m)</div>
<div><br>
</div>
<div>The error message in your earlier e-mail pointed to line 529.</div>
<div><br>
</div>
<div>Jan-Mathijs</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<Screen Shot 2019-05-22 at 09.48.49.png><br>
<div>
<blockquote type="cite">
<div>On 22 May 2019, at 09:42, Irene Varela Leniz <<a href="mailto:irene.varela@alumni.mondragon.edu" target="_blank">irene.varela@alumni.mondragon.edu</a>> wrote:</div>
<br class="gmail-m_-7690022541708529962gmail-m_-6822762809677964255Apple-interchange-newline">
<div>
<div dir="ltr">
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif">Dear Shoffelen, </div>
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><br>
</div>
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif">I am working with last Fieldtrip and MATLAB version so I'm afraid that's not the problem.</div>
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><br>
</div>
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif">Best wishes, </div>
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><br>
</div>
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif">Irene</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">El mié., 22 may. 2019 a las 9:38, Schoffelen, J.M. (Jan Mathijs) (<<a href="mailto:jan.schoffelen@donders.ru.nl" target="_blank">jan.schoffelen@donders.ru.nl</a>>) escribió:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>Hi Irene,
<div><br>
</div>
<div>Please check which version of the code you are using, and update to a more recent version to FieldTrip, and try again. The line + error you report does not match the ones in the current version of Fieldtrip.</div>
<div><br>
</div>
<div>Best wishes,</div>
<div>Jan-Mathijs</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
<div>
<div>
<blockquote type="cite">
<div>On 22 May 2019, at 09:21, Irene Varela Leniz <<a href="mailto:irene.varela@alumni.mondragon.edu" target="_blank">irene.varela@alumni.mondragon.edu</a>> wrote:</div>
<br class="gmail-m_-7690022541708529962gmail-m_-6822762809677964255gmail-m_-2232218543815307315Apple-interchange-newline">
<div>
<div dir="ltr">
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif">Dear Fieldtripers, </div>
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><br>
</div>
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif">I am trying to replicate the well-known
<i>tutorial:salzburg [FielTrip] (</i><a href="http://old.fieldtriptoolbox.org/tutorial/salzburg" style="font-family:Arial,Helvetica,sans-serif" target="_blank">http://old.fieldtriptoolbox.org/tutorial/salzburg</a>). Anyway, I am getting some
errors that I could not manage to solve. I would be really grateful if someone could lend me a hand<span style="color:rgb(60,60,60);font-family:Arial,sans-serif">.</span></div>
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><span style="color:rgb(60,60,60);font-family:Arial,sans-serif"><br>
</span></div>
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><span style="color:rgb(60,60,60);font-family:Arial,sans-serif">I am working on section called "</span><span style="font-family:arial,sans-serif;color:rgb(45,45,45)">Localizing
auditory evoked fields using beamforming techniques in parceled brain space". </span><span style="font-family:Arial,Helvetica,sans-serif">I managed to compute the
<i>sourcemode</i>l as explained in the tutorial without any problem. But now, when "Computing the leadfield" I get an error message related with
<i>sourcemodel.inside </i>field, </span><span style="font-family:Arial,Helvetica,sans-serif">which makes it impossible for me to create the leadfield. The structure is the following:</span></div>
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><span style="font-family:Arial,Helvetica,sans-serif"><br>
</span></div>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><i><font size="1">sourcemodel =
</font></i></div>
</blockquote>
</blockquote>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><i><font size="1"> struct with fields:</font></i></div>
</blockquote>
</blockquote>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><i><font size="1"> pos: [6426×3 double]</font></i></div>
</blockquote>
</blockquote>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><i><font size="1"> dim: [17 21 18]</font></i></div>
</blockquote>
</blockquote>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><i><font size="1"> unit: 'm'</font></i></div>
</blockquote>
</blockquote>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><i><font size="1"> inside: [17×21×18 logical]</font></i></div>
</blockquote>
</blockquote>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><i><font size="1"> cfg: [1×1 struct]</font></i></div>
</blockquote>
</blockquote>
</blockquote>
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><span style="font-family:Arial,Helvetica,sans-serif"><br>
</span></div>
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><span style="font-family:Arial,Helvetica,sans-serif">The structure for computing the leadfield:</span></div>
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><span style="font-family:Arial,Helvetica,sans-serif"><br>
</span></div>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif"> <font size="1">
<i> cfg = [];<br>
cfg.label = data.label;<br>
cfg.elec = data.elec;<br>
cfg.vol = hdm;<br>
cfg.lcmv.reducerank = 2; % I am working with EEG data<br>
cfg.grid = sourcemodel;<br>
[grid] = ft_prepare_leadfield(cfg)</i></font></div>
</blockquote>
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><span style="font-family:Arial,Helvetica,sans-serif"><br>
</span></div>
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><span style="font-family:Arial,Helvetica,sans-serif">An the error I get:</span></div>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><span style="font-family:Arial,Helvetica,sans-serif"><font color="#ff0000" size="1"><br>
</font></span></div>
</blockquote>
</blockquote>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><font color="#ff0000" size="1">Operands to the || and && operators must be convertible to logical scalar values.</font></div>
</blockquote>
</blockquote>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><font color="#ff0000" size="1"><br>
</font></div>
</blockquote>
</blockquote>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><font color="#ff0000" size="1">Error in ft_checkconfig (line 529)</font></div>
</blockquote>
</blockquote>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><font color="#ff0000" size="1"> elseif isfield(cfg, 'grid') && isfield(cfg.grid, 'inside') && any(cfg.grid.inside>1)</font></div>
</blockquote>
</blockquote>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><font color="#ff0000" size="1"><br>
</font></div>
</blockquote>
</blockquote>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><font color="#ff0000" size="1">Error in ft_prepare_leadfield (line 156)</font></div>
</blockquote>
</blockquote>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><font color="#ff0000" size="1">cfg = ft_checkconfig(cfg, 'inside2logical', 'yes');</font></div>
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><font color="#ff0000" size="1"><br>
</font></div>
</blockquote>
</blockquote>
</blockquote>
<font color="#ff0000" face="arial, helvetica, sans-serif" size="1"><span class="gmail_default" style="font-family:arial,helvetica,sans-serif"></span></font>I think the error comes from the fact that
<i>source<span class="gmail_default" style="font-family:arial,helvetica,sans-serif">model</span>.inside</i> is a 3-dimensional logical array<span class="gmail_default" style="font-family:arial,helvetica,sans-serif">. The operation -
<span style="color:rgb(255,0,0);font-size:x-small">any(cfg.grid.inside>1)</span> does not output a logical scalar value because<i> sourcemodel.inside</i> is in 3 dimensions. </span>
<div><span class="gmail_default" style="font-family:arial,helvetica,sans-serif">So far I have always worked with models whose inside parameter was of one dimension. Anyway, I'm not sure if this is the problem, please correct me if I'm wrong.</span><font color="#ff0000" face="arial, helvetica, sans-serif" size="1"><span class="gmail_default" style="font-family:arial,helvetica,sans-serif"></span><br>
</font></div>
<div><font color="#ff0000" face="arial, helvetica, sans-serif" size="1"><span class="gmail_default" style="font-family:arial,helvetica,sans-serif"><br>
</span></font></div>
<div><span style="font-family:arial,helvetica,sans-serif">Has anyone encountered this same problem, and does anyone know how to fix it?</span> <font color="#ff0000" face="arial, helvetica, sans-serif" size="1"><span class="gmail_default" style="font-family:arial,helvetica,sans-serif"><br>
</span></font></div>
<div><font color="#ff0000" face="arial, helvetica, sans-serif" size="1"><span class="gmail_default" style="font-family:arial,helvetica,sans-serif"><br>
</span></font></div>
<div><font face="arial, helvetica, sans-serif"><span class="gmail_default" style="font-family:arial,helvetica,sans-serif">Thank you very much for your attention, </span></font></div>
<div><font face="arial, helvetica, sans-serif"><span class="gmail_default" style="font-family:arial,helvetica,sans-serif"><br>
</span></font></div>
<div><font face="arial, helvetica, sans-serif"><span class="gmail_default" style="font-family:arial,helvetica,sans-serif"><br>
</span></font></div>
<div><font face="arial, helvetica, sans-serif"><span class="gmail_default" style="font-family:arial,helvetica,sans-serif">Irene</span></font></div>
<div><font color="#ff0000" face="arial, helvetica, sans-serif" size="1"><span class="gmail_default" style="font-family:arial,helvetica,sans-serif"><br>
</span></font></div>
<div><font color="#ff0000" face="arial, helvetica, sans-serif" size="1"><span class="gmail_default" style="font-family:arial,helvetica,sans-serif"><br>
</span></font></div>
</div>
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