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I will be out of offie from December 21st to 4th of January and will be checking my email only infrequently during this time. I will respond to your email when I return.<br>
<br>
Best<br>
Anke <br>
<br>
On 26 Dec 2021, at 17.45, Tibor Auer via fieldtrip <fieldtrip@science.ru.nl> wrote:<br>
<br>
<div class="EmailQuote"><font face="Calibri" size="+1" color="black">Dear Emilie,<br>
 <br>
It is usually due to rank deficiency in the leadfield. I suggest removing the affected sources. See how it is implemented in Automatic Analysis:<br>
</font><font face="Calibri" size="+1" color="#0B4CB4"><u><a href="https://github.com/tiborauer/automaticanalysis/blob/82f7a2beac3b690b966933a7aad9c60f2c12a48d/aa_modules/aamod_meeg_sourcereconstruction.m#L185-L221">https://github.com/tiborauer/automaticanalysis/blob/82f7a2beac3b690b966933a7aad9c60f2c12a48d/aa_modules/aamod_meeg_sourcereconstruction.m#L185-L221</a></u></font><font face="Calibri" size="+1" color="black"><br>
I hope it helps.<br>
 <br>
Kind regards,<br>
Tibor <br>
 <br>
</font><font face="Calibri" size="+1" color="#191F28"><b>Dr Tibor Auer, MD., PhD.</b></font><font face="Calibri" size="+1" color="black"><br>
</font><font face="Calibri" size="+1" color="#0B4CB4"><u>tibor.auer@gmail.com</u></font><font face="Calibri" size="+1" color="black"><br>
+44-7906-863837<br>
</font><font face="Calibri" size="+1" color="#0B4CB4"><u>@TiborAuer</u></font><font face="Calibri" size="+1" color="black"><br>
 <br>
</font><font face="Calibri" size="+1" color="black"><b>Feladó:</b></font><font face="Calibri" size="+1" color="black"> fieldtrip <fieldtrip-bounces@science.ru.nl>
</font><font face="Calibri" size="+1" color="black"><b>E személy nevében: </b></font><font face="Calibri" size="+1" color="black">Emilie Caspar via fieldtrip<br>
</font><font face="Calibri" size="+1" color="black"><b>Küldve:</b></font><font face="Calibri" size="+1" color="black"> 09 December 2021 11:16<br>
</font><font face="Calibri" size="+1" color="black"><b>Címzett:</b></font><font face="Calibri" size="+1" color="black"> FieldTrip discussion list <fieldtrip@science.ru.nl><br>
</font><font face="Calibri" size="+1" color="black"><b>Másolatot kap:</b></font><font face="Calibri" size="+1" color="black"> Emilie Caspar <ecaspar@ulb.ac.be><br>
</font><font face="Calibri" size="+1" color="black"><b>Tárgy:</b></font><font face="Calibri" size="+1" color="black"> [FieldTrip] Source Reconstruction - Leadfield has NaNs<br>
 <br>
Dear Fieldtripper, <br>
I am currently trying to compute a source reconstruction on my EEG data (Biosemi, 64 electrodes).<br>
 <br>
I use the following code:<br>
 <br>
</font></div>
<div class="EmailQuote"><font face="Courier" size="-1" color="black">load </font>
<font face="Courier" size="-1" color="#A01FF0">Subject01_sourcemodel_15684</font><font face="Courier" size="-1" color="black">;</font><font face="Calibri" size="+1" color="black"><br>
</font></div>
<div class="EmailQuote"><font face="Courier" size="-1" color="black">headmodel = ft_read_headmodel(</font><font face="Courier" size="-1" color="#A01FF0">'headmodel/standard_bem.mat'</font><font face="Courier" size="-1" color="black">);</font><font face="Calibri" size="+1" color="black"><br>
</font></div>
<div class="EmailQuote"><font face="Courier" size="-1" color="black">electr_pos=ft_read_sens(</font><font face="Courier" size="-1" color="#A01FF0">'Biosemi-Cap64.sfp’</font><font face="Courier" size="-1" color="black">);</font><font face="Calibri" size="+1" color="black"><br>
</font></div>
<div class="EmailQuote"><font face="Courier" size="-1" color="black"> </font><font face="Calibri" size="+1" color="black"><br>
</font></div>
<div class="EmailQuote"><font face="Courier" size="-1" color="black">load(</font><font face="Courier" size="-1" color="#A01FF0">'GA_GroupPerpetrators_Parents_Neutral_DOUL.mat'</font><font face="Courier" size="-1" color="black">)</font><font face="Calibri" size="+1" color="black"><br>
 <br>
</font></div>
<div class="EmailQuote"><font face="Courier" size="-1" color="black">cfg = [];</font><font face="Calibri" size="+1" color="black"><br>
</font></div>
<div class="EmailQuote"><font face="Courier" size="-1" color="black">cfg.method =
</font><font face="Courier" size="-1" color="#A01FF0">'interactive'</font><font face="Courier" size="-1" color="black">;</font><font face="Calibri" size="+1" color="black"><br>
</font></div>
<div class="EmailQuote"><font face="Courier" size="-1" color="black">cfg.elec = electr_pos;</font><font face="Calibri" size="+1" color="black"><br>
</font></div>
<div class="EmailQuote"><font face="Courier" size="-1" color="black">cfg.headshape = headmodel.bnd(1);
</font><font face="Courier" size="-1" color="forestgreen">%1 = skin</font><font face="Calibri" size="+1" color="black"><br>
</font></div>
<div class="EmailQuote"><font face="Courier" size="-1" color="black">elec = ft_electroderealign(cfg, electr_pos);</font><font face="Calibri" size="+1" color="black"><br>
</font></div>
<div class="EmailQuote"><font face="Courier" size="-1" color="forestgreen"> </font><font face="Calibri" size="+1" color="black"><br>
</font></div>
<div class="EmailQuote"><font face="Courier" size="-1" color="black">cfg         = [];</font><font face="Calibri" size="+1" color="black"><br>
</font></div>
<div class="EmailQuote"><font face="Courier" size="-1" color="black">cfg.elec = elec;  
</font><font face="Courier" size="-1" color="forestgreen">% sensor information</font><font face="Calibri" size="+1" color="black"><br>
</font></div>
<div class="EmailQuote"><font face="Courier" size="-1" color="black">cfg.channel = elec.label;</font><font face="Courier" size="-1" color="forestgreen">%;  % the used channels</font><font face="Calibri" size="+1" color="black"><br>
</font></div>
<div class="EmailQuote"><font face="Courier" size="-1" color="black">cfg.sourcemodel    = sourcemodel;  
</font><font face="Courier" size="-1" color="forestgreen">% source points</font><font face="Calibri" size="+1" color="black"><br>
</font></div>
<div class="EmailQuote"><font face="Courier" size="-1" color="black">cfg.headmodel = headmodel;  
</font><font face="Courier" size="-1" color="forestgreen">% volume conduction model</font><font face="Calibri" size="+1" color="black"><br>
</font></div>
<div class="EmailQuote"><font face="Courier" size="-1" color="black">cfg.singleshell.batchsize = 5000;
</font><font face="Courier" size="-1" color="forestgreen">% speeds up the computation</font><font face="Calibri" size="+1" color="black"><br>
</font></div>
<div class="EmailQuote"><font face="Courier" size="-1" color="black">leadfield   = ft_prepare_leadfield(cfg);</font><font face="Calibri" size="+1" color="black"><br>
</font></div>
<div class="EmailQuote"><font face="Courier" size="-1" color="forestgreen">%%</font><font face="Calibri" size="+1" color="black"><br>
</font></div>
<div class="EmailQuote"><font face="Courier" size="-1" color="black">cfg               = [];</font><font face="Calibri" size="+1" color="black"><br>
</font></div>
<div class="EmailQuote"><font face="Courier" size="-1" color="black">cfg.method        =
</font><font face="Courier" size="-1" color="#A01FF0">'mne'</font><font face="Courier" size="-1" color="black">;</font><font face="Calibri" size="+1" color="black"><br>
</font></div>
<div class="EmailQuote"><font face="Courier" size="-1" color="black">cfg.elec = elec;</font><font face="Calibri" size="+1" color="black"><br>
</font></div>
<div class="EmailQuote"><font face="Courier" size="-1" color="black">cfg.grid          = leadfield;</font><font face="Calibri" size="+1" color="black"><br>
</font></div>
<div class="EmailQuote"><font face="Courier" size="-1" color="black">cfg.headmodel     = headmodel;</font><font face="Calibri" size="+1" color="black"><br>
</font></div>
<div class="EmailQuote"><font face="Courier" size="-1" color="black">cfg.mne.prewhiten =
</font><font face="Courier" size="-1" color="#A01FF0">'yes'</font><font face="Courier" size="-1" color="black">;</font><font face="Calibri" size="+1" color="black"><br>
</font></div>
<div class="EmailQuote"><font face="Courier" size="-1" color="black">cfg.mne.lambda    = 3;</font><font face="Calibri" size="+1" color="black"><br>
</font></div>
<div class="EmailQuote"><font face="Courier" size="-1" color="black">cfg.mne.scalesourcecov =
</font><font face="Courier" size="-1" color="#A01FF0">'yes'</font><font face="Courier" size="-1" color="black">;</font><font face="Calibri" size="+1" color="black"><br>
</font></div>
<div class="EmailQuote"><font face="Courier" size="-1" color="black"> </font><font face="Calibri" size="+1" color="black"><br>
</font></div>
<div class="EmailQuote"><font face="Courier" size="-1" color="black">source_GA_GroupPerpetrators_Parents_Neutral_DOUL = ft_sourceanalysis(cfg, GA_GroupPerpetrators_Parents_Neutral_DOUL);</font><font face="Calibri" size="+1" color="black"><br>
</font></div>
<div class="EmailQuote"><font face="Courier" color="black"> </font><font face="Calibri" size="+1" color="black"><br>
However, I got the following error when computing the ft_sourceanalysis:<br>
 <br>
</font></div>
<div class="EmailQuote"><font face="Calibri" color="#FC0107">Error using svd</font></div>
<div class="EmailQuote"><font face="Calibri" size="+1" color="black"><br>
</font></div>
<div class="EmailQuote"><font face="Calibri" color="#FC0107">Input to SVD must not contain NaN or Inf.</font></div>
<div class="EmailQuote"><font face="Calibri" size="+1" color="black"><br>
 <br>
</font></div>
<div class="EmailQuote"><font face="Calibri" color="#FC0107">Error in beamformer_lcmv>pinv (line 415)</font></div>
<div class="EmailQuote"><font face="Calibri" size="+1" color="black"><br>
</font></div>
<div class="EmailQuote"><font face="Calibri" color="#FC0107">  [U,S,V] = svd(A,0);</font></div>
<div class="EmailQuote"><font face="Calibri" size="+1" color="black"><br>
 <br>
</font></div>
<div class="EmailQuote"><font face="Calibri" color="#FC0107">Error in beamformer_lcmv (line 297)</font></div>
<div class="EmailQuote"><font face="Calibri" size="+1" color="black"><br>
</font></div>
<div class="EmailQuote"><font face="Calibri" color="#FC0107">    filt = pinv(lf' * invCy * lf) * lf' * invCy;              % van Veen eqn.</font></div>
<div class="EmailQuote"><font face="Calibri" size="+1" color="black"><br>
</font></div>
<div class="EmailQuote"><font face="Calibri" color="#FC0107">    23, use PINV/SVD to cover rank deficient leadfield</font></div>
<div class="EmailQuote"><font face="Calibri" size="+1" color="black"><br>
 <br>
</font></div>
<div class="EmailQuote"><font face="Calibri" color="#FC0107">Error in ft_sourceanalysis (line 950)</font></div>
<div class="EmailQuote"><font face="Calibri" size="+1" color="black"><br>
</font></div>
<div class="EmailQuote"><font face="Calibri" color="#FC0107">      dip(i) = beamformer_lcmv(grid, sens, headmodel, squeeze_avg, squeeze_Cy,</font></div>
<div class="EmailQuote"><font face="Calibri" size="+1" color="black"><br>
</font></div>
<div class="EmailQuote"><font face="Calibri" color="#FC0107">      optarg{:});</font></div>
<div class="EmailQuote"><font face="Calibri" size="+1" color="black"><br>
 <br>
I checked in all the datafiles I use, and the only NaN I found are in the leadfield.leadfield but all the previous steps appear to be correct and contain the correct electrode locations, data, covariance matrix etc.<br>
 <br>
I am thus not sure how to solve the problem and why my leadfield.leadfield has NaN (or even if the problem comes from there).<br>
 <br>
Thank you in advance for your help!<br>
 <br>
Emilie<br>
</font></div>
<div class="EmailQuote"><font color="black">_______________________________________________<br>
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