<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><meta http-equiv=Content-Type content="text/html; charset=utf-8"><meta name=Generator content="Microsoft Word 15 (filtered medium)"><style><!--
/* Font Definitions */
@font-face
{font-family:Courier;
panose-1:2 7 4 9 2 2 5 2 4 4;}
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
font-size:11.0pt;
font-family:"Calibri",sans-serif;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:#0563C1;
text-decoration:underline;}
span.E-mailStlus19
{mso-style-type:personal-compose;
font-family:"Calibri",sans-serif;
color:windowtext;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:72.0pt 72.0pt 72.0pt 72.0pt;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]--></head><body lang=EN-GB link="#0563C1" vlink="#954F72" style='word-wrap:break-word'><div class=WordSection1><p class=MsoNormal><span style='mso-fareast-language:EN-US'>Dear Emilie,<o:p></o:p></span></p><p class=MsoNormal><span style='mso-fareast-language:EN-US'><o:p> </o:p></span></p><p class=MsoNormal><span style='mso-fareast-language:EN-US'>It is usually due to rank deficiency in the leadfield. I suggest removing the affected sources. See how it is implemented in Automatic Analysis:<o:p></o:p></span></p><p class=MsoNormal><span style='mso-fareast-language:EN-US'><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><o:p></o:p></span></p><p class=MsoNormal><span style='mso-fareast-language:EN-US'>I hope it helps.<o:p></o:p></span></p><p class=MsoNormal><span style='mso-fareast-language:EN-US'><o:p> </o:p></span></p><p class=MsoNormal><span style='mso-fareast-language:EN-US'>Kind regards,<o:p></o:p></span></p><div><p class=MsoNormal>Tibor <span lang=HU><o:p></o:p></span></p><p class=MsoNormal> <span lang=HU><o:p></o:p></span></p><p class=MsoNormal><b><span style='color:#222A35'>Dr Tibor Auer, MD., PhD.</span></b><span lang=HU><o:p></o:p></span></p><p class=MsoNormal><a href="mailto:tibor.auer@gmail.com"><span style='color:#0563C1'>tibor.auer@gmail.com</span></a><o:p></o:p></p><p class=MsoNormal>+44-7906-863837<span lang=HU><o:p></o:p></span></p><p class=MsoNormal><a href="https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Ftwitter.com%2FTiborAuer&data=04%7C01%7Ct.auer%40surrey.ac.uk%7C5f32dba325f5422f5c5a08d8becc029f%7C6b902693107440aa9e21d89446a2ebb5%7C0%7C0%7C637469131016806177%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=wkpejqTmmo%2Fe4JA9QIaA6Z3%2BzipbFY%2FCEmRXC9UvKJs%3D&reserved=0"><span style='color:#0563C1'>@TiborAuer</span></a><span lang=HU><o:p></o:p></span></p></div><p class=MsoNormal><span style='mso-fareast-language:EN-US'><o:p> </o:p></span></p><div><div style='border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=MsoNormal><b><span lang=HU>Feladó:</span></b><span lang=HU> fieldtrip <fieldtrip-bounces@science.ru.nl> <b>E személy nevében: </b>Emilie Caspar via fieldtrip<br><b>Küldve:</b> 09 December 2021 11:16<br><b>Címzett:</b> FieldTrip discussion list <fieldtrip@science.ru.nl><br><b>Másolatot kap:</b> Emilie Caspar <ecaspar@ulb.ac.be><br><b>Tárgy:</b> [FieldTrip] Source Reconstruction - Leadfield has NaNs<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p><div><div><div><div><div><div><div><div><div><div><div><div><div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;margin-bottom:6.0pt'><span style='color:black'>Dear Fieldtripper, <o:p></o:p></span></p><div><p class=MsoNormal><span style='color:black'>I am currently trying to compute a source reconstruction on my EEG data (Biosemi, 64 electrodes).<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='color:black'>I use the following code:<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='color:black'><o:p> </o:p></span></p></div><div><div><p class=MsoNormal><span style='font-size:7.5pt;font-family:Courier;color:black'>load </span><span style='font-size:7.5pt;font-family:Courier;color:#B245F3'>Subject01_sourcemodel_15684</span><span style='font-size:7.5pt;font-family:Courier;color:black'>;</span><span style='font-size:7.5pt;font-family:Courier;color:#B245F3'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:7.5pt;font-family:Courier;color:black'>headmodel = ft_read_headmodel(</span><span style='font-size:7.5pt;font-family:Courier;color:#B245F3'>'headmodel/standard_bem.mat'</span><span style='font-size:7.5pt;font-family:Courier;color:black'>);<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:7.5pt;font-family:Courier'>electr_pos=ft_read_sens(<span style='color:#B245F3'>'Biosemi-Cap64.sfp’</span>);</span><o:p></o:p></p></div></div><div><p class=MsoNormal><span style='font-size:7.5pt;font-family:Courier;color:black'><o:p> </o:p></span></p></div><div><div><p class=MsoNormal><span style='font-size:7.5pt;font-family:Courier;color:black'>load(</span><span style='font-size:7.5pt;font-family:Courier;color:#B245F3'>'GA_GroupPerpetrators_Parents_Neutral_DOUL.mat'</span><span style='font-size:7.5pt;font-family:Courier;color:black'>)</span><span style='font-size:7.5pt;font-family:Courier;color:#B245F3'><o:p></o:p></span></p></div></div><div><p class=MsoNormal><span style='color:black'><o:p> </o:p></span></p></div><div><div><p class=MsoNormal><span style='font-size:7.5pt;font-family:Courier;color:black'>cfg = [];<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:7.5pt;font-family:Courier;color:black'>cfg.method = </span><span style='font-size:7.5pt;font-family:Courier;color:#B245F3'>'interactive'</span><span style='font-size:7.5pt;font-family:Courier;color:black'>;<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:7.5pt;font-family:Courier;color:black'>cfg.elec = electr_pos;<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:7.5pt;font-family:Courier;color:black'>cfg.headshape = headmodel.bnd(1); </span><span style='font-size:7.5pt;font-family:Courier;color:#25992D'>%1 = skin</span><span style='font-size:7.5pt;font-family:Courier;color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:7.5pt;font-family:Courier;color:black'>elec = ft_electroderealign(cfg, electr_pos);<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:7.5pt;font-family:Courier;color:#25992D'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-size:7.5pt;font-family:Courier;color:black'>cfg = [];<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:7.5pt;font-family:Courier;color:black'>cfg.elec = elec; </span><span style='font-size:7.5pt;font-family:Courier;color:#25992D'>% sensor information<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:7.5pt;font-family:Courier;color:black'>cfg.channel = elec.label;</span><span style='font-size:7.5pt;font-family:Courier;color:#25992D'>%; % the used channels</span><span style='font-size:7.5pt;font-family:Courier;color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:7.5pt;font-family:Courier;color:black'>cfg.sourcemodel = sourcemodel; </span><span style='font-size:7.5pt;font-family:Courier;color:#25992D'>% source points</span><span style='font-size:7.5pt;font-family:Courier;color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:7.5pt;font-family:Courier;color:black'>cfg.headmodel = headmodel; </span><span style='font-size:7.5pt;font-family:Courier;color:#25992D'>% volume conduction model</span><span style='font-size:7.5pt;font-family:Courier;color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:7.5pt;font-family:Courier;color:black'>cfg.singleshell.batchsize = 5000; </span><span style='font-size:7.5pt;font-family:Courier;color:#25992D'>% speeds up the computation</span><span style='font-size:7.5pt;font-family:Courier;color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:7.5pt;font-family:Courier;color:black'>leadfield = ft_prepare_leadfield(cfg);<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:7.5pt;font-family:Courier;color:#25992D'>%%<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:7.5pt;font-family:Courier;color:black'>cfg = [];<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:7.5pt;font-family:Courier;color:black'>cfg.method = </span><span style='font-size:7.5pt;font-family:Courier;color:#B245F3'>'mne'</span><span style='font-size:7.5pt;font-family:Courier;color:black'>;<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:7.5pt;font-family:Courier;color:black'>cfg.elec = elec;<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:7.5pt;font-family:Courier;color:black'>cfg.grid = leadfield;<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:7.5pt;font-family:Courier;color:black'>cfg.headmodel = headmodel;<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:7.5pt;font-family:Courier;color:black'>cfg.mne.prewhiten = </span><span style='font-size:7.5pt;font-family:Courier;color:#B245F3'>'yes'</span><span style='font-size:7.5pt;font-family:Courier;color:black'>;<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:7.5pt;font-family:Courier;color:black'>cfg.mne.lambda = 3;<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:7.5pt;font-family:Courier;color:black'>cfg.mne.scalesourcecov = </span><span style='font-size:7.5pt;font-family:Courier;color:#B245F3'>'yes'</span><span style='font-size:7.5pt;font-family:Courier;color:black'>;<o:p></o:p></span></p></div><p class=MsoNormal style='min-height: 12px'><span style='font-size:7.5pt;font-family:Courier;color:black'> <o:p></o:p></span></p><div><p class=MsoNormal><span style='font-size:7.5pt;font-family:Courier;color:black'>source_GA_GroupPerpetrators_Parents_Neutral_DOUL = ft_sourceanalysis(cfg, GA_GroupPerpetrators_Parents_Neutral_DOUL);<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:Courier;color:black'><o:p> </o:p></span></p></div></div><div><p class=MsoNormal>However, I got the following error when computing the ft_sourceanalysis:<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><div><p class=MsoNormal><span style='font-size:8.5pt;color:#FF2600'>Error using svd</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:8.5pt;color:#FF2600'>Input to SVD must not contain NaN or Inf.</span><o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal><span style='font-size:8.5pt;color:#FF2600'>Error in beamformer_lcmv>pinv (line 415)</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:8.5pt;color:#FF2600'> [U,S,V] = svd(A,0);</span><o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal><span style='font-size:8.5pt;color:#FF2600'>Error in beamformer_lcmv (line 297)</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:8.5pt;color:#FF2600'> filt = pinv(lf' * invCy * lf) * lf' * invCy; % van Veen eqn.</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:8.5pt;color:#FF2600'> 23, use PINV/SVD to cover rank deficient leadfield</span><o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal><span style='font-size:8.5pt;color:#FF2600'>Error in ft_sourceanalysis (line 950)</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:8.5pt;color:#FF2600'> dip(i) = beamformer_lcmv(grid, sens, headmodel, squeeze_avg, squeeze_Cy,</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:8.5pt;color:#FF2600'> optarg{:});</span><o:p></o:p></p></div></div><div><p class=MsoNormal><span style='color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='color:black'>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.<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='color:black'>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).<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='color:black'>Thank you in advance for your help!<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='color:black'>Emilie<o:p></o:p></span></p></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></body></html>