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<p class="MsoNormal"><span style="font-size:11.0pt">I wanted to follow up on this problem in case anyone else was having the same one. I had been following the “Localizing visual gamma and corticomuscular coherence” tutorial, where it stated that the inputs
to ft_sourceanalysis should include your leadfield in cfg.sourcemodel. However, after some debugging it become apparent that this was not recognizing the leadfield, and that the leadfield should instead be specific in cfg.grid. This completely solves the problem
– and may in fact be a version-related issue. <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Hopefully this can help someone else avoid frustration upon encountering a similar error!<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b><span style="color:black">From: </span></b><span style="color:black">"Hussain, Sara (NIH/NINDS) [F]" <sara.hussain@nih.gov><br>
<b>Reply-To: </b>FieldTrip discussion list <fieldtrip@science.ru.nl><br>
<b>Date: </b>Friday, April 10, 2020 at 2:28 PM<br>
<b>To: </b>"fieldtrip@science.ru.nl" <fieldtrip@science.ru.nl><br>
<b>Subject: </b>[FieldTrip] DICS beamforming<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
</div>
<p class="MsoNormal"><span style="font-size:11.0pt">Hi all –</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">I am trying to source localize some broadband oscillatory data using the ‘dics’ beamforming option, as documented in the tutorial “Localizing visual gamma and corticomuscular coherence.” I am currently using
standard mri and segmentation via the fieldtrip templates, and generating a dipole grid with 500 dipoles using the ‘basedonvol’ approach. I then compute the leadfield based on the positions of these dipoles. Up to this point, everything seems ok and checks
out during plotting. But when I try to run ft_sourceanalysis I am getting the following error:</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Warning: dipole lies on boundary of volume model
</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">> In inf_medium_leadfield (line 54)</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> In eeg_leadfieldb (line 92)</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> In ft_compute_leadfield (line 443)</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> In beamformer_dics (line 305)</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> In ft_sourceanalysis (line 674)
</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Error using svd</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Input to SVD must not contain NaN or Inf.</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Error in beamformer_dics>pinv (line 643)</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> [U,S,V] = svd(A,0);</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Error in beamformer_dics (line 336)</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> filt = pinv(lf' * invCf * lf) * lf' * invCf; % Gross eqn. 3, use PINV/SVD</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> to cover rank deficient leadfield</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Error in ft_sourceanalysis (line 674)</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> dip(i) = beamformer_dics(grid, sens, headmodel, [], squeeze_Cf, optarg{:});</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">I’ve seen this error asked in other threads but I’ve tried what those suggest with no luck. I’m assuming this has something to do with the fact that the dipoles aren’t fully embedded in the grey matter – but
I’ve tried changing the inward shift parameter etc during grid generation and it hasn’t solved it. Any suggestions? Code is below..</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">===================</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:forestgreen">% housekeeping</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">clearvars</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:black">basedir=</span><span style="font-size:7.5pt;font-family:Courier;color:#A020F0">'/net/nindsdirfs.ninds.nih.gov/ifs/shares/HCPS/'</span><span style="font-size:7.5pt;font-family:Courier;color:black">;</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:black">addpath([basedir
</span><span style="font-size:7.5pt;font-family:Courier;color:#A020F0">'SaraHussain/Analysis_Tools/fieldtrip-20160718'</span><span style="font-size:7.5pt;font-family:Courier;color:black">]);</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">ft_defaults;</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:forestgreen">% read standard mri</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:black">cd([basedir
</span><span style="font-size:7.5pt;font-family:Courier;color:#A020F0">'SaraHussain/Analysis_Tools/fieldtrip-20160718/template/headmodel'</span><span style="font-size:7.5pt;font-family:Courier;color:black">]);</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:black">mri=load(</span><span style="font-size:7.5pt;font-family:Courier;color:#A020F0">'standard_mri.mat'</span><span style="font-size:7.5pt;font-family:Courier;color:black">);</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">mri=mri.mri;</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:forestgreen">% read standard segmentation</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:black">seg=load(</span><span style="font-size:7.5pt;font-family:Courier;color:#A020F0">'standard_seg.mat'</span><span style="font-size:7.5pt;font-family:Courier;color:black">);</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">seg=seg.mri;</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:forestgreen">% read standard headmodel</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:black">vol=load(</span><span style="font-size:7.5pt;font-family:Courier;color:#A020F0">'standard_bem.mat'</span><span style="font-size:7.5pt;font-family:Courier;color:black">);
</span><span style="font-size:7.5pt;font-family:Courier;color:forestgreen">%vol</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">vol=vol.vol;</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:forestgreen">% create sourcemodel/grid based on standard mri</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">cfg=[];</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">cfg.headmodel=vol;</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">cfg.moveinward=2;</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">cfg.grid.unit=<span style="color:#A020F0">'mm'</span>;</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">grid=ft_prepare_sourcemodel(cfg);</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Courier"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:forestgreen">% check segmentation</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">seg.transform=mri.transform;</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">seg.anatomy=mri.anatomy;</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">cfg=[];</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">cfg.funparameter=<span style="color:#A020F0">'gray'</span>;</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">ft_sourceplot(cfg,seg);</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">pause; close
<span style="color:#A020F0">all</span>;</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:forestgreen">% check volume conduction model</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">figure; ft_plot_mesh(vol.bnd(3),<span style="color:#A020F0">'facecolor'</span>,<span style="color:#A020F0">'none'</span>);
<span style="color:forestgreen">%brain</span></span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">figure; ft_plot_mesh(vol.bnd(2),<span style="color:#A020F0">'facecolor'</span>,<span style="color:#A020F0">'none'</span>);
<span style="color:forestgreen">%skull</span></span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">figure; ft_plot_mesh(vol.bnd(1),<span style="color:#A020F0">'facecolor'</span>,<span style="color:#A020F0">'none'</span>);
<span style="color:forestgreen">%scalp</span></span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">pause; close
<span style="color:#A020F0">all</span>;</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:forestgreen">% check electrode positions</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">figure;</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:black">elec=ft_read_sens(</span><span style="font-size:7.5pt;font-family:Courier;color:#A020F0">'standard_1005.elc'</span><span style="font-size:7.5pt;font-family:Courier;color:black">,</span><span style="font-size:7.5pt;font-family:Courier;color:#A020F0">'senstype'</span><span style="font-size:7.5pt;font-family:Courier;color:black">,</span><span style="font-size:7.5pt;font-family:Courier;color:#A020F0">'eeg'</span><span style="font-size:7.5pt;font-family:Courier;color:black">);</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:black">ft_plot_mesh(vol.bnd(3),</span><span style="font-size:7.5pt;font-family:Courier;color:#A020F0">'edgecolor'</span><span style="font-size:7.5pt;font-family:Courier;color:black">,</span><span style="font-size:7.5pt;font-family:Courier;color:#A020F0">'none'</span><span style="font-size:7.5pt;font-family:Courier;color:black">,</span><span style="font-size:7.5pt;font-family:Courier;color:#A020F0">'facecolor'</span><span style="font-size:7.5pt;font-family:Courier;color:black">,[0.2
0.2 0.2],</span><span style="font-size:7.5pt;font-family:Courier;color:#A020F0">'facealpha'</span><span style="font-size:7.5pt;font-family:Courier;color:black">,0.4,</span><span style="font-size:7.5pt;font-family:Courier;color:#A020F0">'edgecolor'</span><span style="font-size:7.5pt;font-family:Courier;color:black">,</span><span style="font-size:7.5pt;font-family:Courier;color:#A020F0">'none'</span><span style="font-size:7.5pt;font-family:Courier;color:black">,</span><span style="font-size:7.5pt;font-family:Courier;color:#A020F0">'edgealpha'</span><span style="font-size:7.5pt;font-family:Courier;color:black">,0.05);
hold </span><span style="font-size:7.5pt;font-family:Courier;color:#A020F0">on</span><span style="font-size:7.5pt;font-family:Courier;color:black">;</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">ft_plot_mesh(vol.bnd(2),<span style="color:#A020F0">'edgecolor'</span>,<span style="color:#A020F0">'none'</span>,<span style="color:#A020F0">'facealpha'</span>,0.4);</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">ft_plot_mesh(vol.bnd(1),<span style="color:#A020F0">'edgecolor'</span>,<span style="color:#A020F0">'none'</span>,<span style="color:#A020F0">'facecolor'</span>,[0.4 0.6 0.4]);</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">ft_plot_sens(elec,<span style="color:#A020F0">'label'</span>,<span style="color:#A020F0">'yes'</span>);</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">pause; close
<span style="color:#A020F0">all</span></span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:#A020F0"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:forestgreen">% check grid position</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">figure; </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">ft_plot_mesh(vol.bnd(3),<span style="color:#A020F0">'edgecolor'</span>,<span style="color:#A020F0">'none'</span>); hold
<span style="color:#A020F0">on</span>; alpha <span style="color:#A020F0">0.4</span>;
<span style="color:forestgreen">%brain</span></span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">ft_plot_mesh(grid.pos(grid.inside,:));</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">pause; close
<span style="color:#A020F0">all</span>;</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:forestgreen">% load data</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:black">cd([basedir
</span><span style="font-size:7.5pt;font-family:Courier;color:#A020F0">'SaraHussain/SS_42H_63/clean_tep_data'</span><span style="font-size:7.5pt;font-family:Courier;color:black">]);</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">load([peak_subj{jjj}
<span style="color:#A020F0">'_double_cleaned_peak.mat'</span>]);</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:forestgreen">% demean/detrend and update channel names</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">cfg=[];</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">cfg.demean=<span style="color:#A020F0">'yes'</span>;</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">cfg.detrend=<span style="color:#A020F0">'yes'</span>;</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">data=ft_preprocessing(cfg,clean_data);</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">data.label=labels;</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:forestgreen">% select relevant post-stim latencies and channels</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">cfg=[];</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">short=ft_selectdata(cfg,data);</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:forestgreen">% calculate post-stim frequency using mtmfft approach </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">cfg=[];</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">cfg.method=<span style="color:#A020F0">'mtmfft'</span>;</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">cfg.output=<span style="color:#A020F0">'powandcsd'</span>;</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">cfg.tapsmofrq=48;</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">cfg.foi=52;</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">peak=ft_freqanalysis(cfg,short);</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:forestgreen">% create leadfield</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">cfg=[];</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">cfg.headmodel=vol;</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">cfg.grid.pos=grid.pos;</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">cfg.grid.inside=grid.inside;</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">cfg.elec=elec;</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">lead=ft_prepare_leadfield(cfg,peak);</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:forestgreen">% get source localized data</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">cfg=[];</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:black">cfg.elec=elec;</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">cfg.method=<span style="color:#A020F0">'dics'</span>;</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">cfg.sourcemodel=lead;</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">cfg.headmodel=vol;</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier">source_peak=ft_sourceanalysis(cfg,peak);</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:#A020F0"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Courier"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Courier"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
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