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<p style="">Hello Azadeh,<br>
</p>
<p style=""><br>
</p>
<p style="">Again, fieldtrip experts please let me know if I am wrong, I dont want to lead azadeh or myself astray.<br>
</p>
<p style=""><br>
</p>
<p style="">The code I use to create my headmodel is the following:<br>
</p>
<p style=""><br>
</p>
<div>cfg = [];</div>
<div style="">cfg.write = 'no';</div>
<div>cfg.coordsys = 'spm';</div>
<div>cfg.output = { 'scalp', 'skull', 'brain'};</div>
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<div style="">segmentedmri = ft_volumesegment(cfg, mri);</div>
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<div>cfg = [];</div>
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<div>cfg.method = 'iso2mesh';</div>
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<div>cfg.numvertices = 10000;</div>
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<div>bnd = ft_prepare_mesh( cfg, segmentedmri);</div>
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<div><br>
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<div>% fix mesh</div>
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<div>[ bnd( 1).pnt, bnd( 1).tri] = meshresample( bnd( 1).pnt, bnd( 1).tri, 1000/size( bnd( 1).pnt, 1));</div>
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<div>[ bnd( 2).pnt, bnd( 2).tri] = meshresample( bnd( 2).pnt, bnd( 2).tri, 2000/size( bnd( 2).pnt, 1));</div>
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<div>[ bnd( 3).pnt, bnd( 3).tri] = meshresample( bnd( 3).pnt, bnd( 3).tri, 3000/size( bnd( 3).pnt, 1));</div>
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<div>for ii = 1:size( bnd),</div>
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<div> [ bnd( ii).pnt, bnd( ii).tri] = meshcheckrepair( bnd( ii).pnt, bnd( ii).tri, 'dup');</div>
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<div> [ bnd( ii).pnt, bnd( ii).tri] = meshcheckrepair( bnd( ii).pnt, bnd( ii).tri, 'isolated');</div>
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<blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;">
<div> [ bnd( ii).pnt, bnd( ii).tri] = meshcheckrepair( bnd( ii).pnt, bnd( ii).tri, 'deep');</div>
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<div> [ bnd( ii).pnt, bnd( ii).tri] = meshcheckrepair( bnd( ii).pnt, bnd( ii).tri, 'meshfix');</div>
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<div>end</div>
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<div><br>
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<div>% calculate headmodel % reordered to brain skull scalp</div>
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<div>cfg = [];</div>
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<div>cfg.method = 'bemcp'; %openmeeg doesnt work with multiple output from ft_volumesegment</div>
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<div>vol = ft_prepare_headmodel(cfg, bnd);</div>
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<div style="">clear bnd</div>
</blockquote>
</blockquote>
<div style=""><br>
</div>
<div style=""> Also with your previous issue: <br>
</div>
<p style=""><br>
</p>
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<div><em><font size="1">??? Error using ==> svd</font></em></div>
<div><em><font size="1">Input to SVD must not contain NaN or Inf.</font></em></div>
<div><em><font size="1"><br>
</font></em></div>
<div><em><font size="1">Error in ==> beamformer_dics>pinv at 650</font></em></div>
<div><em><font size="1"> [U,S,V] = svd(A,0);</font></em></div>
<div><em><font size="1"><br>
</font></em></div>
<div><em><font size="1">Error in ==> beamformer_dics at 339</font></em></div>
<div><em><font size="1"> filt = pinv(lf' * invCf * lf) * lf' * invCf; % Gross eqn. 3, use PINV/SVD to cover rank</font></em></div>
<div><em><font size="1"> deficient leadfield</font></em></div>
<div><em><font size="1"><br>
</font></em></div>
<div><em><font size="1">Error in ==> ft_sourceanalysis at 572</font></em></div>
<div><em><font size="1"> dip(i) = beamformer_dics(grid, sens, vol, [], squeeze(Cf(i,:,:)), optarg{:});</font></em></div>
<div><em><font size="1"><br>
</font></em></div>
<div><em><font size="1">Error in ==> test_sourceanalysis at 12</font></em></div>
<div><em style=""><font size="1" style="">sourceTF = ft_sourceanalysis(cfg, data_TF);</font></em></div>
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<p style=""><br>
</p>
<p style="">Can you check the variables lf invCf<br>
</p>
<p style="">lf should be: number of channels x 3<br>
</p>
<p style="">invCf should be: number of channels x number of channels<br>
</p>
<p style=""><br>
</p>
<p style="">Previously I would get an error if the number of channels didnt match up because when I select only EEG channels, it doesnt update<br>
</p>
<p style="">the data.elec field. So you may need to check that also.<br>
</p>
<p style=""><br>
</p>
<p style="">Hopefully this works.<br>
</p>
<p style=""><br>
</p>
<p style="">tyler<br>
</p>
<p style=""><br>
</p>
<p style=""><br>
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<div style="font-size:13px">*************************
<div style="font-family:Tahoma"><br>
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<div><font face="Arial"><i>Tyler Grummett ( BBSc, BSc(Hons I))</i></font></div>
<div><font face="Arial"><i>PhD Candidate</i></font></div>
<div><font face="Arial"><i>Brain Signals Laboratory</i></font></div>
<div><font face="Arial"><i>Flinders University</i></font></div>
<div><font face="Arial"><i>Rm 5A301</i></font></div>
<div><font face="Arial"><i>Ext 66124</i></font></div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> fieldtrip-bounces@science.ru.nl <fieldtrip-bounces@science.ru.nl> on behalf of Azadeh Hajihosseini <azadehh@uvic.ca><br>
<b>Sent:</b> Tuesday, 22 July 2014 3:42 AM<br>
<b>To:</b> FieldTrip discussion list<br>
<b>Subject:</b> Re: [FieldTrip] Source analysis of EEG oscillatory activity/ NaN values in the leadfield matrices</font>
<div> </div>
</div>
<div>
<div dir="ltr">
<div dir="ltr"><span style="font-family:arial,sans-serif; font-size:13px">Hi Tyler,</span>
<div style="font-family:arial,sans-serif; font-size:13px"><br>
</div>
<div style="font-family:arial,sans-serif; font-size:13px">Thanks for responding! Actually, I have 51 electrodes. I also checked the units again and they are all 'mm'.</div>
<div style="font-family:arial,sans-serif; font-size:13px"><br>
</div>
<div style="font-family:arial,sans-serif; font-size:13px">It looks like there is a problem in preparing the head model because when I call the line: </div>
<div style="font-family:arial,sans-serif; font-size:13px"><i><br>
</i></div>
<div style="font-family:arial,sans-serif; font-size:13px"><i>vol = ft_prepare_headmodel(cfg, segmentedmri_template), </i> </div>
<div style="font-family:arial,sans-serif; font-size:13px"><br>
</div>
<div style="font-family:arial,sans-serif; font-size:13px">there is this warning:</div>
<div style="font-family:arial,sans-serif; font-size:13px"><br>
</div>
<div style="font-family:arial,sans-serif; font-size:13px"><i>Warning: Matrix is singular, close to singular or badly scaled.</i></div>
<div style="font-family:arial,sans-serif; font-size:13px"><i> Results may be inaccurate. RCOND = NaN. </i></div>
<div style="font-family:arial,sans-serif; font-size:13px"><i><br>
</i></div>
<div style="font-family:arial,sans-serif; font-size:13px"> coming from <i>ft_headmodel_bemcp. </i>Any idea about this?</div>
<div style="font-family:arial,sans-serif; font-size:13px"><br>
</div>
<div style="font-family:arial,sans-serif; font-size:13px">Thanks again!!</div>
<div style="font-family:arial,sans-serif; font-size:13px">Azadeh</div>
</div>
<div class="gmail_extra"><br>
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<div class="HOEnZb">
<div class="h5">
<div class="gmail_extra"><br>
<div class="gmail_quote">On Sun, Jul 20, 2014 at 2:14 AM, Tyler Grummett <span dir="ltr">
<<a href="mailto:tyler.grummett@flinders.edu.au" target="_blank">tyler.grummett@flinders.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex; border-left:1px #ccc solid; padding-left:1ex">
<div dir="auto">
<div>Also are the units the same for your Headmodel, electrodes and sourcemodel(?)<br>
<br>
Sent from my iPad</div>
<div>
<div>
<div><br>
On 20 Jul 2014, at 4:08 pm, "Tyler Grummett" <<a href="mailto:tyler.grummett@flinders.edu.au" target="_blank">tyler.grummett@flinders.edu.au</a>> wrote:<br>
<br>
</div>
<blockquote type="cite">
<div>
<div>I don't know if this advice is at all correct but I usually get that error if I've got a relatively small number of electrodes (~29) or a small data set (30 seconds of data).</div>
<div><br>
</div>
<div>Does that sound familiar?</div>
<div><br>
</div>
<div>I usually clear all and run it again and it will work eventually haha<br>
<br>
Sent from my iPad</div>
<div><br>
On 19 Jul 2014, at 8:01 am, "Azadeh Hajihosseini" <<a href="mailto:azadehh@uvic.ca" target="_blank">azadehh@uvic.ca</a>> wrote:<br>
<br>
</div>
<blockquote type="cite">
<div>
<div dir="ltr">
<div dir="ltr">
<div dir="ltr" style="font-family:arial,sans-serif; font-size:13px">Hello FieldTrip members,
<div><br>
</div>
<div>I am trying to source localize EEG oscillatory activity and have a few problems in constructing the forward model and eventually running the source analysis. I think the problems are related to each other. Here is what happens:</div>
<div><br>
</div>
<div>1- When I run the source analysis, I get this error message:</div>
<div><br>
</div>
</div>
<blockquote style="font-family:arial,sans-serif; font-size:13px; margin:0px 0px 0px 40px; border:none; padding:0px">
<div><i><font size="1">??? Error using ==> svd</font></i></div>
<div><i><font size="1">Input to SVD must not contain NaN or Inf.</font></i></div>
<div><i><font size="1" style=""><br>
</font></i></div>
<div><i><font size="1">Error in ==> beamformer_dics>pinv at 650</font></i></div>
<div><i><font size="1"> [U,S,V] = svd(A,0);</font></i></div>
<div><i><font size="1"><br>
</font></i></div>
<div><i><font size="1">Error in ==> beamformer_dics at 339</font></i></div>
<div><i><font size="1"> filt = pinv(lf' * invCf * lf) * lf' * invCf; % Gross eqn. 3, use PINV/SVD to cover rank</font></i></div>
<div><i><font size="1"> deficient leadfield</font></i></div>
<div><i><font size="1"><br>
</font></i></div>
<div><i><font size="1">Error in ==> ft_sourceanalysis at 572</font></i></div>
<div><i><font size="1"> dip(i) = beamformer_dics(grid, sens, vol, [], squeeze(Cf(i,:,:)), optarg{:});</font></i></div>
<div><i><font size="1"><br>
</font></i></div>
<div><i><font size="1">Error in ==> test_sourceanalysis at 12</font></i></div>
<div><i><font size="1">sourceTF = ft_sourceanalysis(cfg, data_TF);</font></i></div>
</blockquote>
<div dir="ltr" style="font-family:arial,sans-serif; font-size:13px">
<div><br>
</div>
<div>2- Checking the leadfiled matrices, I see there are a lot of NaN values.</div>
<div>3- When I visualize the head model I have created, the plots don't look right. The third field, <i>vol.bnd(3),</i> which is supposed to be the brain tissue, looks like a cube.</div>
<div><br>
</div>
<div>And here are my code lines:</div>
<div><br>
</div>
</div>
<blockquote style="font-family:arial,sans-serif; font-size:13px; margin:0px 0px 0px 40px; border:none; padding:0px">
<div><i><font size="1">% CONSTRUCT A HEAD MODEL from the template mri in FT's template/anatomy</font></i></div>
<div><i><font size="1">mri = ft_read_mri('template\anatomy\single_subj_T1.nii');</font></i></div>
<div><i><font size="1">mri.coordsys = 'spm';</font></i></div>
<div><i><font size="1"><br>
</font></i></div>
<div><i><font size="1">%SEGMENTATION:</font></i></div>
<div><i><font size="1">cfg = [];</font></i></div>
<div><i><font size="1">cfg.output = {'brain','skull','scalp'};</font></i></div>
<div><i><font size="1">segmentedmri_template = ft_volumesegment(cfg, mri); % Using NOT resliced data</font></i></div>
<div><i><font size="1">save segmentedmri_template segmentedmri_template</font></i></div>
<div><i><font size="1"><br>
</font></i></div>
<div><br>
</div>
<div><i><font size="1">%CREATE THE HEAD MODEL (VOLUME CONDUCTION MODEL)</font></i></div>
<div><i><font size="1">cfg = [];</font></i></div>
<div><i><font size="1">cfg.method ='bemcp';</font></i></div>
<div><i><font size="1">cfg.tissue ={'brain','skull','scalp'};</font></i></div>
<div><i><font size="1">% cfg.outputfile = 'template_';</font></i></div>
<div><i><font size="1">vol = ft_prepare_headmodel(cfg, segmentedmri_template);</font></i></div>
<div><i><font size="1">save vol vol</font></i></div>
<div><i><font size="1"><br>
</font></i></div>
<div><i><font size="1">%Visualization of the head model</font></i></div>
<div><i><font size="1">figure;</font></i></div>
<div><i><font size="1">ft_plot_mesh(vol.bnd(1),'facecolor','none'); %scalp </font></i></div>
<div><i><font size="1">figure;</font></i></div>
<div><i><font size="1">ft_plot_mesh(vol.bnd(2),'facecolor','none'); %skull</font></i></div>
<div><i><font size="1">figure;</font></i></div>
<div><i><font size="1">ft_plot_mesh(vol.bnd(3),'facecolor','none'); %brain This one looks like a cube</font></i></div>
<div><i><font size="1"><br>
</font></i></div>
<div><i><font size="1">% Align electrodes </font></i></div>
<div><i><font size="1">elec = ft_read_sens('template\electrode\standard_1020.elc'); </font></i></div>
<div><i><font size="1">% load volume conduction model</font></i></div>
<div><i><font size="1">% load vol; </font></i></div>
<div><i><font size="1"><br>
</font></i></div>
<div><i><font size="1">%interactive allignment</font></i></div>
<div><i><font size="1">cfg = [];</font></i></div>
<div><i><font size="1">cfg.method = 'interactive';</font></i></div>
<div><i><font size="1">cfg.elec = elec;</font></i></div>
<div><i><font size="1">cfg.headshape = vol.bnd(1);</font></i></div>
<div><i><font size="1">elec_aligned = ft_electroderealign(cfg);</font></i></div>
<div><i><font size="1"><br>
</font></i></div>
<div><i><font size="1">save elec_aligned elec_aligned</font></i></div>
<div><i><font size="1"><br>
</font></i></div>
<div><i><font size="1">% Prepare leadfield</font></i></div>
<div><i><font size="1">load data_TF</font></i></div>
<div><i><font size="1">cfg=[];</font></i></div>
<div><i><font size="1">cfg.vol = vol; %structure with volume conduction model</font></i></div>
<div><i><font size="1">cfg.elec = elec_aligned;%structure with electrode positions</font></i></div>
<div><i><font size="1">[grid] = ft_prepare_leadfield(cfg, data_TF);</font></i></div>
<div><i><font size="1"><br>
</font></i></div>
<div><i><font size="1">% Find source</font></i></div>
<div><i><font size="1">cfg = []; </font></i></div>
<div><i><font size="1">cfg.method = 'dics';</font></i></div>
<div><i><font size="1">cfg.frequency = 25; </font></i></div>
<div><i><font size="1">cfg.grid = grid; </font></i></div>
<div><i><font size="1">cfg.vol = vol;</font></i></div>
<div><i><font size="1">cfg.latency = .4;%single number in seconds, for time-frequency analysis</font></i></div>
<div><i><font size="1">cfg.dics.projectnoise = 'yes';</font></i></div>
<div><i><font size="1">cfg.dics.lambda = 0;</font></i></div>
<div><i><font size="1">cfg.elec = elec_aligned;%structure with electrode positions</font></i></div>
<div><i><font size="1"><br>
</font></i></div>
<div><i><font size="1">sourceTF = ft_sourceanalysis(cfg, data_TF);</font></i></div>
</blockquote>
<div dir="ltr" style="font-family:arial,sans-serif; font-size:13px">
<div><br>
</div>
<div>
<div>I am using <i>wavelet </i>with a <i>fourier</i> output for the time-frequency analysis (<i>data_TF)</i>. Do you have any idea what might be wrong here?</div>
<div><br>
</div>
<div>I also have a more general question. What type of time-frequency data can be input to source analysis? <i>ft_freqanalysis</i> provides power, power and cross-spectra, and complex fourier outputs. But is source-localization based on only power data correct?
I couldn't find any explanations regarding this issue in the tutorial.</div>
</div>
<div><br>
</div>
<div>I look forward to hearing from anyone who might have ideas about any of these issues! </div>
</div>
<br clear="all" style="font-family:arial,sans-serif; font-size:13px">
<div style="font-family:arial,sans-serif; font-size:13px">Many thanks,</div>
<div style="font-family:arial,sans-serif; font-size:13px"></div>
</div>
<div><br>
</div>
-- <br>
Azadeh HajiHosseini<br>
<br>
</div>
</div>
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