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<p style="">Fieldtrip,<br>
</p>
<p style=""><br>
</p>
<p style="">Ive got it working now.<br>
</p>
<p style=""><br>
</p>
<p style="">The follow error:<br>
</p>
<p style=""><br>
</p>
<p style="">*****************************************************************<br>
</p>
<p style=""><br>
</p>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; background-color: rgb(255, 255, 255);">
Error using * </div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; background-color: rgb(255, 255, 255);">
Inner matrix dimensions must agree.</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; background-color: rgb(255, 255, 255);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; background-color: rgb(255, 255, 255);">
Error in beamformer_lcmv (line 268)</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; background-color: rgb(255, 255, 255);">
filt = pinv(lf' * invCy * lf) * lf' * invCy; % van Veen eqn. 23, use PINV/SVD to</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; background-color: rgb(255, 255, 255);">
cover rank deficient leadfield</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; background-color: rgb(255, 255, 255);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; background-color: rgb(255, 255, 255);">
Error in ft_sourceanalysis (line 794)</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; background-color: rgb(255, 255, 255);">
dip(i) = beamformer_lcmv(grid, sens, vol, squeeze_avg, squeeze(Cy(i,:,:)), optarg{:});<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; background-color: rgb(255, 255, 255);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; background-color: rgb(255, 255, 255);">
<span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; background-color: rgb(255, 255, 255);">****************************************</span><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; background-color: rgb(255, 255, 255);">*</span><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; background-color: rgb(255, 255, 255);">************************</span><br>
</div>
<p style=""><br>
</p>
<p style="">It is because: <br>
</p>
<p style="">if is 128x3<br>
</p>
<p style="">invCy is 124x124<br>
</p>
<p style=""><br>
</p>
<p style="">When I ran the code:<br>
</p>
<p style=""><br>
</p>
<p style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px;"></p>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px;">
<div> cfg = [];</div>
<div style=""> cfg.channel = 'EEG'; % only works for preprocessing</div>
<div> cfg.vartrllength = 2; % accept variable length trials</div>
<div> cfg.covariance = 'yes';</div>
<div> cfg.covariancewindow = 'all';</div>
<div> cfg.keeptrials = 'no';</div>
<div style=""> timelock = ft_timelockanalysis(cfg, data);<br>
</div>
<br>
</div>
<p style="">It did the timelockanalysis on 124 channels, but it didnt remove the non-EEG channels from timelock.elec<br>
</p>
<p style="">and so the four EOG channels explains the 128.<br>
</p>
<p style=""><br>
</p>
<div>timelock = </div>
<div><br>
</div>
<div> avg: [124x11758 double]</div>
<div> var: [124x11758 double]</div>
<div> time: [1x11758 double]</div>
<div> dof: [124x11758 double]</div>
<div> label: {1x124 cell}</div>
<div> dimord: 'chan_time'</div>
<div> cov: [124x124 double]</div>
<div> elec: [1x1 struct]</div>
<div style=""> cfg: [1x1 struct]<br>
</div>
<div style=""><br>
</div>
<div style="">timelock.elec = <br>
</div>
<div style=""><br>
</div>
<div style="">
<div> chanpos: [128x3 double]</div>
<div> elecpos: [128x3 double]</div>
<div> label: {1x128 cell}</div>
<div> type: 'eeg1005'</div>
<div style=""> unit: 'mm'<br>
</div>
<div style=""><br>
</div>
<div style="">I dont know if this is a bug or not. Please advise.<br>
</div>
<div style=""><br>
</div>
<div style="">Tyler<br>
</div>
<br>
</div>
<p style=""><br>
</p>
<div>
<p><br>
</p>
<div name="divtagdefaultwrapper" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:; margin:0">
<div style="font-family:Tahoma; font-size:13px">
<div style="font-family:Tahoma; font-size:13px">
<div style="font-family:Tahoma; font-size:13px">
<div style="font-size:13px">*************************
<div style="font-family:Tahoma"><br>
</div>
<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>
</div>
</div>
</div>
</div>
</div>
</div>
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<hr tabindex="-1" style="display:inline-block; width:98%">
<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 Tyler Grummett <tyler.grummett@flinders.edu.au><br>
<b>Sent:</b> Tuesday, 8 April 2014 12:18 PM<br>
<b>To:</b> FieldTrip discussion list<br>
<b>Subject:</b> [FieldTrip] ft_sourceanalysis using LCMV beamformer and grid from ft_prepare_leadfield</font>
<div> </div>
</div>
<div>
<div style="font-size:12pt; color:#000000; background-color:#FFFFFF; font-family:Calibri,Arial,Helvetica,sans-serif">
<p style="">Hello fieldtrip,<br>
</p>
<p style=""><br>
</p>
<p style="">I am trying to perform an LCMV beamformer on timelockanalysis data.<br>
</p>
<p style=""><br>
</p>
<p style="">timelock = <br>
</p>
<div> avg: [124x20517 double]</div>
<div> var: [124x20517 double]</div>
<div> time: [1x20517 double]</div>
<div> dof: [124x20517 double]</div>
<div> label: {1x124 cell}</div>
<div> dimord: 'chan_time'</div>
<div> cov: [124x124 double]</div>
<div> elec: [1x1 struct]</div>
<div style=""> cfg: [1x1 struct]<br>
</div>
<div style=""><br>
</div>
<div style="">I first run ft_prepare_leadfield<br>
</div>
<div style=""><br>
</div>
<div style="">
<div style=""><span> </span><span> </span><span> </span>cfg = [];</div>
<div> cfg.elec = timelock.elec;</div>
<div> cfg.vol = vol;</div>
<div style=""><span style="font-size:12pt"> cfg.grid.resolution = 1; % use a 3-D grid with a 1 cm resolution</span><br>
</div>
<div> cfg.grid.unit = 'cm';</div>
<div> cfg.normalize = 'yes'; % if you are not contrasting the activity of interest again another condition or baseline time-window</div>
<div style=""> grid = ft_prepare_leadfield( cfg);<br>
</div>
<div style=""><br>
</div>
<div style="">grid = <br>
</div>
<div style="">
<div> xgrid: [-5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8]</div>
<div> ygrid: [-6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7]</div>
<div> zgrid: [0 1 2 3 4 5 6 7 8 9 10 11 12]</div>
<div> dim: [14 14 13]</div>
<div> pos: [2548x3 double]</div>
<div> unit: 'cm'</div>
<div> inside: [1x1409 double]</div>
<div> outside: [1x1139 double]</div>
<div> cfg: [1x1 struct]</div>
<div style=""> leadfield: {1x2548 cell}<br>
</div>
<div style=""><br>
</div>
<div style="">I then try to run the ft_sourceanalysis code:<br>
</div>
<div style="">
<div style=""><span style="font-size:12pt"> </span></div>
<div style="">
<div style=""><span> </span><span> </span><span> </span>cfg = [];</div>
<div> cfg.channel = timelock.label;</div>
<div> cfg.method = 'lcmv';</div>
<div> cfg.grid = grid;</div>
<div> cfg.vol = vol;</div>
<div> cfg.keepfilter = 'yes';</div>
<div style=""> source = ft_sourceanalysis( cfg, timelock);<br>
</div>
<br>
</div>
<br>
</div>
And it crashes with the error message:<br>
</div>
<div style=""><br>
</div>
<div style="">
<div>Error using * </div>
<div>Inner matrix dimensions must agree.</div>
<div><br>
</div>
<div>Error in beamformer_lcmv (line 268)</div>
<div> filt = pinv(lf' * invCy * lf) * lf' * invCy; % van Veen eqn. 23, use PINV/SVD to</div>
<div> cover rank deficient leadfield</div>
<div><br>
</div>
<div>Error in ft_sourceanalysis (line 794)</div>
<div style=""> dip(i) = beamformer_lcmv(grid, sens, vol, squeeze_avg, squeeze(Cy(i,:,:)), optarg{:});<br>
</div>
<div style=""><br>
</div>
<div style=""><br>
</div>
<div style=""><br>
</div>
<div style="">However, the code does work if it is:<br>
</div>
<div style=""><br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px; background-color:rgb(255,255,255)">
<span> </span><span> </span><span> </span>cfg = [];</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px; background-color:rgb(255,255,255)">
cfg.channel = timelock.label;</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px; background-color:rgb(255,255,255)">
cfg.method = 'lcmv';</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px; background-color:rgb(255,255,255)">
cfg.grid.inside = grid.inside;</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px; background-color:rgb(255,255,255)">
cfg.vol = vol;</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px; background-color:rgb(255,255,255)">
cfg.keepfilter = 'yes';</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px; background-color:rgb(255,255,255)">
source = ft_sourceanalysis( cfg, timelock);<br>
</div>
<br>
</div>
However, I run the sourceplot code produces something that looks like the picture attached.<br>
</div>
<div style=""><br>
</div>
<div style="">What is interesting is that when I run the interp code:<br>
</div>
<div style=""><br>
</div>
<div style="">
<div style=""><span> </span>the input is source data with 16777216 positions on a [256 256 256] grid</div>
<div style=""><span> </span>not plotting anatomy<br>
</div>
</div>
<div style=""><br>
</div>
<div style="">But when you run the same code from sourcePost_nocon from the beamformer tutorial, you get the following when you run the code:<br>
</div>
<div style=""><br>
</div>
<div style="">
<div style=""><span> </span>the input is source data with 3042 positions on a [18 13 13] grid</div>
<div style=""><span> </span>the input is volume data with dimensions [256 256 256]<br>
</div>
<div style=""><br>
</div>
<div style="">I have used the same mri file for both.<br>
</div>
<br>
</div>
<div style="">Please help, I cant work out the issue.<br>
</div>
<div style=""><br>
</div>
<div style="">Tyler<br>
</div>
<p style=""><br>
</p>
<div>
<p><br>
</p>
<div name="divtagdefaultwrapper" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:; margin:0">
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<div style="font-family:Tahoma; font-size:13px">
<div style="font-family:Tahoma; font-size:13px">
<div style="font-size:13px">*************************
<div style="font-family:Tahoma"><br>
</div>
<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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