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<p class="MsoNormal"><span lang="EN-US">Dear Fieldtrip users,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">I’m following the tutorial of beamformers (<a href="http://fieldtrip.fcdonders.nl/tutorial/beamformer">Source Analysis: Contrast activity to another interval</a>) to estimate oscillatory sources using DICS. I’ve checked
the surface created after segmentation and the grid generated from the electrode positions and the headmodel. That seems to work ok. However, at the step of source analysis, I get the following error:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Error using * <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Inner matrix dimensions must agree.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Error in beamformer_dics (line 339)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> filt = pinv(lf' * invCf * lf) * lf' * invCf; % Gross eqn. 3, use PINV/SVD to cover rank<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> deficient leadfield<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Error in ft_sourceanalysis (line 567)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> dip(i) = beamformer_dics(grid, sens, vol, [], squeeze(Cf(i,:,:)), optarg{:});<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Does anybody have an idea of what I’m doing wrong?<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Thank you in advance for any help or suggestion!<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">-----------------------------------------------------------------<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">This is my code:<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:forestgreen">%% 1 - Preparation of MRI- source space</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:forestgreen">% Read MRI</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">mrifile =
</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:#A020F0">'Subject01\Subject01.mri'</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">;</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">mri = ft_read_mri(mrifile);</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:forestgreen">% Reslice to reorient images</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">cfg = [];
</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">cfg.dim = [256 256 256];
</span><span style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">mri = ft_volumereslice(cfg,mri);
</span><span style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:forestgreen">% Segment compartments</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">cfg = [];</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">cfg.output = {</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:#A020F0">'brain'</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">,</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:#A020F0">'skull'</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">,</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:#A020F0">'scalp'</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">};</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">segmentedmri = ft_volumesegment(cfg, mri);</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:forestgreen">% Prepare mesh</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">cfg=[];</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">cfg.tissue={</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:#A020F0">'brain'</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">,
</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:#A020F0">'skull'</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">,</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:#A020F0">'scalp'</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">};</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">cfg.numvertices = [3000 2000 1000];</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">bnd=ft_prepare_mesh(cfg,segmentedmri);</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:forestgreen">% Prepare headmodel</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">cfg = [];</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">cfg.method =</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:#A020F0">'bemcp'</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">;</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">vol = ft_prepare_headmodel(cfg, bnd);</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black"></span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:forestgreen">%% 2- Prepare leadfield - Creating grid</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">load
</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:#A020F0">elec_aligned2</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">
</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:forestgreen">% Obtained after adjusting electrodes on scalp surface interactively</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:forestgreen">% Three fiducial markers were added to the electrode file, and now they're</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:forestgreen">% removed so that the electrode structure has the same number of channels as the data</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">elec_aligned2.chanpos = elec_aligned2.chanpos(1:128, :);</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">elec_aligned2.elecpos = elec_aligned2.elecpos(1:128, :);</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">elec_aligned2.label = elec_aligned2.label(1:128, :);</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">cfg =[];</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">cfg.vol = vol;</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">cfg.elec = elec_aligned2;</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">cfg.grid.resolution = 10;
</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">cfg.grid.unit =
</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:#A020F0">'mm'</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">;
</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">[grid] = ft_prepare_leadfield(cfg);
</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:forestgreen">%% 3- Join rest and task data</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:forestgreen">% data_rs: resting state data</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:forestgreen">% data4: data during task</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">dataAll = ft_appenddata([], data_rs, data4);</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">cfg = [];</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">cfg.method =
</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:#A020F0">'mtmfft'</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">;</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">cfg.output =
</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:#A020F0">'powandcsd'</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">;
</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">cfg.tapsmofrq = 4;</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">cfg.foilim = [18 18];</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">freqAll = ft_freqanalysis(cfg, dataAll);</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:forestgreen">%----------------------------------</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:forestgreen">% all seems normal until here<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:forestgreen">%----------------------------------<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:forestgreen">%% 4- Estimate source of all data</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">
</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">cfg = [];</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">cfg.method =
</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:#A020F0">'dics'</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">;</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">cfg.frequency = 18;</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">cfg.grid = grid;</span><span style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black">cfg.vol = vol;</span><span style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">cfg.elec = elec_aligned2;</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">cfg.dics.projectnoise =
</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:#A020F0">'yes'</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">;</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">cfg.dics.lambda =
</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:#A020F0">'5%'</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">;</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">cfg.dics.keepfilter =
</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:#A020F0">'yes'</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">;</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">cfg.dics.realfilter =
</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:#A020F0">'yes'</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">;</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">sourceAll = ft_sourceanalysis(cfg, freqAll);</span><span lang="EN-US" style="font-size:12.0pt;font-family:"Courier New""><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Cheers,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:NL-BE">Laura Rueda Delgado<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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