<div dir="ltr"><div>Hello eveyone,</div><div><br></div><div>I am a research fellow working in the area of brain connectivity analysis and its applicability in Deep Brain stimulation for Parkinsons patients.</div><div>So, for this I created a model of the human head using FieldTrip and then simulated two dipoles inside this head model with thier predefined time series and collected the synthetic EEG data.<br></div><div>Then, I created a source model to reconstruct these two dipoles again inside the head model using LCMV inverse method.</div><div>But, the reconstrcuted dipoles are way too far from the original dipoles in terms of their location.</div><div>I think that even if they are deviated from the original positions it should be a little difference but my results show too much difference. <br></div><div>I am attaching my results obtained below and also providing the code that I've used. Please let me know where am I going wrong.</div><div><br></div><div>% READ MRI<br></div><div>mri = ft_read_mri('Subject01.mri');</div><div> </div><div>%SEGMENTATION<br></div><div>cfg = [];<br>cfg.output = {'gray','white','csf','skull',<wbr>'scalp'};<br>segmentedmri = ft_volumesegment(cfg, mri);</div><div><br></div><div>%MESH GENERATION<br></div><div>cfg = [];<br>cfg.shift = 0.3;<br>cfg.method = 'hexahedral';<br>mesh = ft_prepare_mesh(cfg,<wbr>segmentedmri);</div><div><br></div><div>% HEAD MODEL CREATION<br></div><div>cfg = [];<br>cfg.method ='simbio';<br>cfg.conductivity = [0.33 0.14 1.79 0.01 0.43]; <br>vol = ft_prepare_headmodel(cfg, mesh); <br></div><div><br></div><div>%EEG SENSOR ALIGNMENT<br></div><div>elec = ft_read_sens('standard_1020.<wbr>elc'); <br>cfg = [];<br>cfg.method = 'interactive';<br>cfg.elec = elec;<br>cfg.headshape = vol;<br>elec_aligned = ft_electroderealign(cfg);<br></div><div><br></div><div>% DIPOLE SIMULATION<br></div><div>cfg = [];<br>cfg.vol = vol; <br>cfg.elec = elec_aligned; <br>cfg.dip.pos = [<br> 28.5 -5.5 50.5 % dipole 1<br> 26.5 14.5 41.5 % dipole 2<br> ];<br>cfg.dip.mom = ... % the vector represents [qx1 qy1 qz1 qx2 qy2 qz2]<br> [ 1 0 0 0 0 0 ]' + ...% this is how signal1 contributes to the 6 dipole components<br> [ 0 0 0 1 0 0 ]'; % this is how signal2 contributes to the 6 dipole components<br> <br>time = (0:199)/200; % manually create a time axis<br>signal1 = data.trial{1, 1}(1,:);<br>signal2 = data.trial{1, 1}(3,:); <br>cfg.dip.signal = {[signal1; signal2]}; % one trial only<br>cfg.fsample = 200; % Hz<br>raw = ft_dipolesimulation(cfg);<br>avg = ft_timelockanalysis([], raw);</div><div><br></div><div>%SOURCE MODEL<br></div><div>ftpath = 'C:\Users\sushain\fieldtrip-20180129'; <br>load(fullfile(ftpath, 'template/sourcemodel/standard_sourcemodel3d10mm'));<br>template_grid = sourcemodel;<br>clear sourcemodel;</div><div><br></div><div>cfg = [];<br>cfg.grid.warpmni = 'yes';<br>cfg.grid.template = template_grid;<br>cfg.grid.nonlinear = 'yes';<br>cfg.mri = mri;<br>cfg.grid.unit ='mm';<br>grid = ft_prepare_sourcemodel(cfg);</div><div><br></div><div>%LEADFIELD CREATION<br></div><div>cfg = [];<br>cfg.elec = elec_aligned; % gradiometer distances<br>cfg.headmodel = vol; % volume conduction headmodel<br>cfg.grid = grid; % normalized grid positions<br>cfg.normalize = 'yes'; % to remove depth bias <br>lf = ft_prepare_leadfield(cfg);</div><div><br></div><div>%LCMV SOURCE RECONSTRUCTION</div><div><br></div><div>cfg = [];<br>cfg.method = 'lcmv';<br>cfg.grid = lf; % leadfield, which has the grid information<br>cfg.vol = vol; % volume conduction model (headmodel)<br>cfg.keepfilter = 'yes';<br>cfg.lcmv.fixedori = 'yes'; <br>lcmv_reconstructed_sources = ft_sourceanalysis(cfg, avg);<br><br></div><div>
<pre class="gmail-code"><font face="arial,helvetica,sans-serif">In the LCMV results I plotted the two dipoles showing the maximum power at two grid locations.Note that the originally placed dipoles are red and the reconstructed dipoles are blue in colour.<br>But the results show that these reconstructed dipoles are really deviated from their original locations.<br><br>It would be really helpful for me if I could get some suggestions on what could I possibly be doing wrong.<br><br></font></pre><pre class="gmail-code"><font face="arial,helvetica,sans-serif">Thanking you.<br></font></pre><pre class="gmail-code"><font face="arial,helvetica,sans-serif">Kind Regards,<br></font></pre><pre class="gmail-code"><font face="arial,helvetica,sans-serif">Sushain Magotra<br><span style="font-family:monospace,monospace">Research Fellow IRTG ELAINE<br>University of Rostock<br>Institute of General Electrical Engineering<br>Albert-Einstein-Str. 2<br>D-18059 Rostcok<br>Germany</span><br></font></pre><pre class="gmail-code"><font face="arial,helvetica,sans-serif"><br></font></pre>
<br></div><div><br></div><div><br></div></div>