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Good evening, </div>
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hope you are all doing fine!</div>
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We are trying to compute the source analysis on our 180 channels EEG recording and we are experiencing some issues. </div>
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Unfortunately, we don't have either single-subject MRI and the electrode position registration, therefore we are relying on Fieldtrips' sourcemodel and headmodel files. </div>
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We first aligned our EEG channel location to the headmodel (standard_BEM) using the command:</div>
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<p class="p1" style="margin:0px;font:10px Courier">elec= freqPre.elec;</p>
<p class="p1" style="margin:0px;font:10px Courier">headtemp= ft_convert_units(headmodel,<span class="s1" style="color:rgb(178, 69, 243)">'cm'</span>);</p>
<p class="p2" style="margin:0px;font:10px Courier;min-height:12px"><span class="Apple-converted-space"> </span></p>
<p class="p1" style="margin:0px;font:10px Courier">cfg = [];</p>
<p class="p1" style="margin:0px;font:10px Courier">cfg.method<span class="Apple-converted-space">
</span>= <span class="s1" style="color:rgb(178, 69, 243)">'project'</span>;</p>
<p class="p1" style="margin:0px;font:10px Courier">cfg.elec<span class="Apple-converted-space">
</span>= elec;</p>
<p class="p1" style="margin:0px;font:10px Courier">cfg.channel <span class="Apple-converted-space">
</span>= lay.label;</p>
<p class="p1" style="margin:0px;font:10px Courier">cfg.headshape = headtemp.bnd;</p>
<p class="p1" style="margin:0px;font:10px Courier">elec_aligned = ft_electroderealign(cfg);</p>
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and checked the solution using the function ft_prepare_vol_sens</div>
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<p class="p2" style="margin:0px;font:10px Courier">cfg= [];</p>
<p class="p1" style="margin:0px;font:10px Courier;color:rgb(37, 153, 45)"><span class="s1" style="color:rgb(0, 0, 0)">cfg.headmodel= headtemp;
</span>%structure with volume conductor definition</p>
<p class="p1" style="margin:0px;font:10px Courier;color:rgb(37, 153, 45)"><span class="s1" style="color:rgb(0, 0, 0)">cfg.sens
<span class="Apple-converted-space"> </span>= elec_aligned; </span>%elec_aligned; %structure with gradiometer or electrode definition</p>
<p class="p2" style="margin:0px;font:10px Courier">[headmodel, elec_new] = ft_prepare_vol_sens(headtemp, elec_aligned);</p>
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</p>
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<p style="margin:0in 0in 0.0001pt"><span style="margin:0px; font-size:12pt; color:black">We then loaded the sourcemodel "standard_sourcemodel3d10mm.mat" <span style="background-color:rgb(255, 255, 255);display:inline !important">from the Fieldtrip sourcemodel
template<span> and </span></span></span><span style="color: black; font-size: 12pt;">computed the leadfield with the following command:</span></p>
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</span></p>
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</span></p>
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<p class="p1" style="margin:0px;font:10px Courier">cfg<span class="Apple-converted-space">
</span>= []; </p>
<p class="p1" style="margin:0px;font:10px Courier">cfg.elec <span class="Apple-converted-space">
</span>= elec_new;</p>
<p class="p1" style="margin:0px;font:10px Courier">cfg.headmodel<span class="Apple-converted-space">
</span>= headmodel;</p>
<p class="p1" style="margin:0px;font:10px Courier">cfg.sourcemodel<span class="Apple-converted-space">
</span>= sourcemodel;</p>
<p class="p1" style="margin:0px;font:10px Courier">cfg.resolution <span class="Apple-converted-space">
</span>= 1;<span class="Apple-converted-space"> </span></p>
<p class="p1" style="margin:0px;font:10px Courier">cfg.sourcemodel.unit = <span class="s1" style="color:rgb(178, 69, 243)">
'cm'</span>;</p>
<p class="p1" style="margin:0px;font:10px Courier">sourcemodel_and_leadfield = ft_prepare_leadfield(cfg);</p>
<p style="margin:0in 0in 0.0001pt"><span style="margin:0px; font-size:12pt; color:black"><br>
</span></p>
<p style="margin:0in 0in 0.0001pt"><span style="margin:0px; font-size:12pt; color:black">Although the leadfield structure contains values in mV, when we try to plot the leadfield (as displayed in this Fieldtrip tutorial:<a href="https://www.fieldtriptoolbox.org/workshop/oslo2019/forward_modeling/" id="LPlnk942480">https://www.fieldtriptoolbox.org/workshop/oslo2019/forward_modeling/</a>)
our voltage distribution is zero. </span></p>
<p style="margin:0in 0in 0.0001pt"><span style="color: black; font-size: 12pt;">We also tried to change the source index but we are never able to obtain a voltage distribution. </span></p>
<p style="margin:0in 0in 0.0001pt"><span style="color: black; font-size: 12pt;"><br>
</span></p>
<p style="margin:0in 0in 0.0001pt"><span style="color: black; font-size: 12pt;">Are we missing a necessary step? Does somebody have any advice? </span></p>
<p style="margin:0in 0in 0.0001pt"><span style="color: black; font-size: 12pt;"><br>
</span></p>
<p style="margin:0in 0in 0.0001pt"><span style="color: black; font-size: 12pt;">Any advice would be greatly appreciated! </span></p>
<p style="margin:0in 0in 0.0001pt"><span style="color: black; font-size: 12pt;"><br>
</span></p>
<p style="margin:0in 0in 0.0001pt"><span style="color: black; font-size: 12pt;">Thank you in advance for your attention.</span></p>
<p style="margin:0in 0in 0.0001pt"><span style="color: black; font-size: 12pt;"><br>
</span></p>
<p style="margin:0in 0in 0.0001pt"><span style="color: black; font-size: 12pt;">Elisa and Francesca</span></p>
<p style="margin:0in 0in 0.0001pt"><span style="color: black; font-size: 12pt;"><br>
</span></p>
<p style="margin:0in 0in 0.0001pt"><span style="color: black; font-size: 12pt;"><br>
</span></p>
<p style="margin:0in 0in 0.0001pt"><span style="margin:0px; font-size:12pt; color:black"><br>
</span></p>
<p style="margin:0in 0in 0.0001pt"><span style="margin:0px; font-size:12pt; color:black">Below we report the code we used to plot the leadfield: </span></p>
<p style="margin:0in 0in 0.0001pt"><span style="margin:0px; font-size:12pt; color:black"><br>
</span></p>
<p style="margin:0in 0in 0.0001pt"><span style="margin:0px; font-size:12pt; color:black"></span></p>
<pre class="highlight" style="box-sizing:border-box;font-family:SFMono-Regular, Menlo, Monaco, Consolas, "Liberation Mono", "Courier New", monospace;font-size:13.2px;margin-top:0px;margin-bottom:0px;overflow:auto;display:block;color:rgb(33, 37, 41);background:rgb(240, 240, 240);text-align:left"><code style="box-sizing:border-box"><span class="nb" style="box-sizing:border-box;color:rgb(0, 112, 32)">figure</span><span class="p" style="box-sizing:border-box">(</span><span class="s1" style="box-sizing:border-box;color:rgb(64, 112, 160)">'units'</span><span class="p" style="box-sizing:border-box">,</span> <span class="s1" style="box-sizing:border-box;color:rgb(64, 112, 160)">'normalized'</span><span class="p" style="box-sizing:border-box">,</span> <span class="s1" style="box-sizing:border-box;color:rgb(64, 112, 160)">'outerposition'</span><span class="p" style="box-sizing:border-box">,</span> <span class="p" style="box-sizing:border-box">[</span><span class="mi" style="box-sizing:border-box;color:rgb(64, 160, 112)">0</span> <span class="mi" style="box-sizing:border-box;color:rgb(64, 160, 112)">0</span> <span class="mf" style="box-sizing:border-box;color:rgb(64, 160, 112)">0.5</span> <span class="mf" style="box-sizing:border-box;color:rgb(64, 160, 112)">0.5</span><span class="p" style="box-sizing:border-box">])</span>
<span class="n" style="box-sizing:border-box">source_index</span> <span class="o" style="box-sizing:border-box;color:rgb(102, 102, 102)">=</span> <span class="mi" style="box-sizing:border-box;color:rgb(64, 160, 112)">1200</span><span class="p" style="box-sizing:border-box">;</span> <span class="c1" style="box-sizing:border-box;color:rgb(96, 160, 176);font-style:italic">%% a superficial sources</span>
<span class="n" style="box-sizing:border-box">sensory_dipole_current</span> <span class="o" style="box-sizing:border-box;color:rgb(102, 102, 102)">=</span> <span class="mf" style="box-sizing:border-box;color:rgb(64, 160, 112)">100e-9</span><span class="p" style="box-sizing:border-box">;</span> <span class="c1" style="box-sizing:border-box;color:rgb(96, 160, 176);font-style:italic">% Am (realistic)</span>
<span class="n" style="box-sizing:border-box">n_sensors</span> <span class="o" style="box-sizing:border-box;color:rgb(102, 102, 102)">=</span> <span class="nb" style="box-sizing:border-box;color:rgb(0, 112, 32)">length</span><span class="p" style="box-sizing:border-box">(</span><span class="n" style="box-sizing:border-box">elec_realigned</span><span class="o" style="box-sizing:border-box;color:rgb(102, 102, 102)">.</span><span class="n" style="box-sizing:border-box">label</span><span class="p" style="box-sizing:border-box">);</span>
<span class="n" style="box-sizing:border-box">inside_sources</span> <span class="o" style="box-sizing:border-box;color:rgb(102, 102, 102)">=</span> <span class="nb" style="box-sizing:border-box;color:rgb(0, 112, 32)">find</span><span class="p" style="box-sizing:border-box">(</span><span class="n" style="box-sizing:border-box">sourcemodel_and_leadfield</span><span class="o" style="box-sizing:border-box;color:rgb(102, 102, 102)">.</span><span class="n" style="box-sizing:border-box">inside</span><span class="p" style="box-sizing:border-box">);</span>
<span class="n" style="box-sizing:border-box">inside_index</span> <span class="o" style="box-sizing:border-box;color:rgb(102, 102, 102)">=</span> <span class="n" style="box-sizing:border-box">inside_sources</span><span class="p" style="box-sizing:border-box">(</span><span class="n" style="box-sizing:border-box">source_index</span><span class="p" style="box-sizing:border-box">);</span>
<span class="n" style="box-sizing:border-box">lead</span> <span class="o" style="box-sizing:border-box;color:rgb(102, 102, 102)">=</span> <span class="n" style="box-sizing:border-box">sourcemodel_and_leadfield</span><span class="o" style="box-sizing:border-box;color:rgb(102, 102, 102)">.</span><span class="n" style="box-sizing:border-box">leadfield</span><span class="p" style="box-sizing:border-box">{</span><span class="n" style="box-sizing:border-box">inside_index</span><span class="p" style="box-sizing:border-box">};</span>
<span class="n" style="box-sizing:border-box">xs</span> <span class="o" style="box-sizing:border-box;color:rgb(102, 102, 102)">=</span> <span class="nb" style="box-sizing:border-box;color:rgb(0, 112, 32)">zeros</span><span class="p" style="box-sizing:border-box">(</span><span class="mi" style="box-sizing:border-box;color:rgb(64, 160, 112)">1</span><span class="p" style="box-sizing:border-box">,</span> <span class="n" style="box-sizing:border-box">n_sensors</span><span class="p" style="box-sizing:border-box">);</span>
<span class="n" style="box-sizing:border-box">ys</span> <span class="o" style="box-sizing:border-box;color:rgb(102, 102, 102)">=</span> <span class="nb" style="box-sizing:border-box;color:rgb(0, 112, 32)">zeros</span><span class="p" style="box-sizing:border-box">(</span><span class="mi" style="box-sizing:border-box;color:rgb(64, 160, 112)">1</span><span class="p" style="box-sizing:border-box">,</span> <span class="n" style="box-sizing:border-box">n_sensors</span><span class="p" style="box-sizing:border-box">);</span>
<span class="n" style="box-sizing:border-box">zs</span> <span class="o" style="box-sizing:border-box;color:rgb(102, 102, 102)">=</span> <span class="nb" style="box-sizing:border-box;color:rgb(0, 112, 32)">zeros</span><span class="p" style="box-sizing:border-box">(</span><span class="mi" style="box-sizing:border-box;color:rgb(64, 160, 112)">1</span><span class="p" style="box-sizing:border-box">,</span> <span class="n" style="box-sizing:border-box">n_sensors</span><span class="p" style="box-sizing:border-box">);</span>
<span class="n" style="box-sizing:border-box">voltages</span> <span class="o" style="box-sizing:border-box;color:rgb(102, 102, 102)">=</span> <span class="nb" style="box-sizing:border-box;color:rgb(0, 112, 32)">zeros</span><span class="p" style="box-sizing:border-box">(</span><span class="mi" style="box-sizing:border-box;color:rgb(64, 160, 112)">1</span><span class="p" style="box-sizing:border-box">,</span> <span class="n" style="box-sizing:border-box">n_sensors</span><span class="p" style="box-sizing:border-box">);</span>
<span class="n" style="box-sizing:border-box">titles</span> <span class="o" style="box-sizing:border-box;color:rgb(102, 102, 102)">=</span> <span class="p" style="box-sizing:border-box">{</span><span class="s1" style="box-sizing:border-box;color:rgb(64, 112, 160)">'Lead field (x)'</span> <span class="s1" style="box-sizing:border-box;color:rgb(64, 112, 160)">'Lead field (y)'</span> <span class="s1" style="box-sizing:border-box;color:rgb(64, 112, 160)">'Lead field (z)'</span><span class="p" style="box-sizing:border-box">};</span>
<span class="c1" style="box-sizing:border-box;color:rgb(96, 160, 176);font-style:italic">% get the xyz and norm</span>
<span class="k" style="box-sizing:border-box;color:rgb(0, 112, 32);font-weight:bold">for</span> <span class="n" style="box-sizing:border-box">sensor_index</span> <span class="o" style="box-sizing:border-box;color:rgb(102, 102, 102)">=</span> <span class="mi" style="box-sizing:border-box;color:rgb(64, 160, 112)">1</span><span class="p" style="box-sizing:border-box">:</span><span class="n" style="box-sizing:border-box">n_sensors</span>
<span class="n" style="box-sizing:border-box">this_x</span> <span class="o" style="box-sizing:border-box;color:rgb(102, 102, 102)">=</span> <span class="n" style="box-sizing:border-box">lead</span><span class="p" style="box-sizing:border-box">(</span><span class="n" style="box-sizing:border-box">sensor_index</span><span class="p" style="box-sizing:border-box">,</span> <span class="mi" style="box-sizing:border-box;color:rgb(64, 160, 112)">1</span><span class="p" style="box-sizing:border-box">);</span>
<span class="n" style="box-sizing:border-box">this_y</span> <span class="o" style="box-sizing:border-box;color:rgb(102, 102, 102)">=</span> <span class="n" style="box-sizing:border-box">lead</span><span class="p" style="box-sizing:border-box">(</span><span class="n" style="box-sizing:border-box">sensor_index</span><span class="p" style="box-sizing:border-box">,</span> <span class="mi" style="box-sizing:border-box;color:rgb(64, 160, 112)">2</span><span class="p" style="box-sizing:border-box">);</span>
<span class="n" style="box-sizing:border-box">this_z</span> <span class="o" style="box-sizing:border-box;color:rgb(102, 102, 102)">=</span> <span class="n" style="box-sizing:border-box">lead</span><span class="p" style="box-sizing:border-box">(</span><span class="n" style="box-sizing:border-box">sensor_index</span><span class="p" style="box-sizing:border-box">,</span> <span class="mi" style="box-sizing:border-box;color:rgb(64, 160, 112)">3</span><span class="p" style="box-sizing:border-box">);</span>
<span class="n" style="box-sizing:border-box">this_norm</span> <span class="o" style="box-sizing:border-box;color:rgb(102, 102, 102)">=</span> <span class="nb" style="box-sizing:border-box;color:rgb(0, 112, 32)">norm</span><span class="p" style="box-sizing:border-box">(</span><span class="n" style="box-sizing:border-box">lead</span><span class="p" style="box-sizing:border-box">(</span><span class="n" style="box-sizing:border-box">sensor_index</span><span class="p" style="box-sizing:border-box">,</span> <span class="p" style="box-sizing:border-box">:));</span>
<span class="n" style="box-sizing:border-box">xs</span><span class="p" style="box-sizing:border-box">(</span><span class="n" style="box-sizing:border-box">sensor_index</span><span class="p" style="box-sizing:border-box">)</span> <span class="o" style="box-sizing:border-box;color:rgb(102, 102, 102)">=</span> <span class="n" style="box-sizing:border-box">this_x</span> <span class="o" style="box-sizing:border-box;color:rgb(102, 102, 102)">*</span> <span class="n" style="box-sizing:border-box">sensory_dipole_current</span><span class="p" style="box-sizing:border-box">;</span>
<span class="n" style="box-sizing:border-box">ys</span><span class="p" style="box-sizing:border-box">(</span><span class="n" style="box-sizing:border-box">sensor_index</span><span class="p" style="box-sizing:border-box">)</span> <span class="o" style="box-sizing:border-box;color:rgb(102, 102, 102)">=</span> <span class="n" style="box-sizing:border-box">this_y</span> <span class="o" style="box-sizing:border-box;color:rgb(102, 102, 102)">*</span> <span class="n" style="box-sizing:border-box">sensory_dipole_current</span><span class="p" style="box-sizing:border-box">;</span>
<span class="n" style="box-sizing:border-box">zs</span><span class="p" style="box-sizing:border-box">(</span><span class="n" style="box-sizing:border-box">sensor_index</span><span class="p" style="box-sizing:border-box">)</span> <span class="o" style="box-sizing:border-box;color:rgb(102, 102, 102)">=</span> <span class="n" style="box-sizing:border-box">this_z</span> <span class="o" style="box-sizing:border-box;color:rgb(102, 102, 102)">*</span> <span class="n" style="box-sizing:border-box">sensory_dipole_current</span><span class="p" style="box-sizing:border-box">;</span>
<span class="n" style="box-sizing:border-box">voltages</span><span class="p" style="box-sizing:border-box">(</span><span class="n" style="box-sizing:border-box">sensor_index</span><span class="p" style="box-sizing:border-box">)</span> <span class="o" style="box-sizing:border-box;color:rgb(102, 102, 102)">=</span> <span class="n" style="box-sizing:border-box">this_norm</span> <span class="o" style="box-sizing:border-box;color:rgb(102, 102, 102)">*</span> <span class="n" style="box-sizing:border-box">sensory_dipole_current</span><span class="p" style="box-sizing:border-box">;</span>
<span class="k" style="box-sizing:border-box;color:rgb(0, 112, 32);font-weight:bold">end</span>
<span class="c1" style="box-sizing:border-box;color:rgb(96, 160, 176);font-style:italic">% plot xyz</span>
<span class="nb" style="box-sizing:border-box;color:rgb(0, 112, 32)">axes</span> <span class="o" style="box-sizing:border-box;color:rgb(102, 102, 102)">=</span> <span class="p" style="box-sizing:border-box">{</span><span class="n" style="box-sizing:border-box">xs</span> <span class="n" style="box-sizing:border-box">ys</span> <span class="n" style="box-sizing:border-box">zs</span><span class="p" style="box-sizing:border-box">};</span>
<span class="k" style="box-sizing:border-box;color:rgb(0, 112, 32);font-weight:bold">for</span> <span class="n" style="box-sizing:border-box">axis_index</span> <span class="o" style="box-sizing:border-box;color:rgb(102, 102, 102)">=</span> <span class="mi" style="box-sizing:border-box;color:rgb(64, 160, 112)">1</span><span class="p" style="box-sizing:border-box">:</span><span class="mi" style="box-sizing:border-box;color:rgb(64, 160, 112)">3</span>
<span class="n" style="box-sizing:border-box">this_axis</span> <span class="o" style="box-sizing:border-box;color:rgb(102, 102, 102)">=</span> <span class="nb" style="box-sizing:border-box;color:rgb(0, 112, 32)">axes</span><span class="p" style="box-sizing:border-box">{</span><span class="n" style="box-sizing:border-box">axis_index</span><span class="p" style="box-sizing:border-box">};</span>
<span class="nb" style="box-sizing:border-box;color:rgb(0, 112, 32)">subplot</span><span class="p" style="box-sizing:border-box">(</span><span class="mi" style="box-sizing:border-box;color:rgb(64, 160, 112)">1</span><span class="p" style="box-sizing:border-box">,</span> <span class="mi" style="box-sizing:border-box;color:rgb(64, 160, 112)">3</span><span class="p" style="box-sizing:border-box">,</span> <span class="n" style="box-sizing:border-box">axis_index</span><span class="p" style="box-sizing:border-box">)</span>
<span class="nb" style="box-sizing:border-box;color:rgb(0, 112, 32)">hold</span> <span class="n" style="box-sizing:border-box">on</span>
<span class="n" style="box-sizing:border-box">ft_plot_topo3d</span><span class="p" style="box-sizing:border-box">(</span><span class="n" style="box-sizing:border-box">elec_realigned</span><span class="o" style="box-sizing:border-box;color:rgb(102, 102, 102)">.</span><span class="n" style="box-sizing:border-box">chanpos</span><span class="p" style="box-sizing:border-box">,</span> <span class="n" style="box-sizing:border-box">this_axis</span><span class="p" style="box-sizing:border-box">,</span> <span class="s1" style="box-sizing:border-box;color:rgb(64, 112, 160)">'facealpha'</span><span class="p" style="box-sizing:border-box">,</span> <span class="mf" style="box-sizing:border-box;color:rgb(64, 160, 112)">0.8</span><span class="p" style="box-sizing:border-box">)</span>
<span class="k" style="box-sizing:border-box;color:rgb(0, 112, 32);font-weight:bold">if</span> <span class="nb" style="box-sizing:border-box;color:rgb(0, 112, 32)">strcmp</span><span class="p" style="box-sizing:border-box">(</span><span class="n" style="box-sizing:border-box">headmodel</span><span class="o" style="box-sizing:border-box;color:rgb(102, 102, 102)">.</span><span class="nb" style="box-sizing:border-box;color:rgb(0, 112, 32)">type</span><span class="p" style="box-sizing:border-box">,</span> <span class="s1" style="box-sizing:border-box;color:rgb(64, 112, 160)">'dipoli'</span><span class="p" style="box-sizing:border-box">)</span>
<span class="nb" style="box-sizing:border-box;color:rgb(0, 112, 32)">caxis</span><span class="p" style="box-sizing:border-box">([</span><span class="o" style="box-sizing:border-box;color:rgb(102, 102, 102)">-</span><span class="mf" style="box-sizing:border-box;color:rgb(64, 160, 112)">10e-6</span><span class="p" style="box-sizing:border-box">,</span> <span class="mf" style="box-sizing:border-box;color:rgb(64, 160, 112)">10e-6</span><span class="p" style="box-sizing:border-box">])</span>
<span class="k" style="box-sizing:border-box;color:rgb(0, 112, 32);font-weight:bold">end</span>
<span class="n" style="box-sizing:border-box">c</span> <span class="o" style="box-sizing:border-box;color:rgb(102, 102, 102)">=</span> <span class="nb" style="box-sizing:border-box;color:rgb(0, 112, 32)">colorbar</span><span class="p" style="box-sizing:border-box">(</span><span class="s1" style="box-sizing:border-box;color:rgb(64, 112, 160)">'location'</span><span class="p" style="box-sizing:border-box">,</span> <span class="s1" style="box-sizing:border-box;color:rgb(64, 112, 160)">'southoutside'</span><span class="p" style="box-sizing:border-box">);</span>
<span class="n" style="box-sizing:border-box">c</span><span class="o" style="box-sizing:border-box;color:rgb(102, 102, 102)">.</span><span class="n" style="box-sizing:border-box">Label</span><span class="o" style="box-sizing:border-box;color:rgb(102, 102, 102)">.</span><span class="n" style="box-sizing:border-box">String</span> <span class="o" style="box-sizing:border-box;color:rgb(102, 102, 102)">=</span> <span class="s1" style="box-sizing:border-box;color:rgb(64, 112, 160)">'Lead field (V)'</span><span class="p" style="box-sizing:border-box">;</span>
<span class="nb" style="box-sizing:border-box;color:rgb(0, 112, 32)">axis</span> <span class="n" style="box-sizing:border-box">tight</span>
<span class="n" style="box-sizing:border-box">ft_plot_mesh</span><span class="p" style="box-sizing:border-box">(</span><span class="n" style="box-sizing:border-box">mesh_brain</span><span class="p" style="box-sizing:border-box">,</span> <span class="s1" style="box-sizing:border-box;color:rgb(64, 112, 160)">'facealpha'</span><span class="p" style="box-sizing:border-box">,</span> <span class="mf" style="box-sizing:border-box;color:rgb(64, 160, 112)">0.10</span><span class="p" style="box-sizing:border-box">);</span>
<span class="n" style="box-sizing:border-box">ft_plot_sens</span><span class="p" style="box-sizing:border-box">(</span><span class="n" style="box-sizing:border-box">elec_realigned</span><span class="p" style="box-sizing:border-box">,</span> <span class="s1" style="box-sizing:border-box;color:rgb(64, 112, 160)">'elecsize'</span><span class="p" style="box-sizing:border-box">,</span> <span class="mi" style="box-sizing:border-box;color:rgb(64, 160, 112)">20</span><span class="p" style="box-sizing:border-box">);</span>
<span class="nb" style="box-sizing:border-box;color:rgb(0, 112, 32)">title</span><span class="p" style="box-sizing:border-box">(</span><span class="n" style="box-sizing:border-box">titles</span><span class="p" style="box-sizing:border-box">{</span><span class="n" style="box-sizing:border-box">axis_index</span><span class="p" style="box-sizing:border-box">})</span>
<span class="nb" style="box-sizing:border-box;color:rgb(0, 112, 32)">plot3</span><span class="p" style="box-sizing:border-box">(</span><span class="n" style="box-sizing:border-box">sourcemodel_and_leadfield</span><span class="o" style="box-sizing:border-box;color:rgb(102, 102, 102)">.</span><span class="n" style="box-sizing:border-box">pos</span><span class="p" style="box-sizing:border-box">(</span><span class="n" style="box-sizing:border-box">inside_index</span><span class="p" style="box-sizing:border-box">,</span> <span class="mi" style="box-sizing:border-box;color:rgb(64, 160, 112)">1</span><span class="p" style="box-sizing:border-box">),</span> <span class="k" style="box-sizing:border-box;color:rgb(0, 112, 32);font-weight:bold">...</span>
<span class="n" style="box-sizing:border-box">sourcemodel_and_leadfield</span><span class="o" style="box-sizing:border-box;color:rgb(102, 102, 102)">.</span><span class="n" style="box-sizing:border-box">pos</span><span class="p" style="box-sizing:border-box">(</span><span class="n" style="box-sizing:border-box">inside_index</span><span class="p" style="box-sizing:border-box">,</span> <span class="mi" style="box-sizing:border-box;color:rgb(64, 160, 112)">2</span><span class="p" style="box-sizing:border-box">),</span> <span class="k" style="box-sizing:border-box;color:rgb(0, 112, 32);font-weight:bold">...</span>
<span class="n" style="box-sizing:border-box">sourcemodel_and_leadfield</span><span class="o" style="box-sizing:border-box;color:rgb(102, 102, 102)">.</span><span class="n" style="box-sizing:border-box">pos</span><span class="p" style="box-sizing:border-box">(</span><span class="n" style="box-sizing:border-box">inside_index</span><span class="p" style="box-sizing:border-box">,</span> <span class="mi" style="box-sizing:border-box;color:rgb(64, 160, 112)">3</span><span class="p" style="box-sizing:border-box">),</span> <span class="s1" style="box-sizing:border-box;color:rgb(64, 112, 160)">'bo'</span><span class="p" style="box-sizing:border-box">,</span> <span class="k" style="box-sizing:border-box;color:rgb(0, 112, 32);font-weight:bold">...</span>
<span class="s1" style="box-sizing:border-box;color:rgb(64, 112, 160)">'markersize'</span><span class="p" style="box-sizing:border-box">,</span> <span class="mi" style="box-sizing:border-box;color:rgb(64, 160, 112)">20</span><span class="p" style="box-sizing:border-box">,</span> <span class="s1" style="box-sizing:border-box;color:rgb(64, 112, 160)">'markerfacecolor'</span><span class="p" style="box-sizing:border-box">,</span> <span class="s1" style="box-sizing:border-box;color:rgb(64, 112, 160)">'r'</span><span class="p" style="box-sizing:border-box">)</span>
<span class="k" style="box-sizing:border-box;color:rgb(0, 112, 32);font-weight:bold">end</span>
<span class="c1" style="box-sizing:border-box;color:rgb(96, 160, 176);font-style:italic">% plot norm</span>
<span class="nb" style="box-sizing:border-box;color:rgb(0, 112, 32)">figure</span><span class="p" style="box-sizing:border-box">(</span><span class="s1" style="box-sizing:border-box;color:rgb(64, 112, 160)">'units'</span><span class="p" style="box-sizing:border-box">,</span> <span class="s1" style="box-sizing:border-box;color:rgb(64, 112, 160)">'normalized'</span><span class="p" style="box-sizing:border-box">,</span> <span class="s1" style="box-sizing:border-box;color:rgb(64, 112, 160)">'outerposition'</span><span class="p" style="box-sizing:border-box">,</span> <span class="p" style="box-sizing:border-box">[</span><span class="mi" style="box-sizing:border-box;color:rgb(64, 160, 112)">0</span> <span class="mi" style="box-sizing:border-box;color:rgb(64, 160, 112)">0</span> <span class="mf" style="box-sizing:border-box;color:rgb(64, 160, 112)">0.5</span> <span class="mf" style="box-sizing:border-box;color:rgb(64, 160, 112)">0.85</span><span class="p" style="box-sizing:border-box">])</span>
<span class="nb" style="box-sizing:border-box;color:rgb(0, 112, 32)">hold</span> <span class="n" style="box-sizing:border-box">on</span>
<span class="n" style="box-sizing:border-box">ft_plot_topo3d</span><span class="p" style="box-sizing:border-box">(</span><span class="n" style="box-sizing:border-box">elec_realigned</span><span class="o" style="box-sizing:border-box;color:rgb(102, 102, 102)">.</span><span class="n" style="box-sizing:border-box">chanpos</span><span class="p" style="box-sizing:border-box">,</span> <span class="n" style="box-sizing:border-box">voltages</span><span class="p" style="box-sizing:border-box">,</span> <span class="s1" style="box-sizing:border-box;color:rgb(64, 112, 160)">'facealpha'</span><span class="p" style="box-sizing:border-box">,</span> <span class="mf" style="box-sizing:border-box;color:rgb(64, 160, 112)">0.8</span><span class="p" style="box-sizing:border-box">)</span>
<span class="k" style="box-sizing:border-box;color:rgb(0, 112, 32);font-weight:bold">if</span> <span class="nb" style="box-sizing:border-box;color:rgb(0, 112, 32)">strcmp</span><span class="p" style="box-sizing:border-box">(</span><span class="n" style="box-sizing:border-box">headmodel</span><span class="o" style="box-sizing:border-box;color:rgb(102, 102, 102)">.</span><span class="nb" style="box-sizing:border-box;color:rgb(0, 112, 32)">type</span><span class="p" style="box-sizing:border-box">,</span> <span class="s1" style="box-sizing:border-box;color:rgb(64, 112, 160)">'dipoli'</span><span class="p" style="box-sizing:border-box">)</span>
<span class="nb" style="box-sizing:border-box;color:rgb(0, 112, 32)">caxis</span><span class="p" style="box-sizing:border-box">([</span><span class="mi" style="box-sizing:border-box;color:rgb(64, 160, 112)">0</span><span class="p" style="box-sizing:border-box">,</span> <span class="mf" style="box-sizing:border-box;color:rgb(64, 160, 112)">10e-6</span><span class="p" style="box-sizing:border-box">])</span>
<span class="k" style="box-sizing:border-box;color:rgb(0, 112, 32);font-weight:bold">end</span>
<span class="n" style="box-sizing:border-box">c</span> <span class="o" style="box-sizing:border-box;color:rgb(102, 102, 102)">=</span> <span class="nb" style="box-sizing:border-box;color:rgb(0, 112, 32)">colorbar</span><span class="p" style="box-sizing:border-box">(</span><span class="s1" style="box-sizing:border-box;color:rgb(64, 112, 160)">'location'</span><span class="p" style="box-sizing:border-box">,</span> <span class="s1" style="box-sizing:border-box;color:rgb(64, 112, 160)">'eastoutside'</span><span class="p" style="box-sizing:border-box">);</span>
<span class="n" style="box-sizing:border-box">c</span><span class="o" style="box-sizing:border-box;color:rgb(102, 102, 102)">.</span><span class="n" style="box-sizing:border-box">Label</span><span class="o" style="box-sizing:border-box;color:rgb(102, 102, 102)">.</span><span class="n" style="box-sizing:border-box">String</span> <span class="o" style="box-sizing:border-box;color:rgb(102, 102, 102)">=</span> <span class="s1" style="box-sizing:border-box;color:rgb(64, 112, 160)">'Lead field (V)'</span><span class="p" style="box-sizing:border-box">;</span>
<span class="nb" style="box-sizing:border-box;color:rgb(0, 112, 32)">axis</span> <span class="n" style="box-sizing:border-box">tight</span>
<span class="n" style="box-sizing:border-box">ft_plot_mesh</span><span class="p" style="box-sizing:border-box">(</span><span class="n" style="box-sizing:border-box">mesh_brain</span><span class="p" style="box-sizing:border-box">,</span> <span class="s1" style="box-sizing:border-box;color:rgb(64, 112, 160)">'facealpha'</span><span class="p" style="box-sizing:border-box">,</span> <span class="mf" style="box-sizing:border-box;color:rgb(64, 160, 112)">0.10</span><span class="p" style="box-sizing:border-box">);</span>
<span class="n" style="box-sizing:border-box">ft_plot_sens</span><span class="p" style="box-sizing:border-box">(</span><span class="n" style="box-sizing:border-box">elec_realigned</span><span class="p" style="box-sizing:border-box">,</span> <span class="s1" style="box-sizing:border-box;color:rgb(64, 112, 160)">'elecsize'</span><span class="p" style="box-sizing:border-box">,</span> <span class="mi" style="box-sizing:border-box;color:rgb(64, 160, 112)">20</span><span class="p" style="box-sizing:border-box">);</span>
<span class="nb" style="box-sizing:border-box;color:rgb(0, 112, 32)">title</span><span class="p" style="box-sizing:border-box">(</span><span class="s1" style="box-sizing:border-box;color:rgb(64, 112, 160)">'Leadfield magnitude'</span><span class="p" style="box-sizing:border-box">)</span>
<span class="nb" style="box-sizing:border-box;color:rgb(0, 112, 32)">plot3</span><span class="p" style="box-sizing:border-box">(</span><span class="n" style="box-sizing:border-box">sourcemodel_and_leadfield</span><span class="o" style="box-sizing:border-box;color:rgb(102, 102, 102)">.</span><span class="n" style="box-sizing:border-box">pos</span><span class="p" style="box-sizing:border-box">(</span><span class="n" style="box-sizing:border-box">inside_index</span><span class="p" style="box-sizing:border-box">,</span> <span class="mi" style="box-sizing:border-box;color:rgb(64, 160, 112)">1</span><span class="p" style="box-sizing:border-box">),</span> <span class="k" style="box-sizing:border-box;color:rgb(0, 112, 32);font-weight:bold">...</span>
<span class="n" style="box-sizing:border-box">sourcemodel_and_leadfield</span><span class="o" style="box-sizing:border-box;color:rgb(102, 102, 102)">.</span><span class="n" style="box-sizing:border-box">pos</span><span class="p" style="box-sizing:border-box">(</span><span class="n" style="box-sizing:border-box">inside_index</span><span class="p" style="box-sizing:border-box">,</span> <span class="mi" style="box-sizing:border-box;color:rgb(64, 160, 112)">2</span><span class="p" style="box-sizing:border-box">),</span> <span class="k" style="box-sizing:border-box;color:rgb(0, 112, 32);font-weight:bold">...</span>
<span class="n" style="box-sizing:border-box">sourcemodel_and_leadfield</span><span class="o" style="box-sizing:border-box;color:rgb(102, 102, 102)">.</span><span class="n" style="box-sizing:border-box">pos</span><span class="p" style="box-sizing:border-box">(</span><span class="n" style="box-sizing:border-box">inside_index</span><span class="p" style="box-sizing:border-box">,</span> <span class="mi" style="box-sizing:border-box;color:rgb(64, 160, 112)">3</span><span class="p" style="box-sizing:border-box">),</span> <span class="s1" style="box-sizing:border-box;color:rgb(64, 112, 160)">'bo'</span><span class="p" style="box-sizing:border-box">,</span> <span class="k" style="box-sizing:border-box;color:rgb(0, 112, 32);font-weight:bold">...</span>
<span class="s1" style="box-sizing:border-box;color:rgb(64, 112, 160)">'markersize'</span><span class="p" style="box-sizing:border-box">,</span> <span class="mi" style="box-sizing:border-box;color:rgb(64, 160, 112)">20</span><span class="p" style="box-sizing:border-box">,</span> <span class="s1" style="box-sizing:border-box;color:rgb(64, 112, 160)">'markerfacecolor'</span><span class="p" style="box-sizing:border-box">,</span> <span class="s1" style="box-sizing:border-box;color:rgb(64, 112, 160)">'r'</span><span class="p" style="box-sizing:border-box">)</span>
<span class="nb" style="box-sizing:border-box;color:rgb(0, 112, 32)">view</span><span class="p" style="box-sizing:border-box">(</span><span class="o" style="box-sizing:border-box;color:rgb(102, 102, 102)">-</span><span class="mi" style="box-sizing:border-box;color:rgb(64, 160, 112)">90</span><span class="p" style="box-sizing:border-box">,</span> <span class="mi" style="box-sizing:border-box;color:rgb(64, 160, 112)">0</span><span class="p" style="box-sizing:border-box">)</span></code></pre>
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<p style="margin:0in 0in 0.0001pt"><span style="margin:0px; font-size:12pt; color:black"><br>
Elisa Tatti, Ph.D</span></p>
<p style="margin:0in 0in 0.0001pt"><span style="margin:0px; font-size:12pt; color:black">Post Doctoral Research Fellow </span><span style="margin:0px; font-family:"Times New Roman",serif,serif,EmojiFont; font-size:12pt"><u></u><u></u></span></p>
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<p style="margin:0in 0in 0.0001pt"><span style="color:black; font-size:12pt">CUNY, School of Medicine </span><br>
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<p style="margin:0in 0in 0.0001pt"><span style="margin:0px; font-size:12pt; color:black">160 Convent ave</span><span style="margin:0px; font-family:"Times New Roman",serif,serif,EmojiFont; font-size:12pt"><u></u><u></u></span></p>
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<p style="margin:0in 0in 0.0001pt"><span style="margin:0px; font-size:12pt; color:black">10031 </span><span style="margin:0px; font-family:"Times New Roman",serif,serif,EmojiFont; font-size:12pt"><u></u><u></u></span></p>
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<p style="margin:0in 0in 0.0001pt"><span style="margin:0px; font-size:12pt; color:black">New York City, NY </span><span style="margin:0px; font-family:"Times New Roman",serif,serif,EmojiFont; font-size:12pt"><u></u><u></u></span></p>
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