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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Hi <font size="2">Julian,</font>
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<div>Thank you very much for your kind reply. Yes I want to compute virtual channel from an atlas area like whole Precentral_L (not from one voxel in this area). So your second explanation helps me. If I understood correctly in the code below I should use <font size="2">all
grid points belong to atlas:</font></div>
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<pre class="code" style="padding: 0.5em; margin-top: 0px; margin-bottom: 1em; margin-left: -10px; font-size: 12px; border: 1px dashed rgb(204, 204, 204); overflow: hidden; font-family: Consolas, 'Andale Mono', Menlo, Monaco, monospace; white-space: pre-wrap; width: 640px; text-align: justify; background-color: rgb(247, 249, 250);"><p class="p1">cfg = []</p><p class="p1">cfg.atlas = atlas;</p><p class="p1">cfg.roi = atlas.tissuelabel(1)</p><p class="p1">cfg.inputcoord = <span class="s1">'mni'</span>;</p><p class="p1">mas = ft_volumelookup(cfg,grid);</p></pre>
<pre class="code" style="padding: 0.5em; margin-top: 0px; margin-bottom: 1em; margin-left: -10px; font-size: 12px; border: 1px dashed rgb(204, 204, 204); overflow: hidden; font-family: Consolas, 'Andale Mono', Menlo, Monaco, monospace; white-space: pre-wrap; width: 640px; text-align: justify; background-color: rgb(247, 249, 250);">cfg = [];
cfg.method = 'lcmv';
cfg.vol = hdm;
<p class="p1">cfg.grid.xgrid = </p><p class="p1">cfg.grid.ygrid = </p><p class="p1">cfg.grid.zgrid = </p>cfg.grid.inside = 1:size(cfg.grid.pos, 1);
cfg.grid.outside = [];
cfg.keepfilter = 'yes';
source_idx = ft_sourceanalysis(cfg, tlock);</pre>
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<div>My problem is how I should use the output of volumelookup here for cfg.grid.xgrid, <span style="font-size: 13.3333px;">cfg.grid.ygrid and </span><span style="font-size: 13.3333px;">cfg.grid.zgrid.</span></div>
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<div><span style="font-size: 13.3333px;">an other question that I have is that: when I compute the maximum index from </span></div>
<div><span style="font-size: 10pt;"> [maxvalr, maxpowindxr] = max(srcetask.avg.pow)</span></div>
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<div><span style="font-size: 10pt;">How I can find the atlas position to this maximum point in my code (I can see this atlas label in the figure that I get from sourceplot, but I want to report this label in matlab)</span></div>
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<div><span style="font-size: 10pt;">Regards,</span></div>
<div><span style="font-size: 10pt;">Parinaz.</span></div>
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<div id="divRpF885871" style="direction: ltr;"><font face="Tahoma" size="2" color="#000000"><b>From:</b> fieldtrip-bounces@science.ru.nl [fieldtrip-bounces@science.ru.nl] on behalf of Julian Keil [julian.keil@gmail.com]<br>
<b>Sent:</b> Monday, December 07, 2015 9:30 AM<br>
<b>To:</b> FieldTrip discussion list<br>
<b>Subject:</b> Re: [FieldTrip] Extracting virtual EEG channel from a patch<br>
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<div>Hi Parinaz,
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<div>I'm not sure if I understood your question correctly.</div>
<div>Do you want to find the atlas label to a given virtual channel? Or do you want to compute a virtual channel on a given atlas label?</div>
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<div>In the first case, you can simply interpolate your virtual EEG channels to the standard MRI and use source plot with an atlas to find the corresponding label.</div>
<div>In the second case, it's a tad more complicated, but here's how I do it:</div>
<div>1. Compute the virtual channels for all grid points in the cortex</div>
<div>2. If you have computed the virtual channels on an individual MRI, make sure that the positions correspond to the standard MRI (I think that's described in the source analysis-tutorial)</div>
<div>3. Build a high-resolution 3D-Grid on the standard MRI</div>
<div>4. Select all grid points from the grid of step 3 which belong to an atlas (see ft_volumelookup)</div>
<div>5. Use pythagoras to find the virtual channels from step 2 closest to the grid points from step 4.</div>
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<div>I hope this helps, let me know otherwise.</div>
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<div>Julian</div>
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<div>Am 04.12.2015 um 20:14 schrieb Babaeeghazvini, P.:</div>
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<div id="divRpF893157" style="direction:ltr"><span style="font-size:10pt; font-family:Tahoma">Hello</span></div>
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<div style="color:rgb(0,0,0); font-family:Tahoma; font-size:10pt">I want to reconstruct a source signal the same as below in page <a href="http://www.fieldtriptoolbox.org/tutorial/shared/virtual_sensors" style="font-size:10pt" target="_blank">http://www.fieldtriptoolbox.org/tutorial/shared/virtual_sensors</a></div>
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<pre class="code" style="padding-top:0.5em; padding-right:0.5em; padding-bottom:0.5em; padding-left:0.5em; margin-top:0px; margin-bottom:1em; margin-left:-10px; font-size:12px; border-top-width:1px; border-right-width:1px; border-bottom-width:1px; border-left-width:1px; border-top-style:dashed; border-right-style:dashed; border-bottom-style:dashed; border-left-style:dashed; border-top-color:rgb(204,204,204); border-right-color:rgb(204,204,204); border-bottom-color:rgb(204,204,204); border-left-color:rgb(204,204,204); overflow-x:hidden; overflow-y:hidden; font-family:Consolas,'Andale Mono',Menlo,Monaco,monospace; white-space:pre-wrap; width:640px; text-align:justify; background-color:rgb(247,249,250)">cfg = [];
cfg.method = 'lcmv';
cfg.vol = hdm;
cfg.grid.pos = sourcemodel.pos([maxcohindx maxpowindx], :);
cfg.grid.inside = 1:size(cfg.grid.pos, 1);
cfg.grid.outside = [];
cfg.keepfilter = 'yes';
source_idx = ft_sourceanalysis(cfg, tlock);</pre>
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<div><span style="font-size:10pt">Not from the voxel indicating maximum power (</span><span style="color:rgb(0,0,0); font-family:Consolas,'Andale Mono',Menlo,Monaco,monospace; font-size:12px; text-align:justify; white-space:pre-wrap; background-color:rgb(247,249,250)">[maxval,
maxpowindx] = max(source_diff.avg.pow);</span><span style="color:rgb(0,0,0); font-family:Tahoma; font-size:10pt">), but from the atlas area which this voxel belongs to, such as </span>Supp_Motor_Area_L. So my question is: How I can get the atlas range and
atlas label belong to a voxel, and how I can use this atlas area range in this code to reconstruct a signal instead of using (<span style="font-family:Consolas,'Andale Mono',Menlo,Monaco,monospace; font-size:12px; text-align:justify; white-space:pre-wrap; background-color:rgb(247,249,250)">cfg.grid.pos
= sourcemodel.pos([maxcohindx maxpowindx], :)</span><span style="font-size:10pt">).</span></div>
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<div><span style="font-size:10pt">Regards,</span></div>
<div><span style="font-size:10pt">Parinaz.</span></div>
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