<html dir="ltr">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<style type="text/css" id="owaParaStyle"></style>
</head>
<body style="word-wrap:break-word" fpstyle="1" ocsi="0">
<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Hi Julian,
<div><br>
</div>
<div>Thank you very much for your help now it is completely clear for me.</div>
<div><br>
</div>
<div>Parinaz.<br>
<div style="font-family: Times New Roman; color: #000000; font-size: 16px">
<hr tabindex="-1">
<div id="divRpF45187" 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 5:57 PM<br>
<b>To:</b> FieldTrip discussion list<br>
<b>Subject:</b> Re: [FieldTrip] Extracting virtual EEG channel from a patch<br>
</font><br>
</div>
<div></div>
<div>Hi Parinaz,
<div><br>
</div>
<div>
<blockquote type="cite"><span class="Apple-style-span" style="border-collapse:separate; font-family:Helvetica; font-style:normal; font-variant:normal; font-weight:normal; letter-spacing:normal; line-height:normal; orphans:2; text-indent:0px; text-transform:none; white-space:normal; widows:2; word-spacing:0px; font-size:medium">
<div style="word-wrap:break-word">
<div style="direction:ltr; font-family:Tahoma; color:rgb(0,0,0); font-size:10pt">
<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>
</div>
</div>
</span></blockquote>
<div><br>
</div>
You don't. You compute your virtual channels for a regular grid (something like -20:1:20 for x,y and z) and select the virtual channels in your ROI in a second step.</div>
<div>This might be a bit of an overkill, as you don't use most of your channels later on, but maybe you want to extend your analysis to other cortical areas - you never know.</div>
<div><br>
</div>
<div>Anyways, to be more clear: You compute your virtual electrodes on a predefined grid. To find your ROI, you use ft_volumelookup to get a binary matrix which tells you, which voxels of the standard MRI are in your ROI. Then you build a high-resolution grid
based on the standard MRI (It's important to use one grid point per voxel). Using pythagoras, you can now find the closest high-resolution grid points for each of your virtual electrodes. As soon as you have these, you can see which of them have a value of
1 in your binary matrix of ft_volumelookup. Now you know which virtual electrodes are inside your ROI.</div>
<div><br>
</div>
<div>So for example, you have 2000 virtual electrodes on a -20:1:20 regular grid. You then compute a binary matrix and a high-resolution grid based on the standard MRI resulting in ~900000 grid points on a 91x109x91 grid. Using pythagoras, you find that grid
point 6000 is closest to virtual electrode #1. Then you can see if element 6000 from your binary matrix is a 1. If so, your virtual electrode #1 is in your ROI, if not, your virtual electrode is not in your ROI.</div>
<div><br>
</div>
<div>
<blockquote type="cite"><span class="Apple-style-span" style="border-collapse:separate; font-family:Helvetica; font-style:normal; font-variant:normal; font-weight:normal; letter-spacing:normal; line-height:normal; orphans:2; text-indent:0px; text-transform:none; white-space:normal; widows:2; word-spacing:0px; font-size:medium">
<div style="word-wrap:break-word">
<div style="direction:ltr; font-family:Tahoma; color:rgb(0,0,0); font-size:10pt">
<div><span style="font-size:10pt">How I can find the atlas position to this maximum point in my code</span></div>
</div>
</div>
</span></blockquote>
<div><br>
</div>
Do you want to have the coordinates or the actual label? A while ago, I hacked the ft_sourceplot-function to give me the coordinate position as an output, but I can't find the code anymore. I'm sure you can edit the function to also output the label, as this
has to be included as a text element somewhere in the function. But please be aware that editing the FT-functions can severely compromise the functionality.</div>
<div><br>
</div>
<div>Good luck,</div>
<div><br>
</div>
<div>Julian<br>
<br>
</div>
<div><br>
</div>
<div><br>
<div>
<div>Am 07.12.2015 um 12:52 schrieb Babaeeghazvini, P.:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite"><span class="Apple-style-span" style="border-collapse:separate; font-family:Helvetica; font-style:normal; font-variant:normal; font-weight:normal; letter-spacing:normal; line-height:normal; orphans:2; text-indent:0px; text-transform:none; white-space:normal; widows:2; word-spacing:0px; font-size:medium">
<div style="word-wrap:break-word">
<div style="direction:ltr; font-family:Tahoma; color:rgb(0,0,0); font-size:10pt">
Hi <font size="2">Julian,</font>
<div><br>
</div>
<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>
<div><br>
</div>
<div>
<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)"><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-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;
<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>
</div>
<div><br>
</div>
<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>
<div><span style="font-size:13.3333px"><br>
</span></div>
<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>
<div><span style="font-size:10pt"><br>
</span></div>
<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>
<div><span style="font-size:10pt"><br>
</span></div>
<div><span style="font-size:10pt">Regards,</span></div>
<div><span style="font-size:10pt">Parinaz.</span></div>
<p class="p2"><br>
</p>
<div><br>
</div>
<div><br>
</div>
<div>
<div style="font-family:'Times New Roman'; color:rgb(0,0,0); font-size:16px">
<div id="divRpF885871" style="direction:ltr"><font face="Tahoma" size="2" color="#000000"><b>From:</b><span class="Apple-converted-space"> </span><a href="mailto:fieldtrip-bounces@science.ru.nl" target="_blank">fieldtrip-bounces@science.ru.nl</a><span class="Apple-converted-space"> </span>[<a href="mailto:fieldtrip-bounces@science.ru.nl" target="_blank">fieldtrip-bounces@science.ru.nl</a>]
on behalf of Julian Keil [<a href="mailto:julian.keil@gmail.com" target="_blank">julian.keil@gmail.com</a>]<br>
<b>Sent:</b><span class="Apple-converted-space"> </span>Monday, December 07, 2015 9:30 AM<br>
<b>To:</b><span class="Apple-converted-space"> </span>FieldTrip discussion list<br>
<b>Subject:</b><span class="Apple-converted-space"> </span>Re: [FieldTrip] Extracting virtual EEG channel from a patch<br>
</font><br>
</div>
<div></div>
<div>Hi Parinaz,
<div><br>
</div>
<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>
<div><br>
</div>
<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>
<div><br>
</div>
<div>I hope this helps, let me know otherwise.</div>
<div><br>
</div>
<div>Julian</div>
<div><br>
<div>
<div>Am 04.12.2015 um 20:14 schrieb Babaeeghazvini, P.:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite"><span class="Apple-style-span" style="border-collapse:separate; font-family:Helvetica">
<div>
<div style="direction:ltr; font-family:Tahoma; color:rgb(0,0,0); font-size:10pt">
<div style="font-family:'Times New Roman'; color:rgb(0,0,0); font-size:16px">
<div id="divRpF893157" style="direction:ltr"><span style="font-size:10pt; font-family:Tahoma">Hello</span></div>
<div>
<div style="direction:ltr; font-family:Tahoma; color:rgb(0,0,0); font-size:10pt">
<div style="direction:ltr">
<div style="color:rgb(0,0,0); font-family:Tahoma; font-size:10pt"><br>
</div>
<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>
<div style="color:rgb(0,0,0); font-family:Tahoma; font-size:10pt">
<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>
</div>
<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>
<div><span style="font-size:10pt"><br>
</span></div>
<div><span style="font-size:10pt">Regards,</span></div>
<div><span style="font-size:10pt">Parinaz.</span></div>
</div>
</div>
</div>
</div>
</div>
_______________________________________________<br>
fieldtrip mailing list<br>
<a href="mailto:fieldtrip@donders.ru.nl" target="_blank">fieldtrip@donders.ru.nl</a><br>
<a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip" target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a></div>
</span></blockquote>
</div>
<br>
</div>
</div>
</div>
</div>
</div>
_______________________________________________<br>
fieldtrip mailing list<br>
<a href="mailto:fieldtrip@donders.ru.nl" target="_blank">fieldtrip@donders.ru.nl</a><br>
<a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip" target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a></div>
</span></blockquote>
</div>
<br>
</div>
</div>
</div>
</div>
</div>
</body>
</html>