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Hi Juan,
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<div>We’ll look into this specific issue soon, it should work without specifying sensor positions. However, for now and in general I would recommend just using a pre-cooked template grid. These can be found in fieldtrip/template/sourcemodel. This is mentioned
in the tutorial, and I will make this more explicit shortly.</div>
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<div>Best,</div>
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<div>Jan-Mathijs</div>
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<div>On Dec 11, 2015, at 11:43 AM, Juan <<a href="mailto:juangpc@gmail.com">juangpc@gmail.com</a>> wrote:</div>
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<div class="gmail_default" style="font-family:tahoma,sans-serif;color:#333333">Dear Community, <br>
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<div style="font-family:tahoma,sans-serif;color:rgb(51,51,51)">My name is Juan Garcia-Prieto and I am working in Madrid's MEG Lab. Currently I am learning to do beamforming source analysis using Fieldtrip. </div>
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While following the tutorial: "<a href="http://goog_2124598831/" target="_blank"><span></span>Creating a sourcemodel for source-reconstruction of MEG or EEG data</a>
<div style="font-family:tahoma,sans-serif;color:rgb(51,51,51);display:inline"><a href="http:/" target="_blank"><span></span></a>"</div>
<div style="font-family:tahoma,sans-serif;color:rgb(51,51,51);display:inline"></div>
<span style="color:rgb(51,51,51);font-family:tahoma,sans-serif">
<div style="font-family:tahoma,sans-serif;color:rgb(51,51,51);display:inline"> when I reach "</div>
</span>Subject-specific grids that are equivalent across subjects in normalized space
<div style="font-family:tahoma,sans-serif;color:rgb(51,51,51);display:inline">" procedure , there is an example code. This code throws an error when I execute it with a version of Fieldtrip I downloaded yesterday. I think I have downloaded correctly all the
required info (Subject01.zip).</div>
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<div><font color="#333333" face="tahoma, sans-serif">Code: </font></div>
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<pre style="padding: 0.5em; margin-top: 0px; margin-bottom: 1em; 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);"><span style="padding:0px;margin:0px;color:rgb(128,128,128);font-style:italic">% NOTE: the path to the template file is user-specific</span>
template = ft_read_mri<span style="padding:0px;margin:0px;color:rgb(102,204,102)">(</span><span style="padding:0px;margin:0px;color:rgb(128,128,128);font-style:italic">'~/matlab/fieldtrip/external/spm8/templates/T1.nii'</span><span style="padding:0px;margin:0px;color:rgb(102,204,102)">)</span>;
template.<span style="padding:0px;margin:0px;color:rgb(0,102,0)">coordsys</span> = <span style="padding:0px;margin:0px;color:rgb(128,128,128);font-style:italic">'spm'</span>; <span style="padding:0px;margin:0px;color:rgb(128,128,128);font-style:italic">% so that FieldTrip knows how to interpret the coordinate system</span>
<span style="padding:0px;margin:0px;color:rgb(128,128,128);font-style:italic">% segment the template brain and construct a volume conduction model (i.e. head model): </span>
<span style="padding:0px;margin:0px;color:rgb(128,128,128);font-style:italic">% this is needed to describe the boundary that define which dipole locations are 'inside' the brain.</span>
cfg = <span style="padding:0px;margin:0px;color:rgb(102,204,102)">[</span><span style="padding:0px;margin:0px;color:rgb(102,204,102)">]</span>;
template_seg = ft_volumesegment<span style="padding:0px;margin:0px;color:rgb(102,204,102)">(</span>cfg, template<span style="padding:0px;margin:0px;color:rgb(102,204,102)">)</span>;
cfg = <span style="padding:0px;margin:0px;color:rgb(102,204,102)">[</span><span style="padding:0px;margin:0px;color:rgb(102,204,102)">]</span>;
cfg.<span style="padding:0px;margin:0px;color:rgb(0,102,0)">method</span> = <span style="padding:0px;margin:0px;color:rgb(128,128,128);font-style:italic">'singleshell'</span>;
template_headmodel = ft_prepare_headmodel<span style="padding:0px;margin:0px;color:rgb(102,204,102)">(</span>cfg, template_seg<span style="padding:0px;margin:0px;color:rgb(102,204,102)">)</span>;
template_headmodel = ft_convert_units<span style="padding:0px;margin:0px;color:rgb(102,204,102)">(</span>template_headmodel, <span style="padding:0px;margin:0px;color:rgb(128,128,128);font-style:italic">'cm'</span><span style="padding:0px;margin:0px;color:rgb(102,204,102)">)</span>; <span style="padding:0px;margin:0px;color:rgb(128,128,128);font-style:italic">% Convert the vol to cm, because the CTF convenction is to express everything in cm.</span>
<span style="padding:0px;margin:0px;color:rgb(128,128,128);font-style:italic">% construct the dipole grid in the template brain coordinates</span>
<span style="padding:0px;margin:0px;color:rgb(128,128,128);font-style:italic">% the negative inwardshift means an outward shift of the brain surface for inside/outside detection</span>
cfg = <span style="padding:0px;margin:0px;color:rgb(102,204,102)">[</span><span style="padding:0px;margin:0px;color:rgb(102,204,102)">]</span>;
cfg.<a href="http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html" title="" style="padding:0px;margin:0px;color:rgb(0,136,204);text-decoration:none" target="_blank"><span style="padding: 0px; margin: 0px; font-weight: bold;">grid</span></a>.<span style="padding:0px;margin:0px;color:rgb(0,102,0)">resolution</span> = <span style="padding:0px;margin:0px;color:rgb(204,102,204)">1</span>;
cfg.<a href="http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html" title="" style="padding:0px;margin:0px;color:rgb(0,136,204);text-decoration:none" target="_blank"><span style="padding: 0px; margin: 0px; font-weight: bold;">grid</span></a>.<span style="padding:0px;margin:0px;color:rgb(0,102,0)">tight</span> = <span style="padding:0px;margin:0px;color:rgb(128,128,128);font-style:italic">'yes'</span>;
cfg.<span style="padding:0px;margin:0px;color:rgb(0,102,0)">inwardshift</span> = -<span style="padding:0px;margin:0px;color:rgb(204,102,204)">1.5</span>;
<div style="font-family:tahoma,sans-serif;color:rgb(51,51,51);display:inline"></div>cfg.<span style="padding:0px;margin:0px;color:rgb(0,102,0)">headmodel</span> = template_headmodel;
<br></pre>
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<div style="font-family:tahoma,sans-serif;color:rgb(51,51,51)">The problem occurs when I execute this line:</div>
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<pre style="padding: 0.5em; margin-top: 0px; margin-bottom: 1em; 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);"><div style="font-family:tahoma,sans-serif;color:rgb(51,51,51);display:inline"></div><div style="font-family:tahoma,sans-serif;color:rgb(51,51,51);display:inline"></div><div style="font-family:tahoma,sans-serif;color:rgb(51,51,51);display:inline"></div><div style="font-family:tahoma,sans-serif;color:rgb(51,51,51);display:inline"></div>template_grid = ft_prepare_sourcemodel<span style="padding:0px;margin:0px;color:rgb(102,204,102)">(</span>cfg<span style="padding:0px;margin:0px;color:rgb(102,204,102)">)</span>;</pre>
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<div><font color="#333333" face="tahoma, sans-serif">Matlab's output: </font></div>
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<span style="color:rgb(51,51,51);font-family:tahoma,sans-serif">>> template_grid = ft_prepare_sourcemodel(cfg);</span><br>
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<div><font color="#333333" face="tahoma, sans-serif">creating dipole grid based on automatic 3D grid with specified resolution</font></div>
<div><font face="tahoma, sans-serif" color="#ff0000">Error using ft_prepare_sourcemodel (line 317)</font></div>
<div><font face="tahoma, sans-serif"><font color="#ff0000">creating a 3D-grid sourcemodel this way requires sensor position information to estimate the extent of the brain
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<div style="font-family:tahoma,sans-serif;color:rgb(51,51,51);display:inline"><br>
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<div style="font-family:tahoma,sans-serif;color:rgb(51,51,51);display:inline">I have managed to look around and found that you can specify the required "sensor position information" by executing this code just before (considering the folder with the information
downloaded for this subject is located just there:</div>
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<div style="font-family:tahoma,sans-serif;color:rgb(51,51,51);display:inline">
<pre style="padding: 0.5em; margin-top: 0px; margin-bottom: 1em; 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);"><div style="font-family:tahoma,sans-serif;color:rgb(51,51,51);display:inline">cfg.gradfile='Subject01\Subject01.ds\Subject01.res4';</div>
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<div>Then the rest of the sample code in the tutorial can be executed with no issues. <br>
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<pre style="padding: 0.5em; margin-top: 0px; margin-bottom: 1em; 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);">template_grid = ft_prepare_sourcemodel<span style="padding:0px;margin:0px;color:rgb(102,204,102)">(</span>cfg<span style="padding:0px;margin:0px;color:rgb(102,204,102)">)</span>;
<span style="padding:0px;margin:0px;color:rgb(128,128,128);font-style:italic">% make a figure with the template head model and dipole grid</span>
<a href="http://www.mathworks.com/access/helpdesk/help/techdoc/ref/figure.html" title="" style="padding:0px;margin:0px;color:rgb(0,136,204);text-decoration:none" target="_blank"><span style="padding: 0px; margin: 0px; font-weight: bold;">figure</span></a>
<a href="http://www.mathworks.com/access/helpdesk/help/techdoc/ref/hold.html" title="" style="padding:0px;margin:0px;color:rgb(0,136,204);text-decoration:none" target="_blank"><span style="padding: 0px; margin: 0px; font-weight: bold;">hold</span></a> on
ft_plot_vol<span style="padding:0px;margin:0px;color:rgb(102,204,102)">(</span>template_vol, <span style="padding:0px;margin:0px;color:rgb(128,128,128);font-style:italic">'facecolor'</span>, <span style="padding:0px;margin:0px;color:rgb(128,128,128);font-style:italic">'cortex'</span>, <span style="padding:0px;margin:0px;color:rgb(128,128,128);font-style:italic">'edgecolor'</span>, <span style="padding:0px;margin:0px;color:rgb(128,128,128);font-style:italic">'none'</span><span style="padding:0px;margin:0px;color:rgb(102,204,102)">)</span>;alpha <span style="padding:0px;margin:0px;color:rgb(204,102,204)">0.5</span>; <a href="http://www.mathworks.com/access/helpdesk/help/techdoc/ref/camlight.html" title="" style="padding:0px;margin:0px;color:rgb(0,136,204);text-decoration:none" target="_blank"><span style="padding: 0px; margin: 0px; font-weight: bold;">camlight</span></a>;
ft_plot_mesh<span style="padding:0px;margin:0px;color:rgb(102,204,102)">(</span>template_grid.<span style="padding:0px;margin:0px;color:rgb(0,102,0)">pos</span><span style="padding:0px;margin:0px;color:rgb(102,204,102)">(</span>template_grid.<span style="padding:0px;margin:0px;color:rgb(0,102,0)">inside</span>,:<span style="padding:0px;margin:0px;color:rgb(102,204,102)">)</span><span style="padding:0px;margin:0px;color:rgb(102,204,102)">)</span>;</pre>
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<div style="font-family:tahoma,sans-serif;color:rgb(51,51,51);display:inline"><br>
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<div style="font-family:tahoma,sans-serif;color:rgb(51,51,51);display:inline">My questions: </div>
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<div style="font-family:tahoma,sans-serif;color:rgb(51,51,51);display:inline"><br>
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<div style="font-family:tahoma,sans-serif;color:rgb(51,51,51)">Is there a better solution for this problem? Maybe I can learn a little bit more about the toolbox with your answers. </div>
<div style="font-family:tahoma,sans-serif;color:rgb(51,51,51)"><br>
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<div style="font-family:tahoma,sans-serif;color:rgb(51,51,51)">I didn't want to correct the wiki because my solution depends on where one is placing the downloaded subject's data, and it is platform dependent. Should I add something to the tutorial anyway?
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I figure this can be interesting to other people.</div>
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<div style="font-family:tahoma,sans-serif;color:rgb(51,51,51)"><br>
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<div style="font-family:tahoma,sans-serif;color:rgb(51,51,51)">Best,</div>
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<div><span style="color:rgb(153,153,153)"><br>
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<div><span style="color:rgb(153,153,153)">Juan</span></div>
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