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<p style="">I then do the following:<br>
</p>
<p style=""><br>
</p>
<div>% look up which virtual channels correspond to particular areas</div>
<div> % of the brain</div>
<div> cfg = [];</div>
<div> cfg.atlas = afni;</div>
<div> cfg.inputcoord = 'mni';</div>
<div> cfg.maskparameter = 'inside';</div>
<div> labels = ft_volumelookup( cfg, source);</div>
<div> </div>
<div> % how many sources found in grey matter</div>
<div> [tmp ind] = sort(labels.count,1,'descend');</div>
<div> sel = find(tmp);</div>
<div> for j = 1:length(sel)</div>
<div> found_areas{j,1} = [num2str(labels.count(ind(j))) ': ' labels.name{ind(j)}];</div>
<div style=""> end<br>
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<div style="">However I dont know how to find out what sources are the 'found_areas', after that I dont know how to cluster the source in a particular area.<br>
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<div style="">Tyler<br>
</div>
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<div><font face="Arial"><i>Tyler Grummett ( BBSc, BSc(Hons I))</i></font></div>
<div><font face="Arial"><i>PhD Candidate</i></font></div>
<div><font face="Arial"><i>Brain Signals Laboratory</i></font></div>
<div><font face="Arial"><i>Flinders University</i></font></div>
<div><font face="Arial"><i>Rm 5A301</i></font></div>
<div><font face="Arial"><i>Ext 66124</i></font></div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> fieldtrip-bounces@science.ru.nl <fieldtrip-bounces@science.ru.nl> on behalf of Tyler Grummett <tyler.grummett@flinders.edu.au><br>
<b>Sent:</b> Wednesday, 28 May 2014 3:53 PM<br>
<b>To:</b> FieldTrip discussion list<br>
<b>Subject:</b> Re: [FieldTrip] granger causality on beamformer data</font>
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<p style="">Hello Julian,<br>
</p>
<p style=""><br>
</p>
<p style="">I think I got a few steps further into what I am trying to do, except I dont know whether I have done the correct thing or not, could you check it?<br>
</p>
<p style=""><br>
</p>
<p style=""></p>
<div style=""> % interpolate sources</div>
<div> mri = ft_read_mri('Subject01.mri');</div>
<div> mri = ft_volumereslice([], mri);</div>
<div> </div>
<div> % read in atlas from fieldtrip template</div>
<div> afni = ft_read_atlas( fullfile( matlabrootpath, 'Matlab/fieldtrip/template/atlas/afni/TTatlas+tlrc.HEAD'));</div>
<div> </div>
<div> % construct grid that lies only in grey matter</div>
<div> cfg = [];</div>
<div> cfg.mri = mri;</div>
<div> cfg.grid.warpmni = 'yes';</div>
<div> cfg.grid = afni;</div>
<div style=""> grid = ft_prepare_sourcemodel( cfg);<br>
</div>
<div> </div>
<div> % Source Analysis: without contrasting condition</div>
<div> cfg = [];</div>
<div> cfg.channel = 'EEG';</div>
<div> cfg.method = 'lcmv';</div>
<div> cfg.grid = grid;</div>
<div> cfg.vol = vol;</div>
<div> cfg.keepfilter = 'yes';</div>
<div style=""> source = ft_sourceanalysis( cfg, timelock);<br>
</div>
<p style=""></p>
<p style="">Tyler<br>
</p>
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<div><font face="Arial"><i>Tyler Grummett ( BBSc, BSc(Hons I))</i></font></div>
<div><font face="Arial"><i>PhD Candidate</i></font></div>
<div><font face="Arial"><i>Brain Signals Laboratory</i></font></div>
<div><font face="Arial"><i>Flinders University</i></font></div>
<div><font face="Arial"><i>Rm 5A301</i></font></div>
<div><font face="Arial"><i>Ext 66124</i></font></div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> fieldtrip-bounces@science.ru.nl <fieldtrip-bounces@science.ru.nl> on behalf of Tyler Grummett <tyler.grummett@flinders.edu.au><br>
<b>Sent:</b> Wednesday, 28 May 2014 10:36 AM<br>
<b>To:</b> FieldTrip discussion list<br>
<b>Subject:</b> Re: [FieldTrip] granger causality on beamformer data</font>
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<p style="">Hey Julian,<br>
</p>
<p style=""><br>
</p>
<p style="">Having trouble making sense of that link. Am I correct in saying that I should be downloading the brede toolbox? because it is taking a long time, plus the functions in the brede toolbox dont make a lot of sense.<br>
</p>
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</p>
<p style="">Would you use ft_prepare_sourcemodel instead of ft_prepare_leadfield? or would you run in before running it?<br>
</p>
<p style=""><br>
</p>
<p style="">Regards,<br>
</p>
<p style=""><br>
</p>
<p style="">Tyler<br>
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<div style="font-family:Tahoma"><br>
</div>
<div><font face="Arial"><i>Tyler Grummett ( BBSc, BSc(Hons I))</i></font></div>
<div><font face="Arial"><i>PhD Candidate</i></font></div>
<div><font face="Arial"><i>Brain Signals Laboratory</i></font></div>
<div><font face="Arial"><i>Flinders University</i></font></div>
<div><font face="Arial"><i>Rm 5A301</i></font></div>
<div><font face="Arial"><i>Ext 66124</i></font></div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><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> Wednesday, 28 May 2014 1:55 AM<br>
<b>To:</b> FieldTrip discussion list<br>
<b>Subject:</b> Re: [FieldTrip] granger causality on beamformer data</font>
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<div>Hi Tyler,<br>
<br>
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I can't comment on the usefulness of directionality between 1400 sources, but keep in mind, that you would have to compute something in the range of 1400*1400
<br>
connections, so I hope you have a fast computer.<br>
<br>
</div>
As for the regions, in case you want to use anatomically defined regions, you an either use the atlases (atlanti? atlae?) that come with fieldtrip or generate a mask from this website:
<a href="http://neuro.imm.dtu.dk/services/jerne/ninf/voi.html">http://neuro.imm.dtu.dk/services/jerne/ninf/voi.html</a><br>
<br>
</div>
<div>The general idea is to build a grid with a gridpoint per voxel of your MRI using ft_prepare_sourcemodel. Then you can check which of your virtual channels is closest to the voxel-gridpoints and thus select the virtual channels that are inside your ROI.<br>
</div>
<div><br>
</div>
In the first case, you can use ft_volumelookup to find the voxels corresponding to your ROI. In the latter case you can just use the mask and check which voxels are 1 (= inside your ROI).<br>
<br>
I hope that helps, if you have specific questions, feel free to ask.<br>
<br>
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Best,<br>
<br>
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Julian<br>
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<div class="gmail_quote">On Tue, May 27, 2014 at 7:44 AM, Tyler Grummett <span dir="ltr">
<<a href="mailto:tyler.grummett@flinders.edu.au" target="_blank">tyler.grummett@flinders.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex; border-left:1px #ccc solid; padding-left:1ex">
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<p>Hello fieldtrippers,<br>
</p>
<p><br>
</p>
<p>I was just wondering whether it would be sensible to do granger causality on all 1400 virtual channels, as calculated using beamformer.<br>
</p>
<p><br>
</p>
<p>Or should you do a PCA reduction of some description beforehand.<br>
</p>
<p><br>
</p>
<p>I was also wondering how to create regions of interest. Some of my colleagues think that we should use some kind of spatial ICA technique.<br>
</p>
<p><br>
</p>
<p>Im open to all suggestions.<br>
</p>
<p><br>
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<p>Tyler<br>
</p>
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<div style="font-size:13px">*************************
<div style="font-family:Tahoma"><br>
</div>
<div><font face="Arial"><i>Tyler Grummett ( BBSc, BSc(Hons I))</i></font></div>
<div><font face="Arial"><i>PhD Candidate</i></font></div>
<div><font face="Arial"><i>Brain Signals Laboratory</i></font></div>
<div><font face="Arial"><i>Flinders University</i></font></div>
<div><font face="Arial"><i>Rm 5A301</i></font></div>
<div><font face="Arial"><i>Ext 66124</i></font></div>
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