Thanks, Arjen and Gio,<br><br>I played around with cfg.inwardshift during ft_sourceanalysis, and adjusting it to somewhere between .25 and .5 gives decent results (it was originally set to 1), i.e. good coverage with no shrinkage. <div>
<br></div><div>I'm actually a little confused about why one might need cfg.inwardshift parameter... Assuming the segmentation into different tissue types goes correctly, is it best to set the inwardshift parameters as close to 0 as possible (or not specify), since we'd want to put dipoles ranging the whole volume of the brain? <div>
<br></div><div>Thanks! Akiko <div><br><div class="gmail_quote">On Thu, Mar 29, 2012 at 5:13 AM, Gio Piantoni <span dir="ltr"><<a href="mailto:g.piantoni@nin.knaw.nl">g.piantoni@nin.knaw.nl</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Akiko,<br>
<br>
Your headmodel looks pretty good and your beamformer plot seems to<br>
cover most of the gray matter.<br>
<br>
However, it's good to check the location of your dipoles in respect to<br>
your headmodel. For example, you can plot the .pos field of your<br>
leadfield. Something like:<br>
<br>
ft_plot_mesh(bnd(3), 'facealpha', .5)<br>
hold on<br>
plot3(lead.pos(:,1), lead.pos(:,2), lead.pos(:,3), '.')<br>
<br>
It might well be that your grid is too coarse and some dipoles just<br>
happen to be over the edge of the brain. Remember that your<br>
"beamformer_result.png" is just an interpolation of the values of this<br>
dipole grid.<br>
<br>
You can either try to make your grid more refined (but remember that<br>
your computation time will significantly increase). Or you can<br>
manipulate the way dipoles are considered inside or outside the brain<br>
with "inwardshift" for ft_prepare_leadfield (although I'd advise<br>
against using a negative value as some dipoles might really end up<br>
outside of your brain mesh, with some numerical instabilities).<br>
Another option (the easiest) is to nudge your grid by, say, a few<br>
millimeters, so that the parietal dipoles will be just inside the<br>
brain mesh.<br>
<br>
HTH,<br>
<br>
Gio<br>
<span class="HOEnZb"><font color="#888888"><br>
--<br>
Giovanni Piantoni, MSc<br>
Dept. Sleep & Cognition<br>
Netherlands Institute for Neuroscience<br>
Meibergdreef 47<br>
1105 BA Amsterdam (NL)<br>
<br>
<a href="tel:%2B31%2020%205665492" value="+31205665492">+31 20 5665492</a><br>
<a href="mailto:gio@gpiantoni.com">gio@gpiantoni.com</a><br>
<a href="http://www.gpiantoni.com" target="_blank">www.gpiantoni.com</a><br>
</font></span><div class="HOEnZb"><div class="h5"><br>
On Thu, Mar 29, 2012 at 00:22, Akiko Ikkai <<a href="mailto:akiko.ikkai@gmail.com">akiko.ikkai@gmail.com</a>> wrote:<br>
> Hi Fieldtrip users,<br>
><br>
> I'm hoping that someone could give me advice on segmentation and beamformer<br>
> on EEG data. I have EEG data set based on 128 channel cap. Thanks to the<br>
> help I got in mid-Feb, I'm now able to create a decent<br>
> segmentation (seg_results image attached) and volume conduction model.<br>
> However, when I run beamformer based on these models, resulting beamforming<br>
> image is often smaller than the brain (beamformer_result attached).<br>
> Particularly posterior parietal and occipital map is NaN.<br>
><br>
> I have tried going back to segmentation and expanded brain by using imdilate<br>
> after ft_volumesegment such as:<br>
><br>
> newbrain = imdilate(seg2.brain,strel_bol(1)); % seg2.brain is original brain<br>
> tissue from segmentation<br>
><br>
> seg2.brain = newbrain;<br>
><br>
> seg2.seg = seg2.scalp + seg2.skull*3 + seg2.brain*6;<br>
><br>
> and run ft_prepare_mesh_new on seg2. Of course, I have to make sure there is<br>
> no intersect between different tissue types, so using imdilate has<br>
> limitation.<br>
><br>
> Could someone explain why this shrinkage might be happening, and how I could<br>
> fix it?<br>
><br>
> Thanks in advance! Akiko<br>
><br>
> --<br>
> Akiko Ikkai, Ph.D.<br>
> Postdoctoral Fellow<br>
> Department of Psychological and Brain Sciences<br>
> Johns Hopkins University<br>
> Ames Hall, 3400 N. Charles St.<br>
> Baltimore, MD 21218<br>
><br>
><br>
><br>
</div></div><div class="HOEnZb"><div class="h5">> _______________________________________________<br>
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<br>
_______________________________________________<br>
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<a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip" target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a></div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br><font><span style="font-family:arial,helvetica,sans-serif">Akiko Ikkai, Ph.D. <br>
Postdoctoral Fellow<br style="font-family:arial,helvetica,sans-serif"></span></font><font style="font-family:arial,helvetica,sans-serif" face="'PrimaSans BT,Verdana,sans-serif'" size="2">Department of
Psychological and Brain Sciences<br>Johns Hopkins University<br>Ames
Hall, 3400 N. Charles St.<br>Baltimore, MD 21218</font><br style="font-family:arial,helvetica,sans-serif"><br><br>
</div></div></div>