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Hi all,<br>
<br>
From the previous email it seems that I'm doing something wrong
then. I have previously used the MNI-aligned subject grid (warped
template) for the positions, hence I didn't encounter any problem.
However, this seems to be wrong, as Jorn suggested. The question is
the following:<br>
<br>
The sourcediff.avg.pow is produced using the warped MNI template,
therefore the grid positions and indexes will be different from the
subject-specific MRI. Specifically in my case, the warped template
has 11000 x 3 pos, whereas the subject-specific has 2652 x 3. <br>
My question is, when I therefore index the maxpos using:<br>
<br>
[maxval, maxind] = max(sourcediff.avg.pow), my index is 3171, which
exceeds the matrix dimensions of the subject-specific MRI (2652). <br>
<br>
Which step am I missing?<br>
<br>
Thanks for your help in advance,<br>
Elisa<br>
<br>
<br>
<br>
<br>
<br>
<br>
<div class="moz-cite-prefix">On 07/08/2013 13:52, "Jörn M. Horschig"
wrote:<br>
</div>
<blockquote cite="mid:52024310.1020109@donders.ru.nl" type="cite">
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<div class="moz-cite-prefix">Dear Charidimos,<br>
<br>
thanks very much for pointing to this, it is indeed an error in
the appendix of the tutorial. cfg.grid.pos should be based on
the subject-specific MRI or sourcemodel. So, correctly it should
say that you need to load sourcemodel.mat (i.e. subject specific
grid) and then use sourcemodel.pos(maxpowindx, :) <br>
The rationale in principle is that the warped grid has the same
size and is indexed the same as the original grid; that is why
you can use the index variable obtained from the MNI-warped
source reconstructed data. The virtual channel reconstruction
should however still be done in whatever coordinate system the
subject's anatomical data is in. I will update the appendix
accordingly.<br>
<br>
Best,<br>
Jörn<br>
<br>
On 8/6/2013 8:24 PM, Charidimos Tzagarakis wrote:<br>
</div>
<blockquote
cite="mid:CAFN2X+fdvTW8jkx1EPS8C+J_FGRTQgTtYL38aYw7Gv6BbLtsxg@mail.gmail.com"
type="cite">Hi there, <br>
I have a question regarding virtual electrodes: How can I double
check that the MNI coordinates that I enter are correctly
interpreted?<br>
More specifically:<br>
I have followed the the extended beamforming tutorial in the
"Appendix" and have been able to transpose it to my data (I have
4D/BTi MEG files and Dicom mri volumes).The part I am not
certain about is the call to the LCMV beamformer.<br>
Here it is in my case ( I just want to get the voxel were the
power is max in the previous analysis):<br>
cfg = [];<br>
cfg.method = 'lcmv';<br>
cfg.vol = volfcm;<br>
cfg.grid.pos = source_diff.pos(maxpowindx, :);<br>
cfg.grid.inside = 1:size(cfg.grid.pos, 1);<br>
cfg.grid.outside = [];<br>
cfg.grad=senscm<br>
source_idx = ft_sourceanalysis(cfg, tlock);<br>
My headmodel does not include MEG channel information so I need
to also define the cfg.grad parameter. What I don't understand
is how cfg.grid.pos (which is in MNI coordinates as per the
previous part of the tutorial) can be correctly applied to the
coordinates of the headmodel and the channels since these 2 are
not in MNI coordinates (in my case they are in 4d/Bti
coordinates and rescaled to cm).In the previous part of the
tutorial this is (if I understand correctly) accomplished
because the leadfield used when calling ft_sourceanalysis was
created using and MNI-warped template. I don't see where the
equivalent part is when estimating the virtual electrode though.<br>
Any advice you may have would be much appreciated.<br>
Best,<br>
Haris<br>
<br>
<br>
Charidimos [Haris] Tzagarakis MD, PhD, MRCPsych <br>
University of Minnesota Dept of Neuroscience and Brain Sciences
Center <br>
<br>
<br>
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<pre class="moz-signature" cols="72">--
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team
P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands
Contact:
E-Mail: <a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:jm.horschig@donders.ru.nl">jm.horschig@donders.ru.nl</a>
Tel: +31-(0)24-36-68493
Web: <a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://www.ru.nl/donders">http://www.ru.nl/donders</a>
Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands</pre>
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