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<div class="moz-cite-prefix">Dear Elisa,<br>
<br>
hard to tell, because you are not telling us exactly what you are
doing :) <br>
The idea in the extended beamforming tutorial is that you first
create an MNI template sourcemodel (or grid). Subsequently, you
use exactly this grid and spatially transform it such that it fits
to the subject-specific brain, based on the MRI. After following
these steps, by definition, the number of grid points in the
subject-specific grid and the MNI grid are the same - just the
place where the grid points end up did change. (Otherwise, it
would also not be possible to replace the .pos field from the
source-reconstructed data by the template grid, as being done in
the plotting part of the tutorial). The problem in the tutorial
was exactly this replacement of the position description (which
iself can be a perfectly fine step as e.g. earlier in the
tutorial). Since we provide a sourcemodel based on the subject's
mri, we need to specify the position based on that mri/sourcemodel
and not based on the MNI template.<br>
<br>
You, obviously, do not have the same number of grid points for the
subject-specific sourcemodel as in the template sourcemodel. I
cannot guarantee that what you did is correct, but at least I can
tell you that what you did is not affects by this - else you would
have had the same number of elements for both sourcemodels. I
cross my fingers that you're doing the right thing :)<br>
<br>
Best,<br>
Jörn<br>
<br>
On 8/8/2013 12:23 PM, Elisa Carrus wrote:<br>
</div>
<blockquote cite="mid:520371B9.8060101@csl.psychol.cam.ac.uk"
type="cite">
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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
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NL-6500 HB Nijmegen
The Netherlands
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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 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 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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