[FieldTrip] question about virtual electrode MNI coordinates
"Jörn M. Horschig"
jm.horschig at donders.ru.nl
Thu Aug 8 13:45:09 CEST 2013
Dear Elisa,
hard to tell, because you are not telling us exactly what you are doing :)
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.
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 :)
Best,
Jörn
On 8/8/2013 12:23 PM, Elisa Carrus wrote:
> Hi all,
>
> 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:
>
> 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.
> My question is, when I therefore index the maxpos using:
>
> [maxval, maxind] = max(sourcediff.avg.pow), my index is 3171, which
> exceeds the matrix dimensions of the subject-specific MRI (2652).
>
> Which step am I missing?
>
> Thanks for your help in advance,
> Elisa
>
>
>
>
>
>
> On 07/08/2013 13:52, "Jörn M. Horschig" wrote:
>> Dear Charidimos,
>>
>> 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, :)
>> 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.
>>
>> Best,
>> Jörn
>>
>> On 8/6/2013 8:24 PM, Charidimos Tzagarakis wrote:
>>> Hi there,
>>> I have a question regarding virtual electrodes: How can I double
>>> check that the MNI coordinates that I enter are correctly interpreted?
>>> More specifically:
>>> 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.
>>> Here it is in my case ( I just want to get the voxel were the power
>>> is max in the previous analysis):
>>> cfg = [];
>>> cfg.method = 'lcmv';
>>> cfg.vol = volfcm;
>>> cfg.grid.pos = source_diff.pos(maxpowindx, :);
>>> cfg.grid.inside = 1:size(cfg.grid.pos, 1);
>>> cfg.grid.outside = [];
>>> cfg.grad=senscm
>>> source_idx = ft_sourceanalysis(cfg, tlock);
>>> 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.
>>> Any advice you may have would be much appreciated.
>>> Best,
>>> Haris
>>>
>>>
>>> Charidimos [Haris] Tzagarakis MD, PhD, MRCPsych
>>> University of Minnesota Dept of Neuroscience and Brain Sciences Center
>>>
>>>
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>>
>> --
>> 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:jm.horschig at donders.ru.nl
>> Tel: +31-(0)24-36-68493
>> Web:http://www.ru.nl/donders
>>
>> Visiting address:
>> Trigon, room 2.30
>> Kapittelweg 29
>> NL-6525 EN Nijmegen
>> The Netherlands
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
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--
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: jm.horschig at donders.ru.nl
Tel: +31-(0)24-36-68493
Web: http://www.ru.nl/donders
Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands
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