[FieldTrip] question about virtual electrode MNI coordinates
Elisa Carrus
elisa at csl.psychol.cam.ac.uk
Fri Aug 9 11:25:15 CEST 2013
Dear Jorn,
ah, I apologise for not writing a complete email! The good news is that
I've done things correctly so far, as I do have the same number of grid
points in both the subject-specific and template, as expected :) I gave
you the wrong indices because I thought that in your previous email you
referred to the MRI rather than the sourcemodel. My bad. Sorry for the
misunderstanding and thanks a lot for explaining this again!
Best,
Elisa
On 08/08/2013 12:45, "Jörn M. Horschig" wrote:
> 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
>> 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
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