[FieldTrip] ft_headmodelplot coordinate system origin problem

[jan-mathijs schoffelen]

Hi Ion,

I'd suggest first to have a look at mri_real. How does it look in ft_determine_coordsys?
In particular, is the z-axis pointing in the correct direction?

JM


On Jan 3, 2012, at 12:45 PM, Ion Lavado wrote:

> Hi Jan,
> I am sorry, I have been trying with your method but now what is incorrect is the segmentation. 
> Here is the script. Maybe you understand better the problem...I am getting crazy. The problem comes from line 53
> Thank you very much,
> Best,
> Ion
> 
> 
> 
> 2012/1/3 jan-mathijs schoffelen <jan.schoffelen at donders.ru.nl>
> Hi Ion,
> 
> What is the coordinate system in which the vol and mri are defined? To me it does not look like the neuromag coordinate system, but rather like MNI-space. I would expect the origin to be a bit (~4 cm) lower and a bit more anterior (because the origin is defined on the line going through the pre-auricular points. In the 'vol.jpg' it seems that the origin is in the anterior commissure. Although in principle it shouldn't matter, it is convention to express the coordinates in the MEG-system's coordinate system, i.e. in neuromag space in this case. Therefore I would say that the vol and grid variables need to be adjusted, rather than the sensor positions. As mentioned in my previoius message, this can be achieved by coregistering the anatomy to the neuromag coordinate system using ft_volumerealign. You need to manually identify the locations of the fiducials that define the coordinate system, i.e. the nasion, lpa and rpa. The required cfg is: cfg.interactive = 'yes', cfg.coordsys = 'neuromag'. Once the anatomy is coregistered you can proceed with creating the vol and grid variables.
> 
> Best,
> 
> Jan-Mathijs
> 
> 
> On Jan 3, 2012, at 11:38 AM, Ion Lavado wrote:
> 
>> Thank you for your help Jan. I tried all you told but i continue with my problem. The coordinates for the head (volume) and mri are the same, with the function ft_determine_coordsys i see this. 
>> I think that the problem is about the sensor (helmet) origin of coordinates. Please see the images i adjunt here, the sensors origin is very low(nearly out of the helmet) and when ploting everything i suppose that every origin align to each other, so that the brain comes a little bit low. 
>> 
>> Best whishes,
>> 
>> Ion
>> 
>> 2012/1/2 jan-mathijs schoffelen <jan.schoffelen at donders.ru.nl>
>> Dear Ion,
>> 
>> Are you sure that the sensor positions are defined in the same coordinate system as are the volume conductor model and the source positions? If not, then this is the likely cause of the shift. You can have a look here for more information about the different coordinate systems: http://fieldtrip.fcdonders.nl/faq/how_are_the_different_head_and_mri_coordinate_systems_defined
>> 
>> In order to coregister the anatomical mri to the sensor array, you can use ft_volumerealign. 
>> 
>> Best wishes,
>> 
>> Jan-Mathijs
>> 
>> 
>> On Jan 2, 2012, at 5:11 PM, Ion Lavado wrote:
>> 
>>> Hello, i'm working with MEG data from Elekta Neuromag. My problem comes when i try to plot the headmodel with the function ft_headmodelplot(cfg). This should plot the head model(volume) + brain grid + sensors. As you can see in the adjunted image, my head volume and grid is not centered and part of the head could not be read by the sensors. Is it possible to modify this so i can center the head in the sensors(helmet)? 
>>> Thank you very much.
>>> 
>>> Ion Lavado 
>>> <headmodelplot.jpg>_______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>> 
>> Jan-Mathijs Schoffelen, MD PhD 
>> 
>> Donders Institute for Brain, Cognition and Behaviour, 
>> Centre for Cognitive Neuroimaging,
>> Radboud University Nijmegen, The Netherlands
>> 
>> Max Planck Institute for Psycholinguistics,
>> Nijmegen, The Netherlands
>> 
>> J.Schoffelen at donders.ru.nl
>> Telephone: +31-24-3614793
>> 
>> 
>> _______________________________________________
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>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>> 
>> <helmet.jpg><vol.jpg>_______________________________________________
>> 
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> 
> 
> Jan-Mathijs Schoffelen, MD PhD 
> 
> Donders Institute for Brain, Cognition and Behaviour, 
> Centre for Cognitive Neuroimaging,
> Radboud University Nijmegen, The Netherlands
> 
> Max Planck Institute for Psycholinguistics,
> Nijmegen, The Netherlands
> 
> J.Schoffelen at donders.ru.nl
> Telephone: +31-24-3614793
> 
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> 
> <script.m>_______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

Jan-Mathijs Schoffelen, MD PhD 

Donders Institute for Brain, Cognition and Behaviour, 
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands

Max Planck Institute for Psycholinguistics,
Nijmegen, The Netherlands

J.Schoffelen at donders.ru.nl
Telephone: +31-24-3614793

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