[FieldTrip] ft_headmodelplot coordinate system origin problem

[Ion Lavado]

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
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> 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
>
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