[FieldTrip] ft_headmodelplot coordinate system origin problem

[Ion Lavado]

The Z axis is pointing to the oposite direction (inferior), so i have the
mri upside down. How can i change this? When Matlab plots the figure it
asks me this:

The positive x-axis is pointing towards the right
The positive y-axis is pointing towards anterior
The positive z-axis is pointing towards superior
Do you want to change the anatomical labels for the axes [y, N]?

I then mark to change the axis and mark the positive z-axis as (i)inferior,
but when plotting again is as the begginig... What do i have to do?

Thank you very much Jan.



2012/1/3 jan-mathijs schoffelen <jan.schoffelen at donders.ru.nl>

> 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
>>>
>>>
>>> _______________________________________________
>>> 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
>>
>
> <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
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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