[FieldTrip] Automatic Alignment of T1 with headshape

[José Ángel Pineda]

Thanks Jan,
Ill try as you said.

cheers
Jose


2013/4/29 jan-mathijs schoffelen <jan.schoffelen at donders.ru.nl>

> José,
>
> Coregistration is a tricky thing, particularly if you start mixing results
> from two different software packages. I'd stick to one package, that's my
> recommendation, unless you really know what all individual steps are
> doing. Are you sure that your Aff_1 is doing what you think it is doing?
> E.g. does it apply to an anatomical volume with the same orientation, FOV,
> etc as the T1.nii?
> Also, I think that for any automatic registration tool you use, it is
> necessary to get the geometric objects in approximate alignment, which
> means you need to select fiducials, otherwise your algorithm will not
> converge to the correct solution. I usually use ft_volumerealign twice. The
> first time to get an approximate registration (cfg.method = 'interactive').
> If you have a headsurface determined with a polhemus device, you can call
> ft_volumerealign a second time (with the output to the first call as the
> input mri), in combination with cfg.method = 'headshape', and cfg.headshape
> = ft_read_headshape('headshapefile.txt')
> Finally, I'd recommend not to re-post the same question too quickly after
> itself.
>
> Best wishes,
> Jan-Mathijs
>
>
>
>
> On Apr 29, 2013, at 12:31 PM, José Ángel Pineda wrote:
>
> Dear experts,
>
> I was using manual selection of the fiducials in order to get the affine
> transformation of the MRI T1 image to the MEG sensor space.
> Now, I have decided to use freesurfer for obtaining the head surface and
> some function for performing an automatic corregistration from head surface
> to fiducials (and polhemus information), in order to avoid manual selection
> of the fiducials for each subject.
>
> So I already have one affine transformation (Aff_1)
>
> I loaded the MRI T1 volume (mri = ft_read_mri(T1.nii)), I change the
> mri.transform to mri.transform*Aff_1, but when I plot the results
> (ft_determine_coordsys) I got what is in the attached snapshot.
>
> Could you please give me any advice to solve this?
>
> Thanks
>
> cheers
>
> Jose
>
> <image.png>
>
>
> --
> José Angel Pineda Pardo
> Center of Biomedical Technology (CTB)
> Parque Científico y Tecnológico de la UPM
> Campus de Montegancedo
> 28223 Pozuelo de Alarcón, Madrid, ES
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> Content preview:  Dear experts, I was using manual selection of the
> fiducials
>
>   in order to get the affine transformation of the MRI T1 image to the MEG
>  sensor space. Now, I have decided to use freesurfer for obtaining the head
>   surface and some function for performing an automatic corregistration
> from
>   head surface to fiducials (and polhemus information), in order to avoid
> manual
>   selection of the fiducials for each subject. [...]
>
> Content analysis details:   (5.0 points, 5.0 required)
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> _______________________________________________
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>
> 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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-- 

José Angel Pineda Pardo

Center of Biomedical Technology (CTB)

Parque Científico y Tecnológico de la UPM

Campus de Montegancedo

28223 Pozuelo de Alarcón, Madrid, ES
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