[FieldTrip] Automatic Alignment of T1 with headshape

[jan-mathijs schoffelen]

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)
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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. [...] 
> 
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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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