[FieldTrip] Alignment problem in tutorial: Create MNI-aligned grids in individual head-space

[jan-mathijs schoffelen]

Hi Anette,

Case 1 does not look good because you are overlaying a low resolution image with a high resolution image. This is due to the cfg.downsample=2 before you call ft_volumesegment. (mri.anatomy is just 2^3 as big as the segmented images. Ft_sourceplot assumes all the to-be-plotted data to have the same physical size.
Note that  you replace the transformation matrix in the seg_MNItutorial variable with the transformation matrix from the mri-variable. This is incorrect, because the original mri has 1-mm resolution, whereas the segmented has 2-mm resolution.

Best,

Jan-Mathijs


On Jun 25, 2012, at 2:23 PM, Anette Giani wrote:

> Dear fieldtrip users,
>  
> I am running the tutorial: “Create MNI-aligned grids in individual head-space” (CASE 1). When using the template mri provided on the homepage (i.e. Subject01.mri), it seems like the grid, the resulting vol and the anatomy are not aligned. And even worse: besides the misalignment there seems to be a scaling. Note however, that I am using the exact same parameter as specified on the homepage. For a better understanding see page 1 of Alignment.pdf attached to this mail.
>  
> I found out that things improve when I use the segmentation procedure specified in the tutorial: “Build a geometrical description of the volume conduction model of the head” (CASE 2). See page 2 of Alignment.pdf.
>  
>  
> In particular, in CASE 1 I do:
>  
> cfg = [];
> cfg.downsample  = 2;
> cfg.coordsys    = 'ctf';
> seg_MNItutorial = ft_volumesegment(cfg, mri);
>  
> % plotting case 1
> seg_MNItutorial.transform = mri.transform;
> seg_MNItutorial.anatomy   = mri.anatomy;
> figure
> cfg.funparameter = 'gray';
> ft_sourceplot(cfg,seg_MNItutorial); %segmented gray matter on top
>  
>  
>  
> While, in CASE 2 I do:
>  
> cfg = [];
> cfg.write      = 'no';
> cfg.coordsys   = 'ctf';
> cfg.output     = {'scalp','skull','brain'};
> seg_headmodelTutorial   = ft_volumesegment(cfg, mri);
>  
> % plotting case 2
> mri_combine = mri;
> mri_combine.seg  = seg_headmodelTutorial.scalp + 3*seg_headmodelTutorial.skull + 6*seg_headmodelTutorial.brain;
> mri_combine.mask = (mri_combine.seg)>0;
> cfg = [];
> cfg.interactive   = 'yes';
> cfg.funparameter  = 'seg';
> cfg.funcolormap   = 'jet';
> cfg.funcolorlim   = [0 7];
> cfg.opacitylim    = [0 1.5];
> cfg.maskparameter = 'mask';
> figure, ft_sourceplot(cfg,mri_combine);
>  
>  
> I am confused, why CASE 2 works, while CASE 1 does not. Could anyone explain the differences to me? Is doing it like in CASE 2 correct at all?
>  
> Thanks a lot in advance!
> Anette
>  
> 
> <Alignment.pdf>_______________________________________________
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> fieldtrip at donders.ru.nl
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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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