[FieldTrip] segmented volume not aligned with individual mri

[Ali Bahramisharif]

Dear Fred,

Why do you enforce:

seg.transform = mri.transform;

after segmentation? I do not do it, and it looks fine!

Cheers,
Ali

>
> Dear all,
>
> I am trying to create mni-aligned grids in individual head-space
> and have followed the code provided in the corresponding example-script
> on the fieldtrip site to the line.
>
> However when I plot the segmented volume it looks as if something
> is going wrong. I am attaching the plots of the gray and white matter,
> as well as of the csf.
>
> I tried flipping the dimensions as suggested in the example script,
> however
> this had zero effect.
>
> My code looks like this.
>
> addpath('/data/common/FieldtripCurrent/fieldtrip-20120105/');
> ft_defaults;
>
> mri = ft_read_mri([path2files,'ID_V2.mri']);
>
> cfg = [];
> cfg.coordsys = 'ctf';
> cfg.downsample = 2;
> seg = ft_volumesegment(cfg,mri);
>
> seg.transform = mri.transform;
> seg.anatomy = mri.anatomy;
>
> figure;
> cfg = [];
> ft_sourceplot(cfg,seg);
> figure;
> cfg = [];
> cfg.funparameter = 'gray';
>
> ft_sourceplot(cfg,seg);
>
> figure;
>
> cfg = [];
>
> cfg.funparameter = 'white';
>
>
> ft_sourceplot(cfg,seg);
>
>
> figure;
>
> cfg = [];
>
> cfg.funparameter = 'csf';
>
>
> ft_sourceplot(cfg,seg);
>
>
>
> Anybody an idea why this is happening?
> Any help would be highly appreciated.
>
> Fred
> --
> Frédéric Roux, PhD student
> Department of Neurophysiology
> Max Planck Institute for Brain Research
> D-60529 Frankfurt am Main
> Frederic.Roux at brain.mpg.de
> +49(0)69630183225
>
>
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