[FieldTrip] segmented volume not aligned with individual mri

[jan-mathijs schoffelen]

Hi Fred,

You specify the seg to be downsampled. Therefore, I guess that the seg.dim and the mri.dim don't match anymore. Nor will the dimensions of the mri.anatomy match those of the seg.gray/white/csf. Also, as Ali suggests, the transformation matrices cannot be exchanged anymore.
I suspect that if you do: cfg = []; cfg.downsample = 2; mri2=ft_volumedownsample(cfg, mri); seg.anatomy = mri2.anatomy (and leave out seg.transform = mri.transform) that things will look a bit better.

JM

On Mar 29, 2012, at 12:37 PM, Frederic Roux wrote:

> 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
> 
> 
> <segmented_1.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

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