[FieldTrip] fieldtrip Digest, Vol 16, Issue 51

[Frederic Roux]

Hi Julian,

thank you for response. That did indeed solve the problem.
I had commented out the section where everything is converted
from mm to cm.

Now the grid is at least on the same scale as the head model.
However, when I compare the template grid (Figure1) with
the individual grid (Figure6) it seems as if there is still a difference.

Is this normal and a consequence of the warping or should the
plot look different?

Best, 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




> From: fieldtrip-request at donders.ru.nl
> Subject: fieldtrip Digest, Vol 16, Issue 51
> To: fieldtrip at donders.ru.nl
> Date: Thu, 29 Mar 2012 17:46:09 +0200
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> Today's Topics:
> 
>    1. alignment channel array, head model & individual grid
>       (Frederic Roux)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Thu, 29 Mar 2012 17:45:52 +0200
> From: Frederic Roux <fredericroux at hotmail.de>
> To: <fieldtrip at donders.ru.nl>
> Subject: [FieldTrip] alignment channel array, head model & individual
> 	grid
> Message-ID: <DUB113-W104C6E0B399243CBB06024BB7480 at phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> 
> Dear all,
> 
> I have trouble finding the right alignment for my head models and individual grids
> with the MEG channel array.
> 
> The code I use is the following:
> 
> addpath('/data/common/FieldtripCurrent/fieldtrip-20120105/');
> addpath('/data/common/FieldtripCurrent/fieldtrip-20120105/fieltdrip_private/');
> ft_defaults;
> 
> spm2path = '/data/common/FieldtripCurrent/fieldtrip-20120105/external/spm2/';
> spm8path = '/data/common/FieldtripCurrent/fieldtrip-20120105/external/spm8/';
> 
> rmpath(spm2path,spm8path);
> 
> 
> mri = ft_read_mri('ID_V2.mri');
> 
> cfg = [];
> cfg.coordsys = 'ctf';
> seg = ft_volumesegment(cfg,mri);
> 
> cfg = [];
> hdm = ft_prepare_singleshell(cfg,seg);
> 
> cfg = [];
> cfg.template = '/data/common/SPM8current/spm8/canonical/single_subj_T1.nii';
> cfg.coordsys = 'ctf';
> cfg.nonlinear = 'no';
> 
> norm = ft_volumenormalise(cfg,mri);
> 
> load template_grid.mat % template created from the SPM8 single_subj_T1.nii template located in the canonical folder of SPM8
> 
> grid = [];
> grid.pos = warp_apply(inv(norm.cfg.final), template_grid.pos, 'homogenous')/10;
> grid.inside = template_gird.inside;
> grid.outside = template_grid.outside;
> 
> transfrom_ctf2spm = norm.cfg.final;
> 
> figure;
> hold on;
> ft_plot_sens(ft_read_sens('ID.ds'));
> ft_plot_vol(hdm);
> ft_plot_mesh(grid.pos(grid.inside,:));
> 
> 
> Would be great if you could help me to figure out what is going wrong here.
> 
> Best,
> Fred
> 
> 
> -- 
> Fr?d?ric 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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