[FieldTrip] Issue aligning volume conduction model with source model

Hamid Mohseni hamid.mohseni at eng.ox.ac.uk
Sat Mar 16 16:27:30 CET 2013


Hi,

I THINK there is a problem with your mri.transform matrix. Basically,
without any pre-processing, when you apply this transformation to the
headshape points 'bnd', it should match the original mri. I checked that
and apparently it dosen't happen. How did you obtain this transformation?

Thanks



On 15 March 2013 22:07, Doshi, Chiran <Chiran.Doshi at childrens.harvard.edu>wrote:

> Hello FieldTrip users,
>
> I am having trouble aligning volume conduction model with source model
>
> The link to the data is
> https://www.dropbox.com/sh/7ejsvewemci8ixe/RpfP3F5ROi
>
> Here are the steps I followed
>
> % Read mri
> mri = ft_read_mri('T1.mgz');
>
> % Determine coordinate system. Neuromag selected +x as r, +y as a, +z as s
> and origin as i. At the end mri.coordsys was equal to 'neuromag'
> mri = ft_determine_coordsys(mri);
>
> % Align volume. Selected l, r, l and z in + z direction
> cfg=[];
> cfg.coordsys='neuromag';
> mri = ft_volumerealign(cfg,mri);
>
> %Volume segment
> cfg=[];
> cfg.coordsys='neuromag';
> cfg.output = {'brain' 'scalp' 'skull' 'tpm'};
> seg = ft_volumesegment(cfg, mri);
>
> % Prepare head model. The model aligns well with sensors
> cfg=[];
> cfg.coordsys='neuromag';
> cfg.method    = 'singleshell';
> vol = ft_prepare_headmodel(cfg, seg);
>
> % compute sourcespace
> bnd =
> ft_read_headshape('ID_000000-ico-5-src.fif','format','mne_source','unit','mm');
> T   = mri.transform*inv(mri.transformorig);
> sourcespace = ft_transform_geometry(T, bnd);
>
> % Plot
> figure;hold on;
> ft_plot_mesh(sourcespace, 'edgecolor', 'none'); camlight
> ft_plot_vol(vol, 'facecolor', 'none');alpha 0.5;
>
>
>
> These surfaces do not align. Any ideas?
>
>
>
> Chiran Doshi, MS
> MEG system technologist
> Department of Neurology
> Boston Childrens Hospital
> Phone: 781-216-1136
> Fax: 781-216-1172
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>



-- 
Hamid R. Mohseni, PhD
Post-Doctoral Research Assistant
Institute of Biomedical Engineering
University of Oxford, OX3 7DQ, UK
Tel: +44 (0) 1865 2 83826
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20130316/5e16d748/attachment.html>


More information about the fieldtrip mailing list