[FieldTrip] Issue aligning volume conduction model with source model

Doshi, Chiran Chiran.Doshi at childrens.harvard.edu
Sat Mar 16 17:10:09 CET 2013


Hi Hamid,
Thanks for the reply. I see what you mean.
When I import the T1, there is a mri.transform already present in it. This is generated by the freesurfer. mri.tranform gets changed when I do the ft_volumerealign, (following right hand system) I mark rpa as r, lpa as l , nas as n and z in the positive z direction. I have vitamin pills at the fiducials ( some also at the forehead) that would help in marking the points.

I cannot figure out where am I messing up. Also I am using the src file in MNE and I do not have this issue.

Chiran Doshi, MS
MEG system technologist
Department of Neurology
Boston Childrens Hospital
Phone: 781-216-1136
Fax: 781-216-1172

________________________________
From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Hamid Mohseni [hamid.mohseni at eng.ox.ac.uk]
Sent: Saturday, March 16, 2013 11:28 AM
To: FieldTrip discussion list
Subject: Re: [FieldTrip] Issue aligning volume conduction model with source model

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<mailto: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

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--
Hamid R. Mohseni, PhD
Post-Doctoral Research Assistant
Institute of Biomedical Engineering
University of Oxford, OX3 7DQ, UK
Tel: +44 (0) 1865 2 83826
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