[FieldTrip] Issue aligning volume conduction model with source model

[Hamid Mohseni]

If you want to do beam former source localization, there is no need to
freesurfer and you can extract the brain shape points from the segmented
MRI using FieldTrip itself and you will not have this problem.

However, if you want to do minimum norm source localisation, you may do a
realignment before applying free surfer, please see this

http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate
On Mar 16, 2013 4:23 PM, "Doshi, Chiran" <Chiran.Doshi at childrens.harvard.edu>
wrote:

>  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>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
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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