[FieldTrip] Issue aligning volume conduction model with source model

Hamid Mohseni hamid.mohseni at eng.ox.ac.uk
Tue Mar 19 16:42:51 CET 2013


Hi,

I had this problem before, and I think it is something with freesurfer: If
you plot the original MRI and its segmented volume in freesurfer, you may
see that they are not in the same coordinate. I think the best way is to
ask freesurfer people, we probably missing a small thing here.

Thanks


On 19 March 2013 14:49, Doshi, Chiran <Chiran.Doshi at childrens.harvard.edu>wrote:

> Hi,
> So I tried form the beginning and it fixed the issue. Any ideas why this
> might be hapenning in the first place?
> The problem is I already have a freesurfer database with reconstructed
> surfaces. If there is any fix like a missing transformation that I can
> compute so I do not have to recon-all again for all subjects.
>
>
> 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 Doshi, Chiran [Chiran.Doshi at childrens.harvard.edu]
> Sent: Monday, March 18, 2013 9:49 AM
> To: FieldTrip discussion list
> Subject: Re: [FieldTrip] Issue aligning volume conduction model with
>  source  model
>
> Thanks for the help,
> I will try again from the beginning. I will let know if I am able to get
> the fix the 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 12:47 PM
> To: FieldTrip discussion list
> Subject: Re: [FieldTrip] Issue aligning volume conduction model with
> source     model
>
> 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<mailto:
> 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<mailto:
> fieldtrip-bounces at science.ru.nl> [fieldtrip-bounces at science.ru.nl<mailto:
> fieldtrip-bounces at science.ru.nl>] on behalf of Hamid Mohseni [
> hamid.mohseni at eng.ox.ac.uk<mailto: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
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl<mailto: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<tel:%2B44%20%280%29%201865%202%2083826>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl<mailto:fieldtrip at donders.ru.nl>
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> _______________________________________________
> 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/20130319/07d5ed10/attachment-0002.html>


More information about the fieldtrip mailing list