[FieldTrip] Coordinate system conversion

[Mohammad Ostadmohammadi]

Dear Eelke

Thanks for your response. I think it solved my problem

On Wed, Jul 17, 2019 at 1:05 PM Eelke Spaak <e.spaak at donders.ru.nl> wrote:

> Hi Mohammad,
>
> I only now read your other email. I would definitely recommend
> following the procedure here for creating your source and head models:
>
> http://www.fieldtriptoolbox.org/tutorial/sourcemodel/#performing-group-analysis-on-3-dimensional-source-reconstructed-data
> It will make your life easier.
>
> Cheers,
> Eelke
>
> On Wed, 17 Jul 2019 at 09:45, Eelke Spaak <e.spaak at donders.ru.nl> wrote:
> >
> > Dear Mohammad,
> >
> > You'll need to somehow obtain a transformation matrix from the
> > Neuromag coordinate system into MNI space. The Neuromag coordinate
> > system (like any MEG subject-space coordinate system) depends on
> > anatomical landmarks of an invididual subject, and is thus different
> > for different subjects. If you have a source model in Neuromag
> > coordinates, apparently somehow somewhere someone had access to the
> > individual fiducial locations and brain anatomy. It would be worth
> > checking whether you can obtain this.
> >
> > *Alternatively*, you could take a template MRI in MNI space and
> > somehow manually realign that to Neuromag space, basically treating
> > the template head as if it were used during the actual MEG recording.
> > That will give you an mni-2-neuromag transformation matrix; taking the
> > pinv() of that will allow you to go the other way. I'm not sure this
> > is wise, though. (In any case, it will be suboptimal compared to using
> > individual anatomy; but specifically for the volume conduction model,
> > I don't know whether such a linear transform messes things up.) All in
> > all, creating a source and head model from scratch in the appropriate
> > coordinate system will probably be easier.
> >
> > Cheers,
> > Eelke
> >
> > On Tue, 16 Jul 2019 at 15:42, Mohammad Ostadmohammadi
> > <mohammad.ostad73 at gmail.com> wrote:
> > >
> > > Yes I asked him about it, but because of large amount of data I wanted
> to know is there any way to convert coordinate systems without creating
> source_model from the scratch
> > >
> > > On Tue, Jul 16, 2019 at 6:05 PM Schoffelen, J.M. (Jan Mathijs) <
> jan.schoffelen at donders.ru.nl> wrote:
> > >>
> > >> You mentioned before that your supervisor provided you with the data
> so far. Have you asked your supervisor to help you out?
> > >>
> > >> Jan-Mathijs
> > >>
> > >>
> > >> On 16 Jul 2019, at 12:23, Mohammad Ostadmohammadi <
> mohammad.ostad73 at gmail.com> wrote:
> > >>
> > >> Hi all,
> > >>
> > >> is it possible to change source_model coordination system from
> neuromag to mni? i don't have access to mri data and only source_model and
> head_model is accessible.
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> > >>
> > >>
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