[FieldTrip] Coordinate system conversion

[Eelke Spaak]

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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