manually specifying fiducial positions in MRI structure

[Vladimir Litvak]

Hi Markus,

When building the head model SPM generated some .gii files that should
be at the same location where your individual MRIs were. If you load
the one corresponding to the cortex with something like:

m = export(gifti('filename.gii'), 'ft');

you can take m.pnt and put it in the source structure instead of
source.pos there. Then you'll have matching coordinate systems. There
are also some other ways to do it but this one is the simplest to
explain.

Best,

Vladimir

On Sat, Apr 17, 2010 at 1:45 AM, Markus Bauer <m.bauer at ucl.ac.uk> wrote:
> Hi
>
> I have been using the new SPM mesh (fitted to the individual MRI by the
> inverse transformation matrix of MRI -> MNI) for creating forward models for
> source-analysis for CTF data in fieldtrip.
>
> That works quite well, however, when trying to plot the results in fieldtrip
> I face the problem that the sources and the MRI (read into fieldtrip using
> read_mri and the SPM8 toolbox) have different coordinate systems.
>
> How can I recompute the coordinates of the MRI so that it is in fieldtrip
> (CTF-head-coordinates) format?
> I have the fiducial info from SPM available...
> Is it possible to do sth like:
>
> pos = mri.transform * mri.ind;
> pos = pos - fiducial.pos; %or whatever - do a translation to the origin of
> the 'new coordinate system'
> mri.transform = pos  / ind;
>
> ??
> or is it also necessary to flip the dimensions / specify further info??
> cause I think MRI's in SPM have the x- and y-axis flipped compared to the
> CTF/fieldtrip headmodel format...
>
> Any suggestions would be appreciated, thanks
> Markus
>
> ----------------------------------
>
> The aim of this list is to facilitate the discussion between users of the
> FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and
> EEG analysis.
>
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>
> http://www.ru.nl/fcdonders/fieldtrip/

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.