manually specifying fiducial positions in MRI structure

[Markus Bauer]

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

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