[Mne_analysis] Converting from CTF to a Neuromag/FreeSurfer coordinate system

[Lau Møller Andersen]

        External Email - Use Caution        

Dear List

I'm analysing a dataset in MNE-Python that has been acquired in a CTF scanner. I also have access to individual MR's for each subject. Both one in the native coordinate system (Niftii) and one converted to the CTF space. Since the data comes from an publicly accessible database, the MR's have been defaced, and therefore it is not possible to correctly get the nasion fiducial correctly placed.

My attempt at solving this has been to run the FreeSurfer pipeline on the MR in the CTF space. Then to get it in the Neuromag Space I've rotated it 90 degrees around the z-axis and translated it 40 cm upwards. This looks reasonable, but now I've gotten worried that this won't work since the FreeSurfer origin is based on the ACPC convention and not between the auricular points as in Neuromag. Does this mean that my co-registration below is likely to be wrong, or is it right to be in the Neuromag coordinate system?

Here's my transformation matrix to go from CTF (left below) to Neuromag (right below)

[cid:part1.F7596179.D5AB9AE9 at ki.se]

[cid:part2.26D2E596.8AE582B7 at ki.se]

Left: before rotation and translation. Right: after rotation and translation.

Best Wishes

Lau

--
Lau Møller Andersen | Ph.D. | Post Doc
NatMEG - The National Research Facility for Magnetoencephalography (MEG)
Department of Clinical Neuroscience
Nobels väg 9: D303 | 171 77 Stockholm
+46 8 524 833 33
lau.moller.andersen at ki.se<mailto:lau.moller.andersen at ki.se> | lau at natmeg.se<mailto:lau at natmeg.se>
ki.se | natmeg.se
_____________________________________
Karolinska Institutet – a medical university

Treasurer: Karolinska Institutet Postdoc Association (KIPA)



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