[Mne_analysis] MNE source points in the MRI coordinate system

[Matti Hamalainen]

The easiest way is to read the source spaces from the source space file in Matlab or Python. The coordinates are then directly the surface RAS coordinates and a simple origin shift is needed to transform to the non-zero origin RAS.

- Matti

On Oct 21, 2014, at 2:14 PM, Jukka Saari <jhsaari at neuro.hut.fi> wrote:

> Dear MNE users,
> 
> I am trying to transform the coordinates of the MNE source points (in
> "Head coordinates") of a subject to the coordinate system of the original
> anatomical MR image of the subject (in "RAS coordinates"?).
> 
> Following the description in the manual
> (http://martinos.org/mne/stable/manual/forward.html) it seems that I have
> to apply two coordinate transformations to these points: from "Head
> coordinates" to "Surface RAS coordinates" and from "Surface RAS" to "RAS
> coordinates".
> 
> I have extracted the two transformations by using these commands:
> mne_show_fiff --in example_subject/mri/T1-neuromag/sets/COR.fif --verbose
> mne_make_cor_set --mgh example_subject/mri/orig.mgz --verbose
> 
> The commands output the following lines:
> 
> head -> MRI (surface RAS)
> 	0.99551 -0.04669 -0.08235     0.57
> 	0.02221  0.96082 -0.27627   -13.19
> 	0.09202  0.27320  0.95754   -22.42
> 	0.00000  0.00000  0.00000     1.00
> 
> 
> Coordinate transformation: MRI (surface RAS) -> RAS (non-zero origin)
> 	 1.000000  0.000000  0.000000	 0.46 mm
> 	 0.000000  1.000000  0.000000	 42.65 mm
> 	 0.000000  0.000000  1.000000	 -11.77 mm
> 	 0.000000  0.000000  0.000000    1.00
> 
> 
> If I understood correctly, applying these transformations to the
> coordinates of the MNE source points listed in the file
> 'example_subject-7-lh.pnt' in the bem directory should then give me the
> source points in the original MRI coordinate system. However, these
> transformed coordinates are nowhere near the cortical surface in the
> original anatomical MR image (they are off tens of centimeters).
> 
> (the first few lines of the 'example_subject-7-lh.pnt' file are as follows:
> # CoordinateSystem "Head"
> # X (mm) Y (mm) Z (mm)
> -15.949615 -101.250862 10.354758
> -11.817389 -99.757225 24.933018
> -8.782373 -99.445816 11.100106
> -15.355161 -100.348282 7.023144
> ...)
> 
> Where is the error in these steps? Is there an easier way to get the MNE
> source points in the original anatomical MRI coordinate system? Any help
> clarifying these coordinate systems and their transformations is
> appreciated.
> 
> 
> Thanks,
> --Jukka Saari
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