[Mne_analysis] MNE source points in the MRI coordinate system

[Jukka Saari]

Reading the source points from the file example_subject-7-src.fif in
Python and transforming these points with the Surface RAS -> RAS
transformation solved the problem. Thank you!

--Jukka


>
> 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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>>
>>
>
>
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