[Mne_analysis] convert from vertex number to MNI

Jon Houck jhouck at unm.edu
Mon Aug 2 15:10:57 EDT 2010
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Hi,

On Tue, Mar 9, 2010 at 6:42 PM, Matti Hamalainen
<msh at nmr.mgh.harvard.edu>wrote:
>
>
> I a few easy steps:
>
> 1. Use mne_collect_transforms to make a fif file containing all the
> coordinate transforms you need, see Section 9.9 in the MNE manual.
>
> In Matlab:
>
> 2. Load the surface(s) of interest using mne_read_surfaces or
> mne_read_source_spaces
>
> 3. Using mne_transform_coordinates, transform the coordinates of the
> vertices in the structures returned in step 2 to the desired coordinate
> frame.
>
>

When I follow these steps I get a series of errors -- I think I'm making
syntax errors somewhere along the way but can't determine where.  I'm doing:

[src] =
mne_read_source_spaces('SUBJECTS_DIR/SUBJECT/bem/SUBJECT-oct-6-src.fif');

and

[trans_pos] =
mne_transform_coordinates('SUBJECT_xforms.fif',src(1,2).tris,'FIFFV_COORD_HEAD','FIFFV_COORD_MNI_TAL');

The errors include:

Error in ==> mne_transform_coordinates at 85
if (from == FIFF.FIFFV_COORD_HEAD && isempty(T0)) || isempty(T1) ||
isempty(T2) ||

??? Error using ==> eq
Matrix dimensions must agree

and

??? Error using ==> mne_transform_coordinates at 103
Input data must be in MEG head or surface RAS coordinates

depending on what I comment out in troubleshooting.  Can you see anything
obvious that I've done wrong?  I've been using the 2009-04-27 version of
mne_transform_coordinates that was included in MNE 2.7.0-3106.  The matrix
from the SUBJECT_xforms.fif file is given below.

Thanks

Jon Houck

Coordinate transformation: MEG device -> head
         0.999839 -0.010549 -0.014511     -0.32 mm
         0.013018  0.983165  0.182259      1.43 mm
         0.012344 -0.182419  0.983144     61.88 mm
         0.000000  0.000000  0.000000     1.00
Coordinate transformation: MRI (surface RAS) -> head
         0.997896  0.029082 -0.057949     -1.16 mm
        -0.011038  0.956921  0.290140     17.67 mm
         0.063891 -0.288890  0.955228     46.51 mm
         0.000000  0.000000  0.000000     1.00
Coordinate transformation: MRI (surface RAS) -> RAS (non-zero origin)
         1.000000  0.000000  0.000000      4.31 mm
         0.000000  1.000000  0.000000     60.02 mm
         0.000000  0.000000  1.000000      3.69 mm
         0.000000  0.000000  0.000000     1.00
Coordinate transformation: RAS (non-zero origin) -> MNI Talairach
         0.972405 -0.036926 -0.098139     -2.42 mm
         0.051778  1.001975  0.163707    -71.57 mm
         0.080551 -0.169009  1.019200      0.88 mm
         0.000000  0.000000  0.000000     1.00
Coordinate transformation: MNI Talairach -> Talairach (MNI z > 0)
         0.990000  0.000000  0.000000      0.00 mm
         0.000000  0.968800  0.046000      0.00 mm
         0.000000 -0.048500  0.918900      0.00 mm
         0.000000  0.000000  0.000000     1.00
Coordinate transformation: MNI Talairach -> Talairach (MNI z < 0)
         0.990000  0.000000  0.000000      0.00 mm
         0.000000  0.968800  0.042000      0.00 mm
         0.000000 -0.048500  0.839000      0.00 mm
         0.000000  0.000000  0.000000     1.00
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