Hi,
I see that in mne_analyze it's possible to get the MNI coordinates for selected vertices. How can I have access to the transformation used there? In other words, if I have a list of vertices in matlab, how can I get their MNI coordinates (and vice-versa)?
Thanks,
Gus
Hi Gus,
I see that in mne_analyze it's possible to get the MNI coordinates
for selected vertices. How can I have access to the transformation
used there? In other words, if I have a list of vertices in matlab,
how can I get their MNI coordinates (and vice-versa)?
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.
I hope this helps,
Matti
Hi,
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_spaces3. 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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