transformation during Brainstorm's importation

[sockeel]

Hello,

I'm a new brainstorm's user and I have a little question :
When I import MRI, surfaces... in Brainstorm, they are all converted into the CTF coordinates system. And when I export them after my work with Brainstorm, they still are in this system. But I'm working with others images (fMRI, DTI...), I haven't import in Brainstorm.
So my question is : Where can I find the transformation Brainstorm made when it imports an image?

Thanks for the help,
Stéphane Sockeel

[Francois]

Dear Stephane,

Indeed, the surfaces and sensors coordinates are converted in SCS (subject coordinates system), which follows the CTF convention, when they are imported. Documentation available at:
http://neuroimage.usc.edu/brainstorm/CoordinateSystems

To convert from a coordinates system to another, you can use the functions in brainstorm3/toolbox/cs. The transform from MRI to SCS is stored in the MRI file, in the field "SCS".

To convert back into MRI coordinates the vertices of a surface :
1) Export the surface to Matlab (right click on surface file > File > Export to Matlab), to a variable called "surf"
2) Export the MRI to Matlab (variable "mri")
3) Typing "scs2mri(mri, surf.Vertices)" in your Matlab command window will give you the positions of the vertices in MRI CS.

Does that help ?
Francois

[sockeel]

Dear François,

I have run the 'scs2mri' code and I observe a little error in the result. The origin is good, but the mesh is too small.
I think is just a problem of units (meter vs mm), because a x1000 homothety resolve it.

Thanks for all,
Stéphane

[Francois]

Hi Stephane,
You're right, I did a little mistake in the function calls. The surfaces coordinates are stored in meters, while the mri2scs function takes millimeters in input.

The correct call to get your vertices in MRI coordinates is:
scs2mri(mri, surf.Vertices * 1000) / 1000

Francois