Get MNI coordinates of cortex vertices

Discussions
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1

Hi

Is there any method in Brainstorm that can help me export the cortex vertices as MNI coordinates?
I have computed the MNI transformation of MRI. When I displayed the cortex file such as cortex_15002V, I also can see the MNI coordinates.
I want to get the MNI coordinates of all the 15002 vertices.

Thanks
Lianyang

2

Hi Linyang,

First you need to export your surface to your Matlab workspace:
http://neuroimage.usc.edu/brainstorm/Tutorials/Scripting#Custom_processing

The vertices are in SCS coordinates:
http://neuroimage.usc.edu/brainstorm/Tutorials/ExploreAnatomy#On_the_hard_drive:_Surface

Then you can convert these SCS coordinates to MNI coordinates:
http://neuroimage.usc.edu/brainstorm/CoordinateSystems#Converting_between_coordinate_systems

Cheers,
Francois

3

FYI, these links do not seem to be working.
Is there any other way to get this information?
Many thanks
Adi

4

Hi Adi,

I fixed the links. Thanks for reporting the issue.

Francois

5

Dear all,

To get MNI coordinates, I exported my surface MRI (cortex_15002V) to Matlab workspace.
Then, I tried to convert SCS coordinates to MNI coordinates using cs_convert function.!
But, only empty matrix was outputted, and I could not get MNI coordinates.
Any idea to solve this problem ?
Best
Sugata

MNI_problem
MNI_problem843×826 73.2 KB

6

To convert to/from SCS, your sMRI structure requires a field .SCS with the transformation MRI=>SCS.
To convert to/from MNI, your sMRI structure requires a field .NCS with the transformation MRI=>MNI.

To get both: import your file in your Brainstorm database, set the NAS/LPA/RPA points and compute the MNI transformation. Then export the MRI as this "sMRI" structure.