Dear FreeSurfer experts,

For the past few days I have been struggling with how to transform points in FreeSurfer surface coordinates to points in functional data (SPM t-values) coordinates.

I can coregister the functional data with FreeSurfer anatomical image using tkregister2. What I'm having trouble with is how to transform FreeSurfer surface coordinates to (any) volume coordinates that can be coregistered with the anatomical image. I have looked at the FreeSurfer wiki page about the coordinates, but I have not been able to understand fully which transformations are needed and where the related matrices are.

I believe that the center of the RAS-coordinate systems (mri_info spmT_0001.img --cras; mri_info wm.mgz --cras) could be helpful as well as a transformation from voxel (volume) coordinates to RAS-coordinates (mri_info spmT_0001.img --vox2ras).

What I'm looking for is the matrix-multiplication that would transform the FreeSurfer surface coordinates (such as those in ?h.white) to the functional data volume coordinates (in spmT_0001.img). I need to know what these matrices are (and where to get them) and in which order to apply the transformation matrices.

I would like to do this with Matlab as much as possible. I have a large number of points and therefore I cannot do it manually for each point.

Any help would be greatly appreciated.

Sincerely,

Patrik Ahvenainen AMI centre Helsinki University of Technology