you'll have to first create a registration file, you can do that with

cd subject/mri tkregister2 --mov orig/001.mgz --targ T1.mgz --regheader --s subject --reg register.dat --noedit

then apply this to the surface with

mri_surf2surf --s $subject --sval-xyz white --hemi lh --reg register.dat orig/001.mgz \ --tval-xyz --tval ./lh.white.001

This creates lh.white.001, and the coordinate will/should be in the "tkregister" coorindates of the 001.mgz space (usually they are in the "tkregister" coords of the T1.mgz space). See https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems?action=AttachFil... for how to get from this space to other spaces.

doug

Seok Lew wrote:

Dear all,

I am trying to transform the reconstructed surface like rh.pial into the original mri's (like 001.mgz) coordinate. I found some matrices in the ./transform directory, but not sure of which one (or a set of matrices) would do the transform?

Seok slew@nmr.mgh.harvard.edu

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer