Hi Shani, I don't know anything about that program and can't vouch for it (which probably means that I wrote it:). Anyway, the way that I would do it would be to compute a new matrix:
K = M*inv(T)*R
where R is the register.dat and T is the  vox2tkrRAS and M is the vox2scannerRAS of the DTI. These can be gotten using
mri_info --vox2ras dti.nii
mri_info --vox2ras-tkr dti.nii
Create a new registration file same format as register.dat but with K instead of R
Run something like:

mri_surf2surf --reg newreg.dat dti.nii --sval-xyz white --hemi lh --tval lh.white.dti --tval-xyz

doug

On 02/01/2013 12:35 PM, Shani Ben Amitay wrote:

Hi Doug

I'm sorry it's fs_read_regdat.m a matlab script I found in the mail archive which converts the register.dat file into ras2ras transformation matrix.I want to use thess surfaces to extract vector normals in the diffusion space.
Hope it's clear now
Thanks!
Shani

On Thu, Jan 31, 2013 at 10:33 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

    Hi Shani, what is fs_read_dat.m? I've never seen it before. Why do you
    need to transform the surface? What are you using to create the
    display
    below (ie, command line)?
    doug

    On 01/31/2013 10:53 AM, Shani Ben Amitay wrote:
    > Dear freesurfers
    > I used bbregister to coregister diffusion images with anatomical.
    > I would like to apply the bbregistration transformation to the white
    > and pial surfaces
    > What I've done is:
    > I calculated new transformation  matrix using fs_read_dat.m and then
    > apply it to the surfaces with mri_surf2surf.
    > When overlaying the new surface on the diffusion data- it seems that
    > the transformation is inaccurate.(screenshot is attached)
    > Any idea why?.
    >
    > Thanks, Shani
    >
    >
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