[Freesurfer] tkregister question

Hi,

Here's a question to Doug / anyone else who mastered the intricate way of volume transformations:

I'm a bit puzzled. According to Free surfer's documentation (fscoordinates.pdf), the way two volumes are registered to each other using tkregister is always using the fixed transformation (tkvox2ras) (see page 6).

However, when I do the following little experiment (using matlab's freesurfer API)

A = '001.nii'; B = '002.nii'; X=MRIread(A); X.vox2ras0(1,4) = 40; MRIwrite(X,B);

tkregister2 --targ 001.nii --mov 002.nii --regheader -reg R.reg

The two volumes are not in alignment when they are loaded into tkregister. Now, what am I missing here? If both were loaded using the fixed transform, they should still be in alignment (i.e., vox2ras should be ignored for registration purposes).

Thanks in advance,

-- Shay Tsao lab Caltech