When you use --regheader, then it uses the vox2ras transform in the header. If you pass it a register.dat file as input, then vox2ras is ignored. doug

On 05/31/2012 06:39 PM, Shay Ohayon wrote:

Hi,

Bump?

Can someone please explain to me the puzzle described below regarding tkregister2 and vox2ras0 (which I thought should be ignored for registration purposes?)

Thanks!

-- Shay

On Sat, May 26, 2012 at 2:23 PM, Shay Ohayon <shay.ohayon@gmail.com mailto:shay.ohayon@gmail.com> wrote:

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

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