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
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 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
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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