Hi Constantin,

No, now I understand what you were doing. The T1 / aparc+asge space is your target and the diffusion space is the moving one. Your mri_vol2vol setup should be accurate as you indicated originally. I think the problem might be that the 2nd registration file that you are saving from tkregister2 does not contain the solution from bbregister. Do you have both of them saved? Could you apply the bbregister solution alone to your T1 and see whether you are getting an acceptable solution? If my hypothesis is true, then you will probably need to concatenate the two solutions and apply that registration to the T1 to get the desired answer.

--Lilla

On Mon, 12 Sep 2011, Constantin Anastasopoulos wrote:

Hello Lilla,

thanks for the answer. I first used

bbregister --s (Freesurfer Directory) --mov b0.nii --reg .dat --dti --init-fsl

Afterwards I made some minor spatial changes to the aparc+aseg, bringing it closer to what i believed its position was on the b0space: tkregister2 --mov b0.img --reg .dat --surf

As far as I understand the aparc+aseg was the target and the b0 the space difining image. Now again the T1 should be the target and the b0 should remain constant. You mean that even if I want to register the T1 to the b0 i have to set the b0 as target?

Thanks Constantin

Quoting Lilla Zollei lzollei@nmr.mgh.harvard.edu:

...

Hi Constantin,

When you used tkregister2 which volume was the target? Acoording to what you write it was the b0 volume. So when you apply the registration to the T1 volume, you should keep it that way.

--mov T1 --targ b0image and no -inv is necessary.

Let me know if I misunderstood what you were doing.

Lilla

On Mon, 12 Sep 2011, Constantin Anastasopoulos wrote:

...

Hellom

I coregistered manually a aparc+aseq.nii file to my DWI-space with tkregister2. I saved the .dat file and applied it later to the T1 image in order to apply the same spatial coregistration as to the aparc+aseg. For woth the aparc+aseg and the T1 I used the command mri_vol2vol --mov was the b0image --targ was the aparc+aseg and T1 respectively --o was the output (a .nii in both cases) --reg was the .dat file and at the and --inv.

While the aparc+aseg registration to the b0 worked, the T1-registration gave a false result (altough it had the same dimensions and was in the same space with the aparc+aseg).

What am I doing wrong? Is the mri_vol2vol command the wrong one? I want to apply the same changes as to the aparc+aseg, as they are saved in the .dat file.

Thanks a lot, Constantin

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