Hi M - You generally want to register the lower-res to the higher-res image. In this case, that’s diffusion to T1. Check the diffusion processing tutorial on the freesurfer wiki for how you can apply the inverse transform to the aparc+aseg to get it into diffusion space.

Best,

a.y

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Michiko H." <michiko.rc@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Friday, February 16, 2018 at 3:57 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] bbregister aparc+aseg to diffusion space

Hi,

I understand that bbregister can be used to register diffusion to T1 space but I'm a lot less certain how this can be done in the reverse way, i.e. registering the entire aparc+aseg file to diffusion B0? Do I also do: bbregister --s $subject --mov bo_brain.nii.gz --reg registration2b0.dat --dti --init-fsl

To follow up, I'm also unclear whether this method is inferior to registering diffusion to T1 - if so, why may this be so?

Thanks a lot in advance, 

M.

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