Hi Sam - You can use mri_vol2vol to apply the transformation that was saved in the registration file nodiffb2orif.dat to any volume that's in the same space as nodif.nii.gz.

a.y ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Sam W samfmri@gmail.com Sent: Saturday, January 18, 2020 6:52:10 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] registration of dwi images

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Hello! I have run eddy on all my dwi images and then run bbregister using the first b0 image as the source image. The b0 image is now well aligned with the anatomical image but how can I apply the same transformation to all other dwi images in my dataset?

After eddy correction I extracted the first b0 image (nodif.nii.gz) and run the bbregister command: bbregister --s sub001 --mov /home/samm/nodif.nii.gz --reg /home/samm/nodiffb2orig.dat --dti --init-fsl --o /home/samm/registered_b0.nii.gz

Thanks! Sam