[Freesurfer] coregistering with bbregister

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Hi, I'm trying to coregister the strucural image to the mean functional image using bbregister, so after reconall I did:

bbregister --t2 --init-fsl --reg /data/bbregister/reg.dat --mov /data/mean_func.nii.gz --s 001

bet /data/structural.nii.gz /data/bet_structural.nii.gz

#brain.nii.gz is the brain.mgz from reconall output (in freesurfer space) mri_vol2vol --mov /data/bet_structural.nii.gz --targ /data/brain.nii.gz --o /data/coregistered_structural.nii.gz --reg /data/bbregister/reg.dat --inv –-nearest

But when I load the coregistered_structural.nii.gz and the mean_func.nii.gz they are not aligned. I'm sure I'm doing something wrong, could someone help me figure it out please?

Thanks in advance, Ben