On the PETsurfer wiki, https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer, I had recommended using mri_coreg to register your PET to the FS anatomical using the following command line:
mri_coreg --s subject --mov template.nii.gz --reg template.reg.lta
This works well for PET scans that do not have much activity outside the head (eg, FDG and many neuroreceptor ligands). However, it can be inaccurate for other ligands that do have lots of uptake outside the head (eg, tspo, maybe tau). In these cases I now recommend using
mri_coreg --s subject --mov template.nii.gz --reg template.reg.lta --ref nu.mgz --no-ref-mask
This command will use the whole head MRI (nu.mgz) instead of the brainmasked MRI (brainmask.mgz); this will align better for these types of scans. This is now documented on the PETsurfer website.
Remember, you should always check your PET-MR registrations manually.
Sorry for any inconvenience this has created.
best doug