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Hi Dr Greve,
If the individual PET frames are named: frame1.nii frame2.nii, frame3.nii ... .... frame10.nii, and the mean for all the ten frames is "frames_mean.nii"
 
I ran mri_corg on one of the fames as follows:
mri_coreg --mov frame1.nii --ref frames_mean.nii --reg reg.dat.

Do I need to run the same command on every frame, or just apply reg.dat on all the frames. If applying reg.dat on all the frames is the correct procedure. How can I do it?

Your guidance is highly appreciated.
John



mri_coreg is the right one for that job





‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐
On July 3, 2018 1:51 PM, John Anderson <John.anderso@protonmail.com> wrote:

Dear Freesurfer experts,
I have ten PET frames for every subject in my database. these frames represent specific time during PET acquisition. Due to head motion during acquisition the frames are not fully overlapped on top of each other. I created template represent the mean of the ten frames. I would like to register each low res frame to this low res template. Which tool in Freesurfer is more robust to achieve this goal.
Any additional suggestions are highly appreciated
Thanks
John