Try following this tutorial. It is for fmri, but you can probably apply 
it to PET
surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_freeview
Also see you PET module:
surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_freeview

On 11/20/2018 06:34 PM, john Anderson wrote:
>
>         External Email - Use Caution
>
> Dear Freesurfer experts,
> I would like to run surface based paired  t test of PET data on 
> surface. For every subject I have visit pre treatment and post 
> treatment. I tried to follow the instructions here 
> https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis but the 
> toturial seems to be for cortical thickness data.
> How can i modify the command mris_preproc to do paired test of PEt 
> data on brain surface
>   mris_preproc --target fsaverage --hemi lh \
>     --meas thickness --out lh.paired-diff.thickness.mgh \
>     --fsgd pairs.fsgd --paired-diff
> thanks for any suggestion
> John
>
>
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