Hi FreeSurfer Experts,

I was reading the document of preproc-sess, and it seems -per-run is recommended instead of -per-session. Here is the part:

-per-run
Motion correct and register using the middle time point of each run.
This is the option that you should use.
-per-session
Motion correct and register using the first time point of the first
run. This is mainly for compatability with version 4.

Is there a reason to preprocess each run separately? I know some people motion correct and register all EPI volumes to the same reference EPI volume, which also works well.

Thanks,

Feilong