Thanks for the reply, Doug!

Best, Feilong

On Wed, Mar 22, 2017 at 1:24 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:

I think the motion correction works a little better if done to a reference inside each run, and there's probably less interpolation in the end

On 3/20/17 11:04 AM, Feilong Ma wrote:

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

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