just the brain. For the spine you probably want to do it manually.
freeview can help with this - draw ROIs in the gray and white matter,
then look at the difference between the means (squared) divided by the
sum of the variance
On Thu, 31 Aug 2017, James Welsh wrote:

>
> Thank you Dr Bruce for the info! Is this command works on T1 images acquired from the spine or just
> the brain? 
>
>
>
>
> ____________________________________________________________________________________________________
> From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of
> Bruce Fischl <fischl@nmr.mgh.harvard.edu>
> Sent: Thursday, August 31, 2017 10:08:17 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] motion estimates  
> Hi James
>
> after running recon-all you can use mri_cnr to measure CNR (which is
> usually more interesting than SNR). Motion is harder. Martin investigated
> this at some point, but I'm not sure where he left it
>
> cheers
> Bruce
> On Thu, 31 Aug 2017,
> James Welsh wrote:
>
> > Dear Freesurfer experts, I want to inquire if there are any tools in freesurfer that can help to
> > evaluate T1 quality regarding motion and SNR.
> >
> > Thanks!
> > James
> >
> >
> >
>
>