External Email

Hi Prad

if you use the cortex.label is will avoid using the non-cortical regions in
the surface, like the midline, so should be a more accurate measure

cheers
Bruce


On Thu, 28 May 2020, Pradyumna Bharadwaj wrote:

>
>         External Email - Use Caution        
>
> Hi,
>
> I had a question about the -label flag in mri_cnr.
>
> 1) When you do not use the -label option and just use the following command:
>  mri_cnr $FREESURFER_HOME/subjects/bert/surf    $FREESURFER_HOME/subjects/be
> rt/mri/norm.mgz
>
> The output is as follows
>
>   white = 96.6+-6.0, gray = 75.7+-13.5, csf = 55.3+-16.6 gray/white CNR = 1.
> 983, gray/csf CNR = 0.907
>
>  lh CNR = 1.445
>
> white = 96.4+-6.0, gray = 76.0+-13.3, csf = 55.6+-16.2 gray/white CNR = 1.95
> 2, gray/csf CNR = 0.943
>
> rh CNR = 1.448
>
>  total CNR = 1.446
>
>
> 2) When you add  -label $FREESURFER_HOME/subjects/bert/label/lh.cortex.label
>  $FREESURFER_HOME/subjects/bert/label/rh.cortex.label to the first command,
> you get different (lower) cnr values.
>
> white = 96.6+-6.0, gray = 73.1+-18.9, csf = 50.8+-20.5 gray/white CNR = 1.38
> 9, gray/csf CNR = 0.644
>
> lh CNR = 1.016
>
> white = 96.4+-6.0, gray = 73.4+-18.8, csf = 51.0+-20.3 gray/white CNR = 1.35
> 3, gray/csf CNR = 0.652
>
> rh CNR = 1.002
>
> total CNR = 1.009
>
> How is the lh.cortex and rh.cortex label changing the CNR computation?
>
> Any inputs or thoughts on this matter are greatly appreciated!
>
> Thanks,
> Prad
>
>_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer