External Email

Hi Prad

what is your goal? What you describe below should work

cheers
Bruce
On Thu, 28 May 2020,
Pradyumna Bharadwaj wrote:

>
>         External Email - Use Caution        
>
> Hi Dr. Fischl,
> Thank you for clarifying that!
>
> As a follow up question, I just wanted to double check that the method
> outlined in this post is still a valid approach to obtaining the CNR values
> for each of the ROIs in the Desikan-Killiany atlas(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg62066.html)
> .
>
> Briefly, you recommended converting the aparc annotation to labels in the
> atlas, and applying mri_cnr to each label.
>
> Best,
> Prad
>
> On Thu, May 28, 2020 at 9:14 AM Bruce Fischl <fischl@nmr.mgh.harvard.edu>
> wrote:
>       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
>
>
>_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer