I see. I think Doug has a more modern stream for this that David Salat
has also used a lot
On Thu, 28 May 2020, Pradyumna Bharadwaj wrote:
External Email - Use Caution
Hi Dr. Fischl,
Thanks for confirming that!
We were broadly interested in testing whether age-related differences in
cortical measures were impacted by the CNR in each ROI.
Best,
Prad
On Thu, May 28, 2020 at 9:33 AM Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
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-Killianyatlas(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
<fis...@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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
