On Thu, May 28, 2020 at 9:46 AM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

External Email

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 <fischl@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
> <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
> > >
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