On Thu, May 28, 2020 at 10:12 AM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

External Email

David and Doug: can you point Prad in the right direction for looking at
gray and white signal changes and ratios?
On Thu, 28 May 2020, Pradyumna
Bharadwaj wrote:

>
>         External Email - Use Caution
>
> Hi Dr. Fischl,
> Thank you for suggesting that.
> Would it be possible to share a link to a page with information about this
> stream or to a patch?
>
> Thanks,
> Prad
>
> 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 theDesikan-Killianyatlas(https://www.mail-archive.com/freesurfer@nmr.mgh.harva
> rd.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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