On Fri, May 29, 2020 at 9:32 AM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

External Email

Hi Prad

for mri_cnr, yes, it samples inwards and outwards 1mm along the surface
normal. And I think pctsurfcon is the tool I meant, but hopefully David
and/or Doug can confirm
cheers
Bruce
On Fri, 29 May 2020, Pradyumna Bharadwaj wrote:

>
>         External Email - Use Caution
>
> Hi Dr. Fischl,
> It looks like pctsurfcon was the tool you were referring to. Is this the
> right one?
>
> Also, would brain.mgz be the appropriate volume to use to extract the G-W
> contrast ratios for the cortical parcels?
>
> Finally, for mri_cnr according to this post, the CNR values are computed
> using the voxels at the interface of the white and pial surface(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg38829.html)
>
> Are these voxels offset from the white and pial surfaces by a specific
> default distance?
>
> Thanks,
> Prad
>
> On Thu, May 28, 2020 at 10:47 AM Pradyumna Bharadwaj
> <prad@email.arizona.edu> wrote:
> Is it the pctsurfcon tool? (
> https://surfer.nmr.mgh.harvard.edu/fswiki/pctsurfcon)
>
> 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 intheDesikan-Killianyatlas(https://www.mail-archive.com/freesurfer@nmr.mgh.ha
> rva
> > 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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