On Fri, May 29, 2020 at 9:45 AM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

External Email

Hi Prad

that is a hard question to answer. brain.mgz has been more aggressively
bias corrected than norm and will have removed most of the variability in
the wm. If gm is all you care about you could use it, but if you also
care about wm you might use the norm (or even the nu)

cheers
Bruce
On Fri, 29 May 2020,
Pradyumna Bharadwaj wrote:

>
>         External Email - Use Caution
>
> Thanks for clarifying that! Just one more question: For either pctsurfcon or
> mri_cnr, is brain.mgz the more appropriate volume to extract the g-w
> contrasts or g-w or g-csf CNR values from cortical parcels? (compared to
> norm.mgz)
>
> Thanks,
> Prad
>
> 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 pialsurface(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg3882
> 9.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 ROIsintheDesikan-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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