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
<p...@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
<fis...@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
<fis...@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
> <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
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
> > <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
>
>
>_______________________________________________
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
