actually, if you convert the aparc annotations to a bunch of labels, you
can run:
mri_cnr -label <left hemi label name> <right hemi label name> ...
and it will limit the calculations to that label. FOr example:
mri_cnr -label ~/links/subjects/bruce.dev//label/lh.cortex.label
~/links/subjects/bruce.dev//label/rh.cortex.label
~/links/subjects/bruce.dev/surf ~/links/subjects/bruce.dev/mri/norm.mgz
reading lh and rh labels from
/homes/4/fischl/links/subjects/bruce.dev//label/lh.cortex.label and
/homes/4/fischl/links/subjects/bruce.dev//label/rh.cortex.label
processing MRI volume
/homes/4/fischl/links/subjects/bruce.dev/mri/norm.mgz...
white = 91.0+-9.7, gray = 57.8+-20.2, csf = 33.6+-15.4
gray/white CNR = 2.204, gray/csf CNR = 0.910
lh CNR = 1.557
white = 90.4+-10.0, gray = 57.6+-19.7, csf = 34.6+-15.2
gray/white CNR = 2.196, gray/csf CNR = 0.851
rh CNR = 1.523
total CNR = 1.540
cheers
Bruce
On Wed, 3
Apr 2019, neuroimage analyst wrote:
External Email - Use Caution
Thanks, Dr. Greve. Where can I find the correspondence between the vertices in
?h.w-g.pct.mgh and
the parcellations?
On Wed, Apr 3, 2019 at 2:41 PM Greve, Douglas N.,Ph.D. <dgr...@mgh.harvard.edu>
wrote:
you can get the contrast from surf/?h.w-g.pct.mgh, which you can average
over each parcellation. Not sure where you would get the noise term from.
On 4/3/19 5:23 PM, neuroimage analyst wrote:
>
> External Email - Use Caution
>
> I apologize, Dr. Fischl, that I wasnt clear.
>
> We are using Desikan-Killany atlas that has 68 surfaces defined on the
> atlas, 34 on each hemisphere.
>
> I might be wrong, but I was thinking that there should be a way to
> define CNR of orbitofrontal cortex (OFC), for example. I know that we
> can get CNR of the whole brain gray/white/CSF but is it possible to
> get the gray/white/CSF CNR of OFC only? If no, then we report the
> difference in cortical thickness as we observe. If yes, we want to
> regress or potentially discard the worst CNR subjects and recompute
> the statistics. the hope is we can get 68 CNRs for each surface in the
> Desikan-Killany atlas.--Kindly let me know your suggestions and
thoughts.
>
> Thanks
>
> On Wed, Apr 3, 2019 at 2:11 PM Bruce Fischl
> <fis...@nmr.mgh.harvard.edu <mailto:fis...@nmr.mgh.harvard.edu>> wrote:
>
> can you clarify what you mean? What 68 surfaces do you mean? And
> what do
> you mean by CNR of a surface?
> On Wed, 3 Apr 2019, neuroimage analyst wrote:
>
> >
> > External Email - Use Caution
> >
> > Hi,
> > We were interested in measuring CNR of each of the 68 surfaces
> in Desikan-Killany atlas and compare
> > between the groups to verify if our results are being biased by
> CNRs in the group?
> >
> > I came across mri_cnr and mris_ms_surface_cnr binaries in the
> FreeSurfer tools and were wondering
> > how to loop it through each subject in the subject_list.txt file
> (each column in subject_list.txt is
> > the subject id) so that we get a text file (similar to ?cortical
> thickness txt file generated using
> > aparcstats2table) that has # of subjects * # of regions txt file
> and the entries within each matrix
> > cell is the CNR value corresponding to surface X of Subject Y.
> >
> > We will greatly appreciate any help or pointers regarding this.
> >
> > Thanks
> >
> > Regards
> >
> > --VM
> >
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