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
> <fischl@nmr.mgh.harvard.edu <mailto:fischl@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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