or you can do it in matlab with read_annotation.m
You can read in the mgh file with MRIread.m
Make sure to account for the fact that the annotation vertices will be
0-based and matlab is 1-based

On 4/3/19 6:15 PM, Bruce Fischl wrote:
> 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.
>> <DGREVE@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
>>       > <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
>>       >     >
>>       >  >_______________________________________________
>>       >     Freesurfer mailing list
>>       >     Freesurfer@nmr.mgh.harvard.edu
>> <mailto: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