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:

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


  _______________________________________________
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Thank you, Drs. Fischl and Greve. I was able to compute the surface CNR following your suggestion.

Regards --VM

On Wed, Apr 3, 2019 at 3:25 PM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:

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

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