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> 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 > 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
