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 > > > > > >_______________________________________________ > > 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
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