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. >> <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 >> >> >> > > _______________________________________________ > 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
