External Email - Use Caution 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. < dgr...@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. > >> <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
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