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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 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 CautionHi, 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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