28 May
2020
28 May
'20
12:32 p.m.
Hi Prad
what is your goal? What you describe below should work
cheers Bruce On Thu, 28 May 2020, Pradyumna Bharadwaj wrote:
External Email - Use Caution
Hi Dr. Fischl, Thank you for clarifying that!
As a follow up question, I just wanted to double check that the method outlined in this post is still a valid approach to obtaining the CNR values for each of the ROIs in the Desikan-Killiany atlas(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg62066.html) .
Briefly, you recommended converting the aparc annotation to labels in the atlas, and applying mri_cnr to each label.
Best, Prad
On Thu, May 28, 2020 at 9:14 AM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: External Email
Hi Prad if you use the cortex.label is will avoid using the non-cortical regions in the surface, like the midline, so should be a more accurate measure cheers Bruce On Thu, 28 May 2020, Pradyumna Bharadwaj wrote: > > External Email - Use Caution > > Hi, > > I had a question about the -label flag in mri_cnr. > > 1) When you do not use the -label option and just use the following command: > mri_cnr $FREESURFER_HOME/subjects/bert/surf $FREESURFER_HOME/subjects/be > rt/mri/norm.mgz > > The output is as follows > > white = 96.6+-6.0, gray = 75.7+-13.5, csf = 55.3+-16.6 gray/white CNR = 1. > 983, gray/csf CNR = 0.907 > > lh CNR = 1.445 > > white = 96.4+-6.0, gray = 76.0+-13.3, csf = 55.6+-16.2 gray/white CNR = 1.95 > 2, gray/csf CNR = 0.943 > > rh CNR = 1.448 > > total CNR = 1.446 > > > 2) When you add -label $FREESURFER_HOME/subjects/bert/label/lh.cortex.label > $FREESURFER_HOME/subjects/bert/label/rh.cortex.label to the first command, > you get different (lower) cnr values. > > white = 96.6+-6.0, gray = 73.1+-18.9, csf = 50.8+-20.5 gray/white CNR = 1.38 > 9, gray/csf CNR = 0.644 > > lh CNR = 1.016 > > white = 96.4+-6.0, gray = 73.4+-18.8, csf = 51.0+-20.3 gray/white CNR = 1.35 > 3, gray/csf CNR = 0.652 > > rh CNR = 1.002 > > total CNR = 1.009 > > How is the lh.cortex and rh.cortex label changing the CNR computation? > > Any inputs or thoughts on this matter are greatly appreciated! > > Thanks, > Prad > >_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer