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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/bert/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 = 1.952, 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 = 1.389, 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 = 1.353, 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