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