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Hello!

I had a couple of questions about how mri_cnr computes the contrast to noise ratio.

From previous posts, a command such as mri_cnr $FREESURFER_HOME/subjects/bert/surf $FREESURFER_HOME/subjects/bert/mri/norm.mgz gives the lh cnr, rh cnr, and total cnr for bert.

1) What exactly is happening when you reference the /surf directory here? 2) Are the CNR values for the norm.mgz volume being computed by using the lh white + lh pial; and rh white + rh pial surfaces? 3) Are the subcortical gm structures somehow involved in this calculation as well?

I'm asking question 3 because when you add a -label $FREESURFER_HOME/subjects/bert /label/lh.cortex.label $FREESURFER_HOME/subjects/bert/label/rh.cortex.label the lh cnr, rh cnr, and total cnr values that you get are now different.

The outputs for bert for each case is as follows (FreeSurfer v6 bert was used here): 1) *With /surf alone*

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) With /surf and -label *

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*

Any inputs or thoughts on this matter are greatly appreciated!

Thanks, Prad