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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:
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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 CautionHi,
I had a question about the -label flag in mri_cnr.
- 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
- 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
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