You could also use these:
1. For CNR you can use the mri_cnr tool:
mri_cnr [options] <surf directory> <vol 1>
For example:
mri_cnr $SUBJECTS_DIR/bert/surf/ $SUBJECTS_DIR/bert/mri/norm.mgz
1. For SNR, you'll have to calculate them as:
* Run the recon-all pipeline to process your MRI data.
* Use the mri_binarize tool to create a binary mask of the ROI in the
image.
* Use the mri_segstats tool to calculate the mean and standard deviation
of the intensity values within the ROI.
* Then your SNR = mean_intensity/std_of_intensity.
Best,
Avnish
________________________________
From: [email protected]
<[email protected]> on behalf of Huang, Yujing
<[email protected]>
Sent: Tuesday, February 7, 2023 9:09 AM
To: Freesurfer support list <[email protected]>
Subject: Re: [Freesurfer] MRI image quality metrics
Hi,
The following is taken from
https://github.com/ComaRecoveryLab/Lesion_Correction as mentioned in this
paper https://www.sciencedirect.com/science/article/pii/S2215016120302144
“
Qualitative and Quantitative Assessment of MRI Data
SNR: We calculated SNR for each subject using the “wm-anat-snr” FreeSurfer tool
available in FreeSurfer v6.0. Voxels from the subject’s normalized T1
(norm.mgz) that containing white matter (WM) as defined by the subject’s
aparc+aseg.mgz are used to calculate SNR with this tool.
SNR = (mean WM)/(stdev WM)
We ran the following command for each subject:
wm-anat-snr –s
CNR: We calculated CNR for each subject using the “mri_cnr” FreeSurfer tool
available in FreeSurfer v6.0. This tool finds the average between two CNRs: the
subject’s (1) WM and gray matter (GM) CNR and (2) gray matter and cerebrospinal
fluid (CSF) CNR. The average CNR is then calculated and reported for each
hemisphere. Finally, the CNR for both hemispheres are averaged to produce a
full brain CNR.
WM-GM CNR = (delta(WM,GM)^2)/(total variance) GM-CSF CNR =
(delta(GM,CSF)^2)/(total variance) Hemisphere CNR = (WM-GM CNR + GM-CSF CNR) x
2 Full Brain CNR = (Left Hemisphere CNR + Right Hemisphere CNR) x 2
“
Best,
Yujing
From: [email protected]
<[email protected]> On Behalf Of MANSON ERIC NAAB
Sent: Tuesday, February 7, 2023 5:26 AM
To: Freesurfer support list <[email protected]>
Subject: [Freesurfer] MRI image quality metrics
External Email - Use Caution
Dear FreeSurfer experts,
Please, I need your assistance and guidance on calculating the
contrast-to-noise ratio (CNR) and signal-to-noise-ratio (SNR) of White matter,
Gray matter, and CSF of the brain after recon-all.
Thank you
_______________________________________________
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