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

2. For SNR, you'll have to calculate them as:

1. Run the recon-all pipeline to process your MRI data.

2. Use the mri_binarize tool to create a binary mask of the ROI in the image.

3. Use the mri_segstats tool to calculate the mean and standard deviation of the intensity values within the ROI.

4. Then your SNR = mean_intensity/std_of_intensity.

Best,

Avnish

---

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edu>
Sent: Tuesday, February 7, 2023 9:09 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] MRI image quality metrics

 

Hi,

 

The following is taken from MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://github.com/ComaRecoveryLab/Lesion_Correction  as mentioned in this paper MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be 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: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of MANSON ERIC NAAB
Sent: Tuesday, February 7, 2023 5:26 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
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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