External Email - Use Caution You might consider the command wm-anat-snr to compute SNR
On Thu, Feb 9, 2023 at 10:38 AM Kumar, Avnish <avnish.ku...@mgh.harvard.edu> wrote: > 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: > 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-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Huang, Yujing < > yhuan...@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 > https://secure-web.cisco.com/1thfo9hWCJUK_nYfNM9axD5kjhrzv1nVC_cWmWT2aic2ttFqLtKhuhi9E6AA5fXRqlBpbp24-HV_sfbVQik2RJDyE7c9eALg8zbpl340Dwhl2aijQIJcCFqj9K_RZhk5xCVRHURT36bgdsm5C36VxQ3fQh7sVLpsmxKo0Ie0hB8HrgI8Rn7JySIK5iCJZWL9q1OqnFWJgdRUgMDrVlJVf356x-vM1sz0IWVGsGErBQNdxLAYcSvFCTWx0fb6tb1mCw7ljDzERXM7qU-fnbvpV-AKWSuj0eVKouZoNRp8SgTUOIA2mR_VbqAJw9K2PU4OKa4g3f30QsCJpd0U1hcNz7Q/https%3A%2F%2Fgithub.com%2FComaRecoveryLab%2FLesion_Correction > as mentioned in > this paper > https://secure-web.cisco.com/1aMzZKpIcKTLwbYP_79ZqCUH8p9h0Xh4xqpm8fsmVREKN8hATdl6DHCSkFDKqidqmKqoAydr5eDqjVLAQDKN0zmR2k2Wckx-sv1P3JgKJVQWfpIVeyrh0tqwnGzqQm3nK9BQGA7rUSYwaCBBjmogAhlrnepeAo1_J0CQXj4rKMM-V_g9sXIIirV1h-sajPjULI9qcQw2orS-vs9tl65xAbfrEtmtZ35-IZO43Wk-1D2CsVkFyKCsuGxT5qcGTg9FV3VSUbHpeA-dKS1qkv8zYKtz4i-JeRm0y4E6YAs_B91ccue5fFsCAMyN4jKTPxkhNk7f7IRaIrbfA6GYyWFCX7A/https%3A%2F%2Fwww.sciencedirect.com%2Fscience%2Farticle%2Fpii%2FS2215016120302144 > > > > “ > > 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-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@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 > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1KDvbAKLrFBoPVGyqH2wpBHTCZi4G5JP4CoyRC23fpSgjgmUjIEIDk5ijfEjY7EcdqD7NMLPnurOJaIh0CESkCjdM-kajpNjDkBcmErgdRD0D7VHpAkbJK2Z0vtuzM98dlYvFfoA5RP_t9tAeeRdA-qZEqMyVFnCZytNMwGX7C6SXBJqlptH_9ue8D3YojwI-o03MasVSWHISnuBb-vLjFPQCtTLtRx7VahTcU3GnkMyiIRc3tk2mxwZDkdAvRHcODMGxX35AEUnYGnF7jDNZBlV8elaazdpSJr7VfItSdTLokLwsLxycodEFhQVZk1M8fBPC2gWDxUKYUo3Ku9AgQg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > The information in this e-mail is intended only for the person to whom it > is addressed. If you believe this e-mail was sent to you in error and the > e-mail contains patient information, please contact the Mass General > Brigham Compliance HelpLine at > https://secure-web.cisco.com/12BoyKcru_t9pVynKUJhc-03UXRo5_HIHSkdKg0g9g92cctClREzONivt7Av0WUs5ZZuFZ4PJaWFmVvl7wmn8NLe7S1Fl06iifPPUZmXnCA1-FqoMNvzj1po9VSXSMXQ05nkJnrA1xU9k2McGHE8ggROHrbaxz-xkYAPmE-RYtFG3jkzcl8ZY5wE6r2RVAShtaNoJImU4iRqvLIFmd-7r-EDo1fWDD_ki2hHNioYIh4bQYxDEJah_o26ujxDxzwGGZBA6L34goBxFC4Jh-vLnNcHGkvp2fA9iWlSWgGPKXmnrjsENdA_DOr3RinxcAeiDypqxTvJdtwxNG2kjfAtcSw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > < > https://secure-web.cisco.com/12BoyKcru_t9pVynKUJhc-03UXRo5_HIHSkdKg0g9g92cctClREzONivt7Av0WUs5ZZuFZ4PJaWFmVvl7wmn8NLe7S1Fl06iifPPUZmXnCA1-FqoMNvzj1po9VSXSMXQ05nkJnrA1xU9k2McGHE8ggROHrbaxz-xkYAPmE-RYtFG3jkzcl8ZY5wE6r2RVAShtaNoJImU4iRqvLIFmd-7r-EDo1fWDD_ki2hHNioYIh4bQYxDEJah_o26ujxDxzwGGZBA6L34goBxFC4Jh-vLnNcHGkvp2fA9iWlSWgGPKXmnrjsENdA_DOr3RinxcAeiDypqxTvJdtwxNG2kjfAtcSw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > . >
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