External Email - Use Caution
Thank you very much for your quick response. I still have a challenge locating the output file after running the suggested command ( mri_cnr $SUBJECTS_DIR/bert/surf/ $SUBJECTS_DIR/bert/mri/norm.mgz) with my subject. Can you please provide me with the full command for calculating contrast-to-noise ratio and signal-to-noise ratio of white matter, gray matter and CSF since am a beginner Or a video link to calculate them.
This is what i see after running the command
mri_cnr /Applications/freesurfer/7.1.1/SUBNEW/PA1//label/lh.cortex.label
mri_cnr -- compute the gray/white/csf contrast-to-noise ratio for volumes.
usage: mri_cnr [options] <surf directory> <vol 1> <vol 2> ...
usage example (assumes fs pipeline has finished for subject subj1): mri_cnr subj1/surf subj1/mri/orig.mgz
Available options:
-s <slope_fname> <dist in> <dist out> <step in> <step out>: compute slope based on given values, write it to slope and offset files labeled <slope_fname> (e.g., `lh.<slope_fname>.slope.mgz')
-t : print only the total CNR to stdout (stderr still contains more information)
-l <logfile>: log cnr to file <logfile>. Will contain 8 values in the following order: gray_white_cnr, gray_csf_cnr, white_mean, gray_mean, csf_mean, sqrt(white_var), sqrt(gray_var), sqrt(csf_var)
label <lh> <rh>: read hemisphere labels from <lh> and <rh>
-u, -?, -help : print usage information and quit
-version : print software version information and quit.
On Thu, Feb 9, 2023 at 3:46 PM John Anderson jb19790001@gmail.com wrote:
External Email - Use CautionYou might consider the command wm-anat-snr to compute SNR
On Thu, Feb 9, 2023 at 10:38 AM Kumar, Avnish < Avnish.Kumar@mgh.harvard.edu> wrote:
You could also use these:
- 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
For SNR, you'll have to calculate them as:
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://secure-web.cisco.com/1yBb2GkovBSvAi4q4ORDMfb9gbA5D1lxhgbEGgbhkKPLCst... 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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1xSgxlzAik8YTDjWAB7qFryOCtl3ASznPC5ZYb3rUdYk5Sx... 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-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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1ZggDbPTzdGw9n6UPfbx6DkxHs3xPFi3eKXLAAkQkDTA-uq... 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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1eKMzT1QuLsmlThN1WG_Vgbfffp6njvxjuNiaWXCgMQWhVK... 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 <*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1eKMzT1QuLsmlThN1WG_Vgbfffp6njvxjuNiaWXCgMQWhVK... 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> .
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1ZggDbPTzdGw9n6UPfbx6DkxHs3xPFi3eKXLAAkQkDTA-uq... 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/1eKMzT1QuLsmlThN1WG_Vgbfffp6njvxjuNiaWXCgMQWhVK... < https://secure-web.cisco.com/1eKMzT1QuLsmlThN1WG_Vgbfffp6njvxjuNiaWXCgMQWhVK... . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.