External Email - Use Caution export SUBJECTS_DIR=<path to your recons>
mri_cnr $SUBJECTS_DIR/<subject name>/surf/ $SUBJECTS_DIR/ <subject name> /mri/norm.mgz > output_CNR.txt wm-anat-snr --s <subject name> check stats/wmsnr.e3.dat .... the output is snr for the whole white matter. if you need snr for every roi in aseg.stats or wmparc.stats, then you can add the flag --snr to the command mri_segstats as follows: mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/freesurfer/6.0/ASegStatsLUT.txt --subject <subjectname> --snr do the same for wmparc.stats: mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject <subjectname> --surf-wm-vol --ctab /usr/local/freesurfer/6.0/WMParcStatsLUT.txt --etiv --snr make sure to change /usr/local/freesurfer/6.0/ASegStatsLUT.txt in the previous command to the FS folder on your system The last two commands update aseg.stats and wmparc.stats. They both will get a new column for SNR values for every roi. On Fri, Feb 10, 2023 at 10:25 PM MANSON ERIC NAAB <enman...@st.ug.edu.gh> wrote: > 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 <jb19790...@gmail.com> wrote: > >> 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 *MailScanner has detected a possible fraud >>> attempt from "secure-web.cisco.com" claiming to be* >>> https://secure-web.cisco.com/15IwpbwQA-WCW8yltQ1qpLfRaQV-8nx8afnQdmUW16GAXDwTUuUE2Uo7ja53lo5m7QrlaFd47dzyShd9KzRS2Es1vj-OVv2KNK8YwnrKMk_THG1mncORT2zcXT-2Z1CQSXJ4fFOwfPkWc8YM1bqAMvG6W_r9RBMqgVA7Jy3u04DIz5Zoov1ua2fuerdE_bRqfR8Qv_7aKjopsHnq6DmBpW392U8ds0q4m2dZ3_ztQfJIqJyH4PPd0ovHK46IAJ7zYw4Ssh70e0XtUfztdvLQFQjVeFQtJkc-E2Kq6USLv6B8cuoQG2e1PO4hoVZ1AhMkJCRIj1tFy8QWMhNJ2s_BUrQ/https%3A%2F%2Fgithub.com%2FComaRecoveryLab%2FLesion_Correction >>> <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/1yJ_L006xWsJhmlYzv5RmfhdySC-5IeAYuWn6pMVGtU1ScZSh4dbdq0Q00DqNIYarr5afo262h72-7niJXMcaNnhgVOsYFRHiTX7nl6URCYU_ZyxCOcXrJM7aLIjjmS6HVFtmzIKpFqj6xaeKJXzQGtuNzdH2Dw5kx8I6INI19xyZ7k3ueNDIKrpdSNZ9JMhb7_RMrhCsKNCnuRPQJdx4oQN_7OmZg2C8hg2Lna4GDZG_8PlJn-qFRlSD9lV6nsV5pwHaE9nr2M2NUtOH7yeHC2j9BQovgiKN1ogVexEhjWXYGWTr3j1m3c6Dj-7qSFMeWpTywHvGJPstr-EnNAdWoQ/https%3A%2F%2Fwww.sciencedirect.com%2Fscience%2Farticle%2Fpii%2FS2215016120302144 >>> <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 >>> *MailScanner has detected a possible fraud attempt from >>> "secure-web.cisco.com" claiming to be* >>> https://secure-web.cisco.com/1447-MTTQzBwszM7-35WcqfkPASOK24AkeGL4yYzpzWVU4wN9GPuqRn8ErKQz4fM-h-9VgPnaUdHpDibnYbn7IYzwjzU00T8uflxdFBMVfu4Z1Hnc8sd9XLHcqvf5VYn6ctgaEpsSXs4sOvQRsCPc1wmpk1Hx-DGjgAtrVaprjp48sI45X1eJx21ZdpNAGfeTtu4R9GwWuIdSt4GYISMQ8YWb5HGU34pJqEixBY5OmwVWIKEGCIHyHQIghcM0hCkGRbETHSVfZF7LAwvGEeds44y9HBMfucFRE_BdnpQj2ZF3SSQqZ3jYX2DpiHGjJopi-4_-16jkDuvWuC70bCE3kw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >>> <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. 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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. >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1447-MTTQzBwszM7-35WcqfkPASOK24AkeGL4yYzpzWVU4wN9GPuqRn8ErKQz4fM-h-9VgPnaUdHpDibnYbn7IYzwjzU00T8uflxdFBMVfu4Z1Hnc8sd9XLHcqvf5VYn6ctgaEpsSXs4sOvQRsCPc1wmpk1Hx-DGjgAtrVaprjp48sI45X1eJx21ZdpNAGfeTtu4R9GwWuIdSt4GYISMQ8YWb5HGU34pJqEixBY5OmwVWIKEGCIHyHQIghcM0hCkGRbETHSVfZF7LAwvGEeds44y9HBMfucFRE_BdnpQj2ZF3SSQqZ3jYX2DpiHGjJopi-4_-16jkDuvWuC70bCE3kw/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/19UvQ2_Te2X2Sz4BxqjeNt73mcRq5Da_jmoE7FBMJS_O8ZeR4Th9YsDIbQ_meNhZ7V4NWgkT3oZr9EilHmSsbUz-NWAmIiS0uzuwUvfaITDnVxDsKDxY8OKCpWM3_ILL9cSc8L5pQhnPXGrgUWI8b8FD6k2fbRBamqvpN9ku_-CXaTjWtBxP5QYf5DjuNhMnydVGtYYr62GVOy6xKDVp6cr-y8Nw-mDNVt4Pa2taWo8nXTFb3ftqG29TP9KIwEq4_ERPTcSKBV0pY9UgjbSeqH4hPXb1urnmL4qjjO1zHfd_bmsseZGO6ExzPDXw6snbap7ZIe2lnj5mAWfgwI6AxJw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > < > https://secure-web.cisco.com/19UvQ2_Te2X2Sz4BxqjeNt73mcRq5Da_jmoE7FBMJS_O8ZeR4Th9YsDIbQ_meNhZ7V4NWgkT3oZr9EilHmSsbUz-NWAmIiS0uzuwUvfaITDnVxDsKDxY8OKCpWM3_ILL9cSc8L5pQhnPXGrgUWI8b8FD6k2fbRBamqvpN9ku_-CXaTjWtBxP5QYf5DjuNhMnydVGtYYr62GVOy6xKDVp6cr-y8Nw-mDNVt4Pa2taWo8nXTFb3ftqG29TP9KIwEq4_ERPTcSKBV0pY9UgjbSeqH4hPXb1urnmL4qjjO1zHfd_bmsseZGO6ExzPDXw6snbap7ZIe2lnj5mAWfgwI6AxJw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > . >
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . 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.
