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We provide example subjects, like bert, as part of the freesurfer distribution. But the install location on the Mac (and linux) is usually write protected and so while you can read data from there, you can’t write data there. You can place your own subject data - or copy the subject data provided in the fresurfer distribution - to somewhere you can write to like your home directory, e.g. … copy in the data … $ cd $HOME$ rm -rf subjects$ (cd /Applications/freesurfer/7.1.1; tar cpf - subjects) | tar xpf - … check it is there … $ ls -d subjects/bert/statssubjects/bert/stats … reset SUBJECTS_DIR to the new location where you can both read and write data … $ export SUBJECTS_DIR=$HOME/subjects … try the command again … $ wm-anat-snr --s bert - R. On Feb 17, 2023, at 19:43, MANSON ERIC NAAB <enman...@st.ug.edu.gh> wrote: External Email - Use Caution Thank you once again for your reply. After running the command wm-anat-snr --s <subject name> to determine the white matter signal-to-noise ratio, I receive an error about the output. It fails to write the output. Please, how do I solve this?MACs-MacBook-Pro:~ mac$ export FREESURFER_HOME=/Applications/freesurfer/7.1.1MACs-MacBook-Pro:~ mac$ export SUBJECTS_DIR=$FREESURFER_HOME/subjectsMACs-MacBook-Pro:~ mac$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-darwin-macOS-7.1.1-20200811-8b40551 --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME /Applications/freesurfer/7.1.1FSFAST_HOME /Applications/freesurfer/7.1.1/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR /Applications/freesurfer/7.1.1/subjectsMNI_DIR /Applications/freesurfer/7.1.1/mniFSL_DIR /Users/mac/fslMACs-MacBook-Pro:~ mac$ cd $SUBJECTS_DIRMACs-MacBook-Pro:subjects mac$ wm-anat-snr --s bertERROR: cannot write to /Applications/freesurfer/7.1.1/subjects/bert/statsOn Sat, Feb 11, 2023 at 2:11 PM John Anderson <jb19790...@gmail.com> wrote: 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> --snrdo 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 --snrmake 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 commandmri_cnr /Applications/freesurfer/7.1.1/SUBNEW/PA1//label/lh.cortex.labelmri_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.mgzAvailable 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 SNROn Thu, Feb 9, 2023 at 10:38 AM Kumar, Avnish <avnish.ku...@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.mgzFor 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,AvnishFrom: 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 AMTo: 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/1GW7LdX41sNV79_a8x11n-kRoiFNfVNYL0Ap-AHHpQ3tHl1qudG4bTlM2bBqPgJL4lYjNAtbjnH37EDsvvGWC_TmsCVrQAqRz0icPpFLUlMd62bW98y6WiA7L1KvUjGp3Vqgo8GiIw_D2fufaiXbxCZNE7JhvUnsac4KTqJlbb3h9s58aIlaBdKsw9tj2CerpuJUFsFMaTlIHvvj5_KyAqxVlPYmyz9DMDn9b0j5MsbIShFwrisZ35jS0HnahqJz9VE8Wn1WEU-skxJmCxqtL62cJNi-cGYX_Vgj4rJo0xANFsTor5SH78BOGp984K6J1/https%3A%2F%2Fgithub..com%2FComaRecoveryLab%2FLesion_Correction%26nbsp; 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/1hQvY1YI8eNsVP8riMVfQKAJE3-zVDvNtjJmOWcjhI4heW-VTsCNh6OkIZEThC1qtU5-snz-F-bstnTIdq04FJAjJd50ucaKtRidbH2wkTwSCowGItwrjjVRe5SHmx0KATUg3HdjqB7yoq5kg3jyhfSM9ftM1DfaFc53VjkSQe8wdI4ZZdT7RiJrI2EcyUD9r8_Be3ojHTZ1pPa2Vud-58KH4xsmG-lM7B97__nPW04IgrFxh4s2xYDghPi7JR9r_kdpUDB7M6W523Q4vpkSRNpiN_iKpPaoZBktx6XByuU_Up7M8Y2jlf8uA4dXydjgAb7fevx0vVvf5-oAuApjD3A/https%3A%2F%2Fwww.sciencedirect.com%2Fscience%2Farticle%2Fpii%2FS2215016120302144%26nbsp;“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 NAABSent: Tuesday, February 7, 2023 5:26 AMTo: 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.. 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