You probably don't have write permission to that folder.
Also, you can try
mri_segstats --qa-stats subject subject.qa.dat
Run mri_segstats with --help to understand what is in the qa.dat file
On 2/17/2023 7:43 PM, MANSON ERIC NAAB 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/7.1.1
MACs-MacBook-Pro:~ mac$ export SUBJECTS_DIR=$FREESURFER_HOME/subjects
MACs-MacBook-Pro:~ mac$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
-------- freesurfer-darwin-macOS-7.1.1-20200811-8b40551 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /Applications/freesurfer/7.1.1
FSFAST_HOME /Applications/freesurfer/7.1.1/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /Applications/freesurfer/7.1.1/subjects
MNI_DIR /Applications/freesurfer/7.1.1/mni
FSL_DIR /Users/mac/fsl
MACs-MacBook-Pro:~ mac$ cd $SUBJECTS_DIR
MACs-MacBook-Pro:subjects mac$ wm-anat-snr --s bert
ERROR: cannot write to /Applications/freesurfer/7.1.1/subjects/bert/stats
On 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>
--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
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-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://github.com/ComaRecoveryLab/Lesion_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://www.sciencedirect.com/science/article/pii/S2215016120302144
<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
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