Hello Freesurfers,
We are beginning to perform QC on our subjects and want to look at signal to noise ratio. I've taken a look at the fsnr.nii overlay files, but we would like to be able to calculate a whole surface value for SNR for each functional run of each subject, so that we can exclude runs if that SNR values falls below our designated threshold. Is there a way to accomplish this?
Thanks,
Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital
There should be an fsnr.dat file in the fsfast analysis directory with the value that you want.
doug
On 12/20/10 1:30 PM, Adam Nitenson wrote:
Hello Freesurfers,
We are beginning to perform QC on our subjects and want to look atsignal to noise ratio. I've taken a look at the fsnr.nii overlay files, but we would like to be able to calculate a whole surface value for SNR for each functional run of each subject, so that we can exclude runs if that SNR values falls below our designated threshold. Is there a way to accomplish this?
Thanks,
Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
Is the fsnr.dat a Stable 5 feature? I'm working on Stable 4, and cannot find this file in my analysis directory,
e.g. /cluster/roffman/users/folate_subjects/FB0011099AA/bold/fmcsm5_functionals
...or anywhere else in the subject directory. All I see are the fsnr.nii overlay files.
-Adam
There should be an fsnr.dat file in the fsfast analysis directory with the value that you want.
doug
On 12/20/10 1:30 PM, Adam Nitenson wrote:
Hello Freesurfers,
We are beginning to perform QC on our subjects and want to look atsignal to noise ratio. I've taken a look at the fsnr.nii overlay files, but we would like to be able to calculate a whole surface value for SNR for each functional run of each subject, so that we can exclude runs if that SNR values falls below our designated threshold. Is there a way to accomplish this?
Thanks,
Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital
yep, stable 5
doug
Adam Nitenson wrote:
Hi Doug,
Is the fsnr.dat a Stable 5 feature? I'm working on Stable 4, andcannot find this file in my analysis directory,
e.g. /cluster/roffman/users/folate_subjects/FB0011099AA/bold/fmcsm5_functionals
...or anywhere else in the subject directory. All I see are the fsnr.nii overlay files.
-Adam
There should be an fsnr.dat file in the fsfast analysis directory with the value that you want.
doug
On 12/20/10 1:30 PM, Adam Nitenson wrote:
Hello Freesurfers,
We are beginning to perform QC on our subjects and want to look atsignal to noise ratio. I've taken a look at the fsnr.nii overlay files, but we would like to be able to calculate a whole surface value for SNR for each functional run of each subject, so that we can exclude runs if that SNR values falls below our designated threshold. Is there a way to accomplish this?
Thanks,
Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital
Is that the only (relatively convenient) way to get this data? I'm not sure if we're ready to start reprocessing all of our subjects. I noticed that the selxavg-sess command had a "-svsnr" argument for "save estimate of SNR to analysis/estsnr". Would this give me the relevant data? My main concern is that I used "selxavg3-sess" instead of "selxavg-sess" during processing; I'm not sure what the difference between the two is, and I am hesitant to use a different command that might change other aspects of our data.
-Adam
yep, stable 5
doug
Adam Nitenson wrote:
Hi Doug,
Is the fsnr.dat a Stable 5 feature? I'm working on Stable 4, andcannot find this file in my analysis directory,
e.g. /cluster/roffman/users/folate_subjects/FB0011099AA/bold/fmcsm5_functionals
...or anywhere else in the subject directory. All I see are the fsnr.nii overlay files.
-Adam
There should be an fsnr.dat file in the fsfast analysis directory with the value that you want.
doug
On 12/20/10 1:30 PM, Adam Nitenson wrote:
Hello Freesurfers,
We are beginning to perform QC on our subjects and want to lookat signal to noise ratio. I've taken a look at the fsnr.nii overlay files, but we would like to be able to calculate a whole surface value for SNR for each functional run of each subject, so that we can exclude runs if that SNR values falls below our designated threshold. Is there a way to accomplish this?
Thanks,
Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital
freesurfer@nmr.mgh.harvard.edu
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