Hi Bruce,

Thanks for the help! I was thinking of the CSF as a homogeneous structure, but I will see what I get with the caudate.

Best wishes,

Max

On dijous 14 abril 2016 14:49 CEST, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

Hi Max

I don't think we output the background std, but depending on your goal you could use the std of some relatively homogenous structure (caudate?) as a proxy. This will probably overestimate it a bit. Alternatively you could draw a background ROI and right click on it in freeview and it will allow you to compute statistics. You could also use mri_vol2vol to map this across subjects using the talairach.m3z and measure it in each one.

cheers Bruce

On Thu, 14 Apr 2016, BAUTISTA-PERPINYA Maximilià wrote:

...

Hi experts,

I wish to calculate signal-to-noise ratio (SNR) of my T1 MRI images. Do you know if I can use freesurfer for this? SNR = mean signal at ROI / standard dev. of background noise. The mean signal at ROI I can obtain from the aseg.stats table, but I cannot seem to find a value describing the standard dev. of the background noise. Does anybody know if freesurfer can output this? Otherwise, how would you recommend to calculate it?

Thank you for your help.

Best,

Max

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

wm-anat-snr will do it for white matter. I've never been able to relate the final measure to the quality of the analysis, but you can try.

On 04/14/2016 08:49 AM, Bruce Fischl wrote:

Hi Max

I don't think we output the background std, but depending on your goal you could use the std of some relatively homogenous structure (caudate?) as a proxy. This will probably overestimate it a bit. Alternatively you could draw a background ROI and right click on it in freeview and it will allow you to compute statistics. You could also use mri_vol2vol to map this across subjects using the talairach.m3z and measure it in each one.

cheers Bruce

On Thu, 14 Apr 2016, BAUTISTA-PERPINYA Maximilià wrote:

...

Hi experts,

I wish to calculate signal-to-noise ratio (SNR) of my T1 MRI images. Do you know if I can use freesurfer for this? SNR = mean signal at ROI / standard dev. of background noise. The mean signal at ROI I can obtain from the aseg.stats table, but I cannot seem to find a value describing the standard dev. of the background noise. Does anybody know if freesurfer can output this? Otherwise, how would you recommend to calculate it?

Thank you for your help.

Best,

Max

---

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