If you have run recon-all on a case, you can use wm-anat-snr to compute the SNR in WM (basically the meanWM/stdWM -- this is not what you are suggesting because it does not use background). You can use freeview to draw your ROIs. You can use mri_segstats to get the mean and std in each ROI

On 9/8/2022 10:08 AM, Marina Fernández wrote:

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Dear experts,

I would like to calculate the SNR by dividing the mean intensity of the signal of interest by the SD of the noise. To do this, I would like to create a small circular ROI and place it within the region of interest and a larger circular ROI and place it within the 'background' region that is parcelled to each subject in apas+head.mgz (ID=130).

Do you know what functions I can use to create these ROIs and place them within the regions I want? Do you know a better method to calculate the SNR?

Thank you in advance.

Best regards,

Marina
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