fedi_dmri_snr

Synopsis

Compute the Signal-to-Noise Ratio (SNR) for diffusion MRI using the subtraction-based method described in Dietrich et al., JMRI 2007. Signal is estimated from the mean of two b=0 volumes and noise from their difference.

Usage

fedi_dmri_snr [-h] -d <file> -a <file> -m <file>

Description

This tool estimates the Signal-to-Noise Ratio (SNR) from two non-diffusion-weighted (b=0) volumes using the difference method, as described in Dietrich et al., JMRI 2007.

The SNR is computed within the provided binary mask as:

\[\mathrm{SNR} = \frac{\mu\left(\frac{S_1 + S_2}{2}\right)}{\sigma\left(\frac{S_1 - S_2}{\sqrt{2}}\right)}\]

where \(S_1\) and \(S_2\) are the two b=0 volumes, \(\mu(\cdot)\) denotes the mean signal, and \(\sigma(\cdot)\) denotes the standard deviation of the noise within the mask.

This method assumes that the two b=0 volumes are acquired independently and without preprocessing-induced duplication. It is appropriate when at least two distinct b=0 images are available.

Options

Help

  • -h, –help Show this help message and exit

Mandatory

  • -d, –dmri <file> Input 4D dMRI NIfTI image (e.g., dmri.nii.gz)

  • -a, –bval <file> Bvals file (e.g., bvals.txt)

  • -m, –mask <file> Binary mask within which SNR will be averaged (e.g., brain_mask.nii.gz)

References

  • Dietrich, O., Heiland, S., Sartor, K., 2007. Measurement of signal-to-noise ratios in MR images: Influence of multichannel coils, parallel imaging, and reconstruction filters. Journal of Magnetic Resonance Imaging, 26(2), 375–385.

  • Snoussi, H., Karimi, D., Afacan, O., Utkur, M. and Gholipour, A., 2025. Haitch: A framework for distortion and motion correction in fetal multi-shell diffusion-weighted MRI. Imaging Neuroscience.