Content-type: text/html Manpage of estimatesnr

estimatesnr

Section: User Commands (1)
Index Return to Main Contents

NAME

estimatesnr - Estimates the signal to noise ratio in b=0 images.

SYNOPSIS

estimatesnr -bgmask <mask> -schemefile <file> [-noiseroi <roi>]

DESCRIPTION

This program estimates the noise variance and the signal to noise ratio in a given ROI, for the b=0 data for a given scan.

The traditional method for estimating the noise is to sample two ROIs, one in brain white matter, and one in the background. Assuming that the background signal contained only noise, we can estimate the noise standard deviation as

sigma = sqrt(2.0 / (4.0 - PI)) * stddev(signal in background region)

where the constant scaling corrects for the Rician distribution of the noise, giving us the standard deviation sigma of the original signal. To synthesize data with the same noise conditions, we would take the true signal S_0 and calculate

S = |[S_0 + N(0, sigma), N(0, sigma)]|

where N(0, sigma) is a random sample drawn from normal distribution with mean 0 and standard deviation sigma.

The two-ROI approach is only valid when the signal in the background follows the distribution

S_b = |[N(0, sigma), N(0, sigma)]|

however, this is often not the case. Dietrich et al [JMRI 26:376-385 (2007)] showed the shortcomings of this approach and evaluated better ways to estimate the noise variance without using a background region.

ALTERNATIVES TO THE TWO-ROI APPROACH

The first method requires two b=0 images. We call this method sigma_diff, because it uses the difference between the two images. If S_{i1} is the signal in voxel i, image 1, and S_{i2} is the signal from the same voxel in image 2, and there are N voxels in the ROI, then

sigma_diff = stddev(S_{11} - S_{12},...,S_{N1} - S_{N2}) / sqrt(2)

The SNR is the mean signal in the ROI divided by sigma_diff, ie

mean(S_{i1} + S_{i2}) / [2.0 * sigma_diff]

The second method requires multiple b=0 images, and defines sigma_mult as the standard deviation of the signal over the ROI, across all K b=0 images. Again, let i be a voxel index, then

sigma_i = stddev(S_{i1},...,S{iK}))

sigma_mult = mean(sigma_1,...,sigma_N)

And finally SNR is

mean(S_{11}, S_{12},...,S_{1K}, S_{21},...,S_{NK}) / sigma_mult

If there are two or more b=0 images, both snr_diff and snr_mult will both be computed. The more b=0 images there are, the better the estimate via sigma_mult, but sigma_diff only ever uses the first two b=0 images.

USES OF NOISE VARIANCE IN CAMINO

The noise variance, or the signal to noise ratio (SNR) in white matter, is used in several Camino programs, such as:

picopdfs - the SNR is required to evaluate the uncertainty in principal directions.

restore - the noise standard deviation is required to do the fitting. However, the RESTORE method contains other parameters which have the same effect as altering the estimate of sigma. Thus you should consider sigma as a starting point for the RESTORE algorithm.

mbalign - this program uses RESTORE, see above.

EXAMPLES

Data exists in a voxel-ordered file, A.Bfloat. A white-matter region WM_ROI.hdr is drawn by hand.

estimatesnr -inputfile A.Bfloat -schemefile A.scheme -bgmask WM_ROI.hdr

Now we compute the same thing, only we use BG_ROI.hdr, which is simply WM_ROI.hdr translated such that the non-zero voxels are all in the background region of the image.

estimatesnr -inputfile A.Bfloat -schemefile A.scheme -bgmask WM_ROI.hdr -noiseroi BG_ROI.hdr

Start from data in a 4D Analyze file

analyze2voxel -inputfile data.hdr | estimatesnr -inputfile A.Bfloat -schemefile A.scheme -bgmask WM_ROI.hdr

OPTIONS

-bgmask <mask>: Path to an image header or raw data file that contains the region of interest. This image should mask out a region of interest that contains an approximately constant unweighted signal. Usually, we would choose a white matter structure for this purpose.
-schemefile <file>: Imaging scheme for the data. The program will select the b=0 measurements for the computation.
-noiseroi <roi>: An ROI placed outside the brain, where the mean signal is zero. If this is supplied, the noise variance is estimated using the "two ROI" technique.
-approxb0meas <x y z...>: Tells the program to use the specified measurements instead of the b=0 measurements. The arguments following The option should be integer indices of measurements that are approximately directionally isotropic. For example, imagine data with no b=0 measurements, but the first three are at b=50 s / mm^2. The program could then be called with the option "-approxb0meas 0 1 2". This option should only be used when signal is homogeneous across the selected measurements and across the ROI. This will not be the case for most diffusion-weighted measurements in the brain.

AUTHORS

Philip Cook <camino@cs.ucl.ac.uk>

BUGS

This document was created by man2html, using the manual pages.
Time: 02:07:11 GMT, December 04, 2017

Estimatesnr