nii.qc.cnr: Contrast-to-Noise Ratio

In TKoscik/nifti.qc: Quality control metrics and reports for NIFTI data

Description

Calculate the the contrast ratio between GM and WM regions relative to background noise.

CNR = |μ_GM - μ_WM| / [√(σ^2_AIR + σ^2_WM + σ^2_GM)]

Magnotta VA, Friedman L, BIRN F. Measurement of signal-to-noise and contrast-to-noise in the fBIRN multicenter imaging study. Journal of digital imaging. 2006 Jun 1;19(2):140-7.

Usage

nii.qc.cnr(img.nii, img.vol=1L, gm.nii, gm.vol=1L, gm.dir="gt", gm.thresh=0, wm.nii, wm.vol=1L, wm.dir="gt", wm.thresh=0, air.nii, air.vol=1L, air.dir="eq", air.thresh=1)

Arguments

img.nii	Full directory listing to desired nifti image (unzipped)
img.vol=1L	For multi volume images; an integer indicating the volume to load (1..N)
gm.nii	Full directory listing to desired nifti image to use for GM (unzipped). Must be identical pixel dimensions to base image.
gm.vol=1L	For multi volume images; an integer indicating the volume to load (1..N)
gm.dir="gt"	Direction to threshold the GM mask image to generate the desired ROI. Options include ("gt") [>] Default, "ge" [>=], "lt" [<], "le" [<=], "eq" [==]
gm.thresh=0	Value at which to threshold the GM mask image to generate an ROI. E.g., for binary masks, where the value 1 indicates the ROI, default of >0, will generate the appropriate mask
wm.nii	Full directory listing to desired nifti image to use for WM (unzipped). Must be identical pixel dimensions to base image.
wm.vol=1L	For multi volume images; an integer indicating the volume to load (1..N)
wm.dir="gt"	Direction to threshold the WM mask image to generate the desired ROI. Options include ("gt") [>] Default, "ge" [>=], "lt" [<], "le" [<=], "eq" [==]
wm.thresh=0	Value at which to threshold the WM mask image to generate an ROI. E.g., for binary masks, where the value 1 indicates the ROI, default of >0, will generate the appropriate mask
air.nii	Full directory listing to desired nifti image to use for identifying the air region around the head (unzipped). Must be identical pixel dimensions to base image.
air.vol=1L	For multi volume images; an integer indicating the volume to load (1..N)
air.dir="gt"	Direction to threshold the air mask image to generate the desired ROI. Options include ("gt") [>] Default, "ge" [>=], "lt" [<], "le" [<=], "eq" [==]
air.thresh=0	Value at which to threshold the air mask image to generate an ROI. E.g., for binary masks, where the value 1 indicates the ROI, default of >0, will generate the appropriate mask

Value

a numeric value indicating contrast-to-noise-ratio relative to air

Author(s)

Timothy R. Koscik <[e-mail]>

TKoscik/nifti.qc documentation built on May 6, 2019, 4:30 p.m.