Description Usage Arguments Value Author(s)
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.
1 | 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)
|
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 |
a numeric value indicating contrast-to-noise-ratio relative to air
Timothy R. Koscik <timkoscik+niiqc@gmail.com>
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