nii.qc.cjv: Coefficient of Joint Variation

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

Description

CJV, a measure related to SNR and CNR that is presented as a proxy for the INU artifact. Lower is better.

CJV = (σ_WM + σ_GM)/|μ_WM - μ_GM|

Ganzetti M, Wenderoth N, Mantini D. Intensity inhomogeneity correction of structural MR images: a data-driven approach to define input algorithm parameters. Frontiers in neuroinformatics. 2016 Mar 15;10:10.

Usage

nii.qc.cjv(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)

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

Value

returns a numeric value corresponding to CJV

Author(s)

Timothy R. Koscik <[e-mail]>

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