MRIaggr-calcControlateral: Compute contraleral normalization values

In bozenne/MRIaggr: Management, Display, and Processing of Medical Imaging Data

Description

Associate each voxel to an hemisphere and compute the difference between the voxel values and their contralateral correspondent.

Usage

## S4 method for signature 'MRIaggr'
calcContralateral(object, param, num = NULL, type = "mean", 
     param.ref = NULL, distband = 1, lambda = 1, 
	 verbose = optionsMRIaggr("verbose"), update.object = FALSE, overwrite = FALSE)

Arguments

object	an object of class MRIaggr. REQUIRED.
param	the contrast parameters to normalize. character vector. REQUIRED.
num	the slices to extract. numeric vector or NULL.
type	the method used to compute the contralateral correspondent of each voxel. Can be "mean", "median" or "1NN_penalised".
param.ref	the parameter to use as a reference for the identification of the contralateral voxel. character or NULL if no reference parameter available.
distband	the distance within which the contralateral values are considered. postive numeric.
lambda	the importance of the penalization. numeric.
verbose	should the execution of the function be traced ? logical.
update.object	should the resulting contralateral parameters be stored in object ? logical.
overwrite	if contrast parameters with the same names are already stored in object@data, can they be overwritten ? logical.

Details

ARGUMENTS:
Information about the num argument can be found in the details section of initNum.

FUNCTION:
To compute the contralateral correspondent of each voxel, the mean or median value of the contralateral observations present in the distband can be used. Otherwise, considering a reference parameter, the contralateral voxel that minimised the difference in contrast (denoted I) with the voxel of interest (denoted x) penalized by the distance is retained :

voxel_{contro} = argmin_{y} \frac{|I(x) - I(y)|}{σ} + λ * dist(x,y) where σ=sd(I)

The param.ref and lambda are active only if type is "1NN_penalized". In this case lambda equal 0 means no penalization.

Value

An list containing :

• [[data]] : a data.frame containing the coordinates and the parameters normalized by the contralateral values.

• [[index_plot]] : two lists containing the observations used to compute the contralateral values, one for each hemisphere.

See Also

calcHemisphere to identify the hemispheres. selectContrast to select the contralateral normalized parameters or the hemisphere parameter.

Examples

## load a MRIaggr object
data("MRIaggr.Pat1_red", package = "MRIaggr")

## associate each voxel to its contralateral correspondant 
## according T1 parameter and compute the normalized parameters
res <- calcContralateral(MRIaggr.Pat1_red, param = c("DWI_t0","T2_FLAIR_t2"), num = NULL,
         type = "mean", param.ref = "T1_t0", distband = 1, lambda = 1, verbose = TRUE)

## display
multiplot(res$data[,c("i","j","k"),drop = FALSE],
             contrast = res$data$DWI_t0_contro
)

multiplot(res$data[,c("i","j","k"), drop = FALSE],
             contrast = res$data$DWI_t0_contro,
             index1 = res$data[res$index_plot$index.plot_lesionR,c("i","j","k"), drop = FALSE],
             index2 = res$data[res$index_plot$index.plot_lesionL,c("i","j","k"), drop = FALSE]
) 

bozenne/MRIaggr documentation built on May 13, 2019, 1:39 a.m.