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Last data update: 2014.03.03

R: Compute regional contrast parameters

calcRegionalContrast

R Documentation

Compute regional contrast parameters

Description

Compute the regional contrast parameters.

Usage

## S4 method for signature 'MRIaggr'
calcRegionalContrast(object,param, bandwidth, power = 2, diagonal = FALSE,
         W = "ifany", W.range, W.spatial_res = c(1,1,1), num = NULL, hemisphere = "both",
         name_newparam = paste(param,"regional", sep = "_"),
         verbose = optionsMRIaggr("verbose"), update.object = FALSE, overwrite = FALSE)

Arguments

`object`	an object of class `MRIaggr`. REQUIRED.
`param`	the contrast parameter(s) from which the regional parameter(s) will be computed. character vector. REQUIRED.
`bandwidth`	the bandwidth of the kernel. postive numeric. REQUIRED.
`power`	the power of the kernel. postive numeric.
`diagonal`	should the diagonal be added to the neighbourhood matrix ? logical.
`W`	the neighbourhood matrix. dgCMatrix or `"ifany"` leading to use the neighbourhood matrix stored in the `object` if possible, else to compute this matrix.
`W.range`	the neighbourhood range. postive numeric. Required only if `W` have to be computed.
`W.spatial_res`	a dilatation factor for the coordinates. positive numeric vector of size 3.
`num`	the slices to use. numeric vector or `NULL`.
`hemisphere`	the hemisphere to use. character.
`verbose`	should the execution of the function be traced ? logical.
`name_newparam`	the name of the new parameters. character vector.
`update.object`	should the resulting regional parameters be stored in `object` ? logical.
`overwrite`	if contrast parameters with the same names are already stored in `object` can they be overwritten ? logical.

Details

This function requires to have installed the Matrix and the spam package to work.

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

Information about the hemisphere arguments can be found in the details section of selectContrast.

Information about bandwidth and power arguments can be found in the details section of EDK.

Value

A data.frame containing in columns the regional parameters.

Examples

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

## compute regional values
res  <- calcRegionalContrast(MRIaggr.Pat1_red, param = c("T2_FLAIR_t2","T1_t0"), bandwidth = 1.875,
                        W.spatial_res = c(1.875,1.875,6), W.range = 6,
                        update.object = TRUE, overwrite = TRUE)

## display
par(mfrow = c(2,4), mar = rep(1.5,4), mgp = c(2,0.5,0))
multiplot(MRIaggr.Pat1_red, param = "T2_FLAIR_t2", num = 1:3,
             window = NULL, main = "raw - slice ")
multiplot(MRIaggr.Pat1_red, param = "T2_FLAIR_t2_regional", num = 1:3,
             window = NULL, main = "regional - slice ")

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(MRIaggr)
Loading required package: Rcpp
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/MRIaggr/MRIaggr-calcRegionaContrast.Rd_%03d_medium.png", width=480, height=480)
> ### Name: calcRegionalContrast
> ### Title: Compute regional contrast parameters
> ### Aliases: calcRegionalContrast calcRegionalContrast,MRIaggr-method
> ### Keywords: methods
> 
> ### ** Examples
> 
> ## load a MRIaggr object
> data("MRIaggr.Pat1_red", package = "MRIaggr")
> 
> ## compute regional values
> res  <- calcRegionalContrast(MRIaggr.Pat1_red, param = c("T2_FLAIR_t2","T1_t0"), bandwidth = 1.875,
+                         W.spatial_res = c(1.875,1.875,6), W.range = 6,
+                         update.object = TRUE, overwrite = TRUE)
 computing W ... W ready 
 param : T2_FLAIR_t2 T1_t0 
allocContrast[MRIaggr] : Cartographies "T2_FLAIR_t2_regional" "T1_t0_regional" 
                         have been allocated 
> 
> ## display
> par(mfrow = c(2,4), mar = rep(1.5,4), mgp = c(2,0.5,0))
> multiplot(MRIaggr.Pat1_red, param = "T2_FLAIR_t2", num = 1:3,
+              window = NULL, main = "raw - slice ")
> multiplot(MRIaggr.Pat1_red, param = "T2_FLAIR_t2_regional", num = 1:3,
+              window = NULL, main = "regional - slice ")
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>