MRIaggr-calcRegionaContrast: Compute regional contrast parameters

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

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.

See Also

selectContrast to select the regional parameter(s).
calcW to compute the neighboring matrix.

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 ")

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