MRIaggr (version 1.1.5)

calcNormalization: Compute normalization values

Description

Compute the normalization values for each contrast parameter.

Usage

"calcNormalization"(object, param, mu_type = "mean", sigma_type = "sd", rm.CSF = FALSE, rm.WM = FALSE, rm.GM = FALSE, 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.

mu_type

the type of centering. Can be "mean" or "median".

sigma_type

the type of scaling. Can be "sd" or "mad".

rm.CSF

should the cerebral spinal fluid observations be excluded ? logical.

rm.GM

should the grey matter observations be excluded ? logical.

rm.WM

should the white matter observations be excluded ? logical.

verbose

should the execution of the function be traced ? logical.

update.object

should the resulting normalization values be stored in object ? logical.

overwrite

if normalization values are already stored in object@normalization, can they be overwritten ? logical.

Value

An list containing the normalization values, one element for each type of normalization.

Details

FUNCTION: If any of the rm.CSF, rm.WM or rm.GM is set to true, then the values of the parameters remaining to FALSE (among CSF, WM and GM) are summed. Voxels with value under 0.5 are discarded. Note that rm.CSF, rm.GM and rm.WM cannot be set simultaneously to TRUE.

See Also

selectNormalization to select the normalization values. calcTissueType to compute a probabilistic classification of the brain observations in WM/GM/CSF.

Examples

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

## compute normalization values
res <- calcNormalization(MRIaggr.Pat1_red, param = c("DWI_t0","T2_FLAIR_t2"),
                         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,
             legend = TRUE, window = NULL, main = "raw - slice ")
multiplot(MRIaggr.Pat1_red, param = "T2_FLAIR_t2", num = 1:3,
			 norm_mu="contralateral", norm_sigma="contralateral",
             legend = TRUE, window = NULL, main = "normalized - slice ")

## extract normalization
selectNormalization(MRIaggr.Pat1_red, type = "global", mu = TRUE, sigma = FALSE)