MRIaggr-calcNormalization: Compute normalization values

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

Description

Compute the normalization values for each contrast parameter.

Usage

## S4 method for signature 'MRIaggr'
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.

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.

Value

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

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)

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