MRIaggr-calcGroupsMask: Compute spatial groups

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

Description

Compute the spatial groups defined by a binary parameter.

Usage

## S4 method for signature 'MRIaggr'
calcGroupsMask(object, mask, numeric2logical = FALSE,
     W = "ifany", W.range, W.spatial_res = c(1,1,1),
	 verbose = optionsMRIaggr("verbose"), update.object = FALSE, overwrite = TRUE)

Arguments

object	an object of class MRIaggr. REQUIRED.
mask	the binary contrast parameter that should be used to identifying the spatial groups. character. REQUIRED.
numeric2logical	should mask be convert to logical ? logical.
W	the neighbourhood matrix. dgCMatrix or "ifany" leading to use the neighbourhood matrix stored in the object if any and else computate this matrix.
W.range	the neighbourhood range. postive numeric. REQUIRED.
W.spatial_res	a dilatation factor for the coordinates. positive numeric vector of size 3.
verbose	should the execution of the function be traced ? logical.
update.object	should the resulting spatial groups be stored in object ? logical.
overwrite	if spatial groups are already stored in object@ls_descStats, can they be overwritten ? logical.

Details

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

FUNCTION:
Call the calcGroupsW function.

Value

An list containing for each parameter:

• [[group]] : a vector containing the group index for each observation.

• [[group_size]] : a vector with the size of each spatial group.

• [[group_number]] : the number of spatial groups. integer vector.

• [[group_max]] : the index of the largest group. integer vector.

See Also

selectDescStats to select the spatial groups.
calcW to compute the neighbourhood matrix.

Examples

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

## compute spatial groups
calcGroupsMask(MRIaggr.Pat1_red, mask = c("MASK_DWI_t0","MASK_T2_FLAIR_t2"),
               W.range = 6, W.spatial_res = c(1.875,1.875,6),
               update.object = TRUE, overwrite = TRUE)

## extract spatial groups
selectDescStats(MRIaggr.Pat1_red, "GroupsLesion")

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