MRIaggr (version 1.1.3)

outlineMRIaggr: Outline a region on a slice

Description

Tool for graphical definition of a spatial region on an image.

Usage

## S3 method for class 'MRIaggr':
outlineMRIaggr(object, param, index1 = NULL, num = NULL, hemisphere = "both",
     numeric2logical = FALSE, xlim = NULL, ylim = NULL, legend = FALSE,
     palette = "terrain.colors", col = NULL, breaks = 25, fill = TRUE, n = 50,
     sequential = TRUE, min_dist = 1, operator_index1 = "none",
     col.outline = c("blue","red","grey"), pch = 20, cex = c(0.75,1,0.75), 
	 name_newparam = "userMask",
	 verbose = optionsMRIaggr("verbose"), update.object = FALSE, overwrite = FALSE)

Arguments

object

an object of class MRIaggr. REQUIRED.

param

the contrast parameter map on which the outline will be drawn. character. REQUIRED.

index1

the coordinates of additionnal points to display. data.frame or list or NULL.

num

the slices on which the outline will be drawn. numeric vector or NULL.

hemisphere

the hemisphere to consider. character.

numeric2logical

if a parameter is specified for the index argument, should it be converted to logical ? logical.

xlim

the y limits of the plot. numeric vector of size 2 or NULL leading to automatic setting of the x limits.

ylim

the y limits of the plot. numeric vector of size 2 or NULL leading to automatic setting of the y limits.

legend

how should the legend be displayed ? logical or NULL.

palette

the colors or the palette to use when associating colors to observation intensities. character vector or character.

col

the color to use to plot the observations. character vector or NULL leading to automatic generation of the colors using the breaks and palette arguments.

breaks

the break points or the number of breakpoints to use to generate the color intervals . numeric vector or postive integer.

fill

should the spatial region be filled ? Otherwise only the edge is used. logical.

n

maximum number of points to define the outline. integer.

sequential

should the region edge be updated on the graphical device after each point ? logical.

min_dist

if the distance between the new point and the initial point is inferior to min_dist, then the definition of the region ends. numeric. Only active if sequential is TRUE.

operator_index1

the operator to apply between the index1 observations and the outlined observations. Can be "none" "intersection" "difference" or "union".

col.outline

the colors in which the user-defined edge points, the interpolated edge points and the interior points should be ploted. character vector[3].

pch

the symbol with which the observations will be displayed. positive integer.

cex

the expansion factor used to plot the edge points, the interpolated edge points and the interior points. positive numeric vector of size 3.

verbose

should the execution of the function be traced ? logical.

name_newparam

the name of the new parameter. character.

update.object

should the new parameter be stored in object ? logical.

overwrite

if a contrast parameter with the same names is already stored in object@data, can it be overwritten ? logical.

Value

• A matrix containing in columns :
  • [,c("i","j","k")]: the coordinates of the observations.
  • [,"index"]: the index of the observation inobject.
  • [,"edge"]: whether each observation is on an edge.
  • [,"surface"]: whether each observation is in the interior.
  • [,"userMask"]: whether each observation belong toindex1(if no not defined, alwaysFALSE).

concept

calc.

Details

ARGUMENTS: Information about the num argument can be found in the details section of initNum. Information about the index1 argument can be found in the details section of initIndex (argument index). Information about the hemisphere argument can be found in the details section of selectContrast. Information about the palette and legend arguments can be found in the details section of initCol. FUNCTION: This function uses the locator function to obtain the coordinates of the cursor. See outline for more details. It will display slice by slice the parameter map and on each slice a region should be drawn. Press Echap and 1 to restart the draw on the same slice. Press Echap and 0 to skip a slice.

Examples

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

## outline the area of interest
res <- outlineMRIaggr(MRIaggr.Pat1_red, param = "DWI_t0",
             num = 1:3, sequential = TRUE, overwrite = TRUE, update.object = TRUE)

multiplot(MRIaggr.Pat1_red, param = "userMask",              
             num = 1:3)


## outline an edge of interest 
res <- outlineMRIaggr(MRIaggr.Pat1_red, param = "DWI_t0", index1 = "MASK_DWI_t0",
            fill = FALSE, num = 1:3, sequential = TRUE, overwrite = TRUE, update.object = TRUE)

multiplot(MRIaggr.Pat1_red, param = "userMask", num = 1:3)

## define an new area as the union of the outlined area and the initial lesion mask
res <- outlineMRIaggr(MRIaggr.Pat1_red, param = "DWI_t0", index1 = "MASK_DWI_t0",
            operator_index1 = "union", num = 3, sequential = TRUE, 
			overwrite = TRUE, update.object = TRUE)

multiplot(MRIaggr.Pat1_red, param = "userMask", num = 3)

## define an new area as the intersection of the outlined area and the initial lesion mask
res <- outlineMRIaggr(MRIaggr.Pat1_red, param = "DWI_t0", index1 = "MASK_DWI_t0",
            operator_index1 = "intersection", num = 3, sequential = TRUE, 
			overwrite = TRUE, update.object = TRUE)

multiplot(MRIaggr.Pat1_red, param = "userMask", num = 3)

## define an new area as the difference between the outlined area and the initial lesion mask
res <- outlineMRIaggr(MRIaggr.Pat1_red, param = "DWI_t0", index1 = "MASK_DWI_t0",
            operator_index1 = "difference", num = 3, sequential = TRUE,
			overwrite = TRUE, update.object = TRUE)

multiplot(MRIaggr.Pat1_red, param = "userMask", num=3)