createMask

Create volumetric mask from dicomContours object

Syntax

BW = createMask(rtContours,roiIndex,spatial)

Description

BW = createMask(rtContours,roiIndex,spatial) creates the volumetric mask BW, a voxel representation of the specified ROI roiIndex from the dicomContours object rtContours. The roiIndex argument specifies which contour in rtContours to create a mask from. spatial specifies the location, resolution, and orientation of the 3-D data in world coordinates.

Examples

Create Mask of dicomContours Object

Read the metadata of a DICOM-RT structure set file.

info = dicominfo("RTSTRUCT-VS-SEG-001.dcm");

Construct a dicomContours object from the metadata.

rtContours = dicomContours(info);

Display all of the ROI information as a table.

rtContours.ROIs

ans=4×5 table
    Number       Name        ContourData    GeometricType       Color    
    ______    ___________    ___________    _____________    ____________

      1       {'TV'     }    {13×1 cell}     {13×1 cell}     {3×1 double}
      2       {'Cochlea'}    { 5×1 cell}     { 5×1 cell}     {3×1 double}
      3       {'Vol2016'}    {12×1 cell}     {12×1 cell}     {3×1 double}
      4       {'*Skull' }    {79×1 cell}     {79×1 cell}     {3×1 double}

Plot the contours of all ROIs by using the plotContours function. This function plots the contours in world coordinates.

plotContour(rtContours)

Create an imref3d object with the same world limits as the plotContours plot, so that the image is in the same space as the contours.

referenceInfo = imref3d([128 128 50],xlim,ylim,zlim);

Create a 3-D logical mask of the first contour, 'Body_Contour', from rtContours, with spatial referencing specified by the imref3d object.

contourIndex = 1;
rtMask = createMask(rtContours,contourIndex,referenceInfo);

Display the mask as a volumetric image.

volshow(rtMask);

Input Arguments

rtContours — DICOM contours

dicomContours object

DICOM contours, specified as a dicomContours object.

Data Types: dicomContours

roiIndex — ROI in DICOM contours object

positive integer | character vector | string scalar

ROI in a DICOM contours object, specified as a positive integer, character vector, or string scalar. The value depends on which ROI identifier in the ROIs table of the dicomContours object you use.

ROI Identifier	Type	Example
Number	Row of the ROI in the ROIs table of the rtContours object, specified as a positive integer. Number is the first column in the ROIs table.	rtMask = createMask(rtContours,1,spatialInfo)
Name	Name of the ROI in the ROIs table of the rtContours object, specified as a character vector or string scalar. Name is the second column in the ROIs table.	rtMask = createMask(rtContours,"Body_Contour",spatialInfo)

Data Types: single | double | int8 | int16 | int32 | int64 | uint8 | uint16 | uint32 | uint64 | char | string

spatial — Spatial referencing information

structure | imref3d object

Spatial referencing information, specified as a structure or an imref3d object. You can use a structure returned by dicomreadVolume that contains the fields PatientPosition, PixelSpacing, and PatientOrientation. Spatial referencing information provides the location, resolution, and orientation of the 3-D coordinate data.

Output Arguments

BW — Volumetric mask

3-D logical array

Volumetric mask, returned as a 3-D logical array. The mask uses the intrinsic image coordinate system defined by spatial.

Extended Capabilities

Thread-Based Environment

Run code in the background using MATLAB® backgroundPool or accelerate code with Parallel Computing Toolbox™ ThreadPool.

This function fully supports thread-based environments. For more information, see Run MATLAB Functions in Thread-Based Environment.

Version History

Introduced in R2020b

R2024b: Support for thread-based environments

createMask now supports thread-based environments.