28/09/2023 10:44 Display Labeled Medical Image Volume in Patient Coordinate System - MATLAB & Simulink - MathWorks France

Display Labeled Medical Image Volume in Patient Coordinate System

This example shows how to display labeled 3-D medical image volumes by using
volshow. The volshow function uses the spatial referencing information from a Try This Example
medicalVolume object to transform intrinsic image coordinates, in voxel units, to
patient coordinates in real-world units such as millimeters. You can visualize labels
 Copy Command
as an overlay by using the OverlayData property of the Volume object created by
volshow. If you do not have Medical Imaging Toolbox™ installed, see volshow
(Image Processing Toolbox™).

Download Image Volume Data

This example uses a subset of the Medical Segmentation Decathlon data set [1]. The subset of data includes two CT
chest volumes and corresponding label images, stored in the NIfTI file format.

Run this code to download the MedicalVolumNIfTIData.zip file from the MathWorks® website, then unzip the file.
The size of the data file is approximately 76 MB.

zipFile = matlab.internal.examples.downloadSupportFile("medical","MedicalVolumeNIfT  Get

filepath = fileparts(zipFile);
unzip(zipFile,filepath)

The folder dataFolder contains the downloaded and unzipped data.

dataFolder = fullfile(filepath,"MedicalVolumeNIfTIData");  Get

Specify the filenames of the CT volume and label image used in this example.

dataFile = fullfile(dataFolder,"lung_043.nii.gz");  Get

labelDataFile = fullfile(dataFolder,"LabelData","lung_043.nii.gz");

Import Image Volume

Create a medical volume object that contains the image data and spatial referencing information for the CT volume.
The Voxels property contains a numeric array of the voxel intensities. The VoxelSpacing property indicates that the
voxels are anisotropic, with a size of 0.7695-by-0.7695-by-2.5 mm.

medVolData = medicalVolume(dataFile)  Get

medVolData =
medicalVolume with properties:

Voxels: [512×512×129 single]

VolumeGeometry: [1×1 medicalref3d]
SpatialUnits: "mm"
Orientation: "transverse"
VoxelSpacing: [0.7695 0.7695 2.5000]
NormalVector: [0 0 -1]
NumCoronalSlices: 512
NumSagittalSlices: 512
NumTransverseSlices: 129
PlaneMapping: ["sagittal" "coronal" "transverse"]
Modality: "unknown"
WindowCenters: 0
WindowWidths: 0

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Import Label Data

Create a medical volume object that contains the label image data. The label image has the same spatial information
as the intensity CT volume.

medvolLabels = medicalVolume(labelDataFile)  Get

medvolLabels =
medicalVolume with properties:

Voxels: [512×512×129 uint8]

VolumeGeometry: [1×1 medicalref3d]
SpatialUnits: "mm"
Orientation: "transverse"
VoxelSpacing: [0.7695 0.7695 2.5000]
NormalVector: [0 0 -1]
NumCoronalSlices: 512
NumSagittalSlices: 512
NumTransverseSlices: 129
PlaneMapping: ["sagittal" "coronal" "transverse"]
Modality: "unknown"
WindowCenters: 0
WindowWidths: 0

Display CT Volume with Tumor Overlay

Create a colormap and transparency map to display the rib cage. The alpha and color values are based on the CT-
bone rendering style from the Medical Image Labeler app. The intensity values have been tuned for this volume
using trial and error.

alpha = [0 0 0.72 1.0];  Get

color = ([0 0 0; 186 65 77; 231 208 141; 255 255 255]) ./ 255;
intensity = [-3024 -700 -400 3071];

queryPoints = linspace(min(intensity),max(intensity),256);
alphamap = interp1(intensity,alpha,queryPoints)';
colormap = interp1(intensity,color,queryPoints);

To display the volume in the patient coordinate system, pass the medicalVolume object as input to volshow. Use the
CinematicRendering rendering style to view the volume with realistic lighting and shadows. Specify the custom
colormap and transparency map. The volshow function uses the spatial details in medVol to set the
Transformation property of the output Volume object, vol. The voxels are scaled to the correct anisotropic
dimensions. The axes display indicators label the inferior/superior (S), left/right (L), and anterior/posterior (P)
anatomical axes.

vol = volshow(medVolData, ...  Get

RenderingStyle="CinematicRendering", ...
Colormap=colormap, ...
Alphamap=alphamap);

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Pause to apply all of the cinematic rendering iterations before updating the display in Live Editor.

pause(4)  Get
drawnow

View the tumor label image as an overlay on the CT volume. You can set the OverlayData and OverlayAlphamap
properties of an existing Volume object, or specify them during creation using volshow. Note that you must set the
OverlayData property to the numeric array in the Voxels property of medVolLabels, rather than the medicalVolume
object itself.

vol.OverlayData = medvolLabels.Voxels;  Get

vol.OverlayAlphamap = 1;

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pause(4)  Get
drawnow

Optionally, you can clean up the viewer window by using the 3-D Scissors tool, , to remove the patient bed. For a
detailed example, see Remove Objects from Volume Display Using 3-D Scissors.

This image shows the final volume after bed removal.

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Display CT Volume as Slice Planes

Visualize the CT volume and label overlay as slice planes. Use the RenderingStyle name-value argument to specify
the rendering style as "SlicePlanes". Specify the tumor label overlay using the OverlayData name-value argument.
Note that you must set the OverlayData property to the numeric array in the Voxels property of medVolLabels,
rather than the medicalVolume object itself.

volSlice = volshow(medVolData, ...  Get

OverlayData=medvolLabels.Voxels, ...
RenderingStyle="SlicePlanes", ...
Alphamap=linspace(0.01,0.2,256), ...
OverlayAlphamap=0.75);

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To scroll through the transverse slices, pause the cursor on the transverse slice until it highlights in blue, then drag
the cursor along the inferior/superior axis.

Drag the cursor to rotate the volume. The tumor overlay is visible in the slices for which the overlay is defined.

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References
[1] Medical Segmentation Decathlon. "Lung." Tasks. Accessed May 10, 2018. http://medicaldecathlon.com/. The
Medical Segmentation Decathlon data set is provided under the CC-BY-SA 4.0 license. All warranties and
representations are disclaimed. See the license for details.

See Also
volshow | Volume Properties | medicalref3d | medicalVolume | intrinsicToWorldMapping

Related Topics
Choose Approach for Medical Image Visualization
Display Medical Image Volume in Patient Coordinate System
Display Volume Using Cinematic Rendering
Remove Objects from Volume Display Using 3-D Scissors

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