na-mic national alliance for medical image computing using annotations in slicer 4.0 yong zhang,...
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NA-MICNational Alliance for Medical Image Computing http://na-mic.org
Using Annotations in Slicer 4.0
Yong Zhang, Kilian Pohl
June 2010
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National Alliance for Medical Image Computing http://na-mic.org
Introduction
• miAnnotation is a free and open source software module integrated with 3D Slicer for users to annotate medical images to capture information latent in the scans.
• miAnnotation has the functionality similar to commercial software packages for image annotation.
“Old Atlas” contains Thalamic Nuclei
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National Alliance for Medical Image Computing http://na-mic.org
Prerequisites
• Slicer version 3.4 or later• Example dataset: download and extract the dataset for this
tutorial: Slicer_miAnnotationData.zip. It contains two data sets that can be use as examples.
• Tutorials to complete first (helpful but not required):
– Slicer3Minute Tutorial – Loading and Viewing Data– http://www.slicer.org/slicerWiki/index.php/Slicer3.4:Training
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National Alliance for Medical Image Computing http://na-mic.org
1. Loading Example Dataset
To get the Example Dataset loaded into Slicer:
1. Menu: File: Add Volume…
2. Select file name “Mri_S01_t01.nhdr” and then click “Apply”
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National Alliance for Medical Image Computing http://na-mic.org
2. Loading Label Map
To get the Label Map loaded into Slicer:
1. Menu: File: Add Volume…
2. Select file name “Lvcm_S01_t01.nhdr” and then click to turn on “Label Map” in Volume Options, then click “Apply”
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National Alliance for Medical Image Computing http://na-mic.org
3. Turn On Label Map Outline
To get the label map outline from the 2D viewers, click the “Display a menu of more options for the slice viewer” button and select “Show label volume outlines” option.
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National Alliance for Medical Image Computing http://na-mic.org
4. miAnnotation Main Panel
• Upper Panel: – 8 different annotation types – controls for mouse modes
• Middle Panel: – A table contains all annotations – Edit annotation properties – Edit annotation table–
• Lower Panel: – Save as text format – Save screen shot – Save entire MRML structure – Save report as HTML format
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National Alliance for Medical Image Computing http://na-mic.org
5. Create Annotations
Click to create ROI node
Click to create Ruler node
Click to create Text node
Click to start the angle node creation: manually click 3 points in the 3D view to create Angle node
Click to create Sticky NoteClick to start the fiducial
node creation: manually click 1 point in the 2D view to create a fiducial node
Click to start the Bidimensional node creation: manually click 2 points in the 3D view to create one line node, then manually click 2 other points to create the orthogonal line node
Click to start the Spline node creation: manually click and drag up to 5 points from the initial position to other locations to create the spline node
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National Alliance for Medical Image Computing http://na-mic.org
5. Create Annotations (cont’d)
An annotation entry is created in the annotation table when a new annotation is created in the viewers
Annotation ID
Hide/Unhide the annotation in the viewers
Lock/unlock the annotation in the viewers
Text Information
Icons for the Annotation
Value for the Annotation
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National Alliance for Medical Image Computing http://na-mic.org
6. Modify Properties of Annotations
By clicking the “edit property” button in the annotation table, a new property dialog is created for users to modify the properties of the annotation
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National Alliance for Medical Image Computing http://na-mic.org
6. Modify Properties of Annotations (Cont’d)
Modify texts
Modify coordinates
Modify text properties (color and text scale)
Modify point properties
Modify line properties
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National Alliance for Medical Image Computing http://na-mic.org
6. Modify Properties of Annotations (Cont’d)
The change to the property is immediately displayed in the viewers when the user is modifying the properties
“OK” to confirm the changes
“Cancel” to discard the changes and the annotation changes back to its original view.
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National Alliance for Medical Image Computing http://na-mic.org
7. Modify Annotation Table
Hide/Unhide selected annotations
Select/Unselect all annotations
Lock/Unlock selected annotations
Move down selected annotation
Delete selected annotations
Move up selected annotation
Restore viewers to their original status
Annotation entries in the table can be modified using the “Edit panel”
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National Alliance for Medical Image Computing http://na-mic.org
8. Interact with Annotations - Ruler
Users can interact with most annotations by mouse clicking and dragging.
Click and Drag the two control points to specify the ruler
The measurement of the ruler is updated in the table
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National Alliance for Medical Image Computing http://na-mic.org
8. Interact with Annotations - Angle
Click and Drag the 3 control points to specify the angle
The measurement of the angle is updated in the table
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National Alliance for Medical Image Computing http://na-mic.org
8. Interact with Annotations - ROI
Click and Drag the 6 control points to change the extensions of the Region of Interest (ROI) node
The measurements of the ROI extensions are updated in the table
Click and drag the central control point to change the location of the ROI
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National Alliance for Medical Image Computing http://na-mic.org
8. Interact with Annotations - Text
Use mouse middle button to click and drag the text node to any places inside the viewer
Use edit button or directly edit the text field of the table to change the text information shown in the viewer
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National Alliance for Medical Image Computing http://na-mic.org
8. Interact with Annotations - Fiducial
Click and drag the fiducial node in either 2D viewers or 3D viewer to change the location of the fiducial node.
Click anywhere in the 2D viewers to create the fiducial node.
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National Alliance for Medical Image Computing http://na-mic.org
8. Interact with Annotations – Bidimensional Node
Click and drag the 4 control points to specify the bidimensional node
The measurements of the bidimensional node are updated in the table
Use mouse middle button to click and move the node
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National Alliance for Medical Image Computing http://na-mic.org
8. Interact with Annotations – Spline Node
Click and drag the 5 control points to specify the spline node
The total length of the spline node is updated in the table
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National Alliance for Medical Image Computing http://na-mic.org
8. Interact with Annotations – Sticky Note
There is no views for a sticky note
A sticky note only contains text information and can be modified by using the edit button or directly editing the text field in the table.
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National Alliance for Medical Image Computing http://na-mic.org
9. Save Annotations
Annotation can be saved by saving entire MRML structures
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National Alliance for Medical Image Computing http://na-mic.org
9. Save Annotations (Cont’d)
Annotation can be saved by saving text MRML information
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National Alliance for Medical Image Computing http://na-mic.org
9. Save Annotations (Cont’d)
Annotation can be saved by saving the screen shots
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National Alliance for Medical Image Computing http://na-mic.org
9. Save Annotations (Cont’d)
Annotation can be saved by saving the HTML report
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National Alliance for Medical Image Computing http://na-mic.org
Acknowledgments
National Alliance for Medical Image ComputingNIH U54 EB005419
Neuroimage Analysis CenterNIH P41 RR13218 (ARRA Supplement)