NA-MICNational Alliance for Medical Image Computing http://na-mic.org

Using Annotations in Slicer 4.0

Yong Zhang, Kilian Pohl

June 2010

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

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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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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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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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.

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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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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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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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

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

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.

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”

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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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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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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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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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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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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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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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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9. Save Annotations

Annotation can be saved by saving entire MRML structures

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9. Save Annotations (Cont’d)

Annotation can be saved by saving text MRML information

National Alliance for Medical Image Computing http://na-mic.org

9. Save Annotations (Cont’d)

Annotation can be saved by saving the screen shots

National Alliance for Medical Image Computing http://na-mic.org

9. Save Annotations (Cont’d)

Annotation can be saved by saving the HTML report

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)