1. NA-MIC National Alliance for Medical Image Computing http://na-mic.org Using Annotations in Slicer 4.0 Yong Zhang, Kilian Pohl June 2010

2. 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

3. 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

4. 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”

5. 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”

6. 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.

7. 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

8. 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 Note Click 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

9. 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

10. 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

11. 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

12. 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.

13. 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”

14. 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

15. 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

16. 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

17. 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

18. 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.

19. 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

20. 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

21. 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.

22. National Alliance for Medical Image Computing http://na-mic.org 9. Save Annotations Annotation can be saved by saving entire MRML structures

23. National Alliance for Medical Image Computing http://na-mic.org 9. Save Annotations (Cont’d) Annotation can be saved by saving text MRML information

24. National Alliance for Medical Image Computing http://na-mic.org 9. Save Annotations (Cont’d) Annotation can be saved by saving the screen shots

25. National Alliance for Medical Image Computing http://na-mic.org 9. Save Annotations (Cont’d) Annotation can be saved by saving the HTML report

26. National Alliance for Medical Image Computing http://na-mic.org Acknowledgments National Alliance for Medical Image Computing NIH U54 EB005419 Neuroimage Analysis Center NIH P41 RR13218 (ARRA Supplement)