Slicer Tutorial Module: DTMRI Data: Dartmouth DTI

1. Slicer TutorialModule: DTMRIData: Dartmouth DTI May 26-27, 2005

2. Pre-requisites • Slicer 2.5 already installed from http://www.na-mic.org/Wiki/index.php/Slicer:Slicer2.5_Getting_Started • Dartmouth DTI Data Set (first of six normals on BIRN servers) downloaded using instructions in http://www.na-mic.org/Wiki/index.php/DataRepository • Dartmouth DTI “protocol” saved in slicer2/Modules/vtkDTMRI/data/ NAMIC-Dartmouth-2b12g-Volume

3. Tutorial: Slicer DTMRI Module • Introducing the Module • Load Diffusion Data • Convert to Tensor • Compute Fractional Anisotropy (FA) • Perform Tractography • Save Tracts and Scene • Use Case from BWH • Compute Statistics on FA of ROI

4. Load Dartmouth DTI images 2: Use the Basic Reader 3: Click File Browse 4: Pick First File 1: Click Add Volume 5: Switch to Manual 6: Click Apply

5. Load Dartmouth images (contd) 7: Set Thickness to 3 11: DWI Images Appear 8: Set Order to Axial SI 9: Little Endian “Yes” 10: Click Apply Q: Where is the MRML file? What does it contain?

6. Convert To Tensors 13: Pick Convert Tab 15: Pick Convert (ignore warning messages) 14: Protocol is NAMIC-Dartmouth-2b12g-Volume 12: Go to DTMRI Module 16: Resulting Viewer window looks like this:

7. Converted Tensor Image 16: Resulting viewer window looks like this: Q: What is it that we are viewing in this image? What is in the protocol file we just used?

8. Aside Adjust Image Win-Level Select “Volumes” and Select the AvGradient volume Adjust Window and Level Resulting Image

9. Tractography Steps • Compute Fractional Anisotropy (FA) • Create Tracts • Individually • From segmented ROI

10. Tractography Step 1: Compute Fractional Anisotropy (FA) Select DTMRI Select Scalars (if you don’t see it, select More until you do) Select FA Resulting Image Apply Q: What does the MRML file contain now? Q1: Where is the MRML file? What does it contain? Q2: How do you read the FA value at a certain RAS location off the screen?

11. Tractography Steps • Compute Fractional Anisotropy (FA) • Create Tracts • Individually • From segmented ROI

12. Tractography Step 2:Create Individual Tracts • Setup color of tracts • Setup 3D view • Create one tract • Add slices to 3D view. Zoom and rotate to optimize view. • Add more tracts individually. • Add tracts using a segmented ROI.

13. Tractography Step 2: Go to Tractography Tab Select Display More Select Tractography

14. Tractography Step 2 (contd):Select color for display of tracts Select Color Click on new color Current Selection of Tract Color

15. Tractography Step 2 (contd): Set up 3D window for viewing tracts Notice volume orientation Click on “A” to orient volume view

16. Tractography Step 2 (contd): Create a single tract To create a single tract originating at a point in the corpus collosum: position mouse on the point and hit the “s” key.

17. Tractography Step 2 (contd):View tract in 3D window See the tiny tract in the 3D window.

18. Tractography Step 2 (contd):Zoom in 3D window Drag Right Mouse Button Down in 3D Window to Zoom In.

19. Tractography Step 2 (contd):Show Slices in 3D window Click “v” to show slices in 3D window.

20. Tractography Step 2 (contd):Show Slices in 3D window Click on the left arrow tip to rotate volume…

21. Tractography Step 2 (contd):Rotate and Zoom Volume to optimize view Drag Left Mouse Button in 3D window to Rotate, and Right Mouse Button to Zoom. Do this until you get to a view you like.

22. Tractography Step 2 (contd):Add more tracts Add tracts by moving mouse to different points in corpus collosum and hitting the “s” key. Watch tracts appear in the volume window. Q: What happens if you hold the “s” key down and drag the mouse in the corpus collosum?

23. Tractography Step 2 (contd):Segment ROI (then use it to seed tracts) Draw Module Start Editor Effects Tab Draw Select new color

24. Tractography Step 2 (contd):Segment ROI (then use it to seed tracts) Draw Outline with Mouse Note name of segmented volume. Hit Apply to Fill Outline.

25. Tractography Step 2 (contd):Generate Tracts from Segmented ROI Resulting Tracts Appear in 3D view.

26. Tractography Step 2 (contd):Generate Tracts from Segmented ROI Zoom and Rotate 3D view by dragging right and left mouse buttons

27. Tractography Step 2 (contd):Generate Tracts from Segmented ROI Add a Slice to 3D view

28. Tractography Steps • Compute Fractional Anisotropy (FA) • Create Tracts • Individually • From segmented ROI • Save Tracts • Save 3D Model of Tracts • Add Model to Current Scene • Save scene

29. Save TractsSave 3D Model of Tracts Give a name such as “savedTractsTutorial” and it Will be saved as “savedTractsTutorial.xml” Q: Can you open this xml file in a web browser? What does it contain? How many models? Why?

30. Save TractsAdd Model to Scene This is the tract File that was just saved

31. Save TractsSave Scene

32. Open Saved Scene

33. Use Case: Measure FA Statistics in ROI

34. Measure FA Statistics in ROI Manually draw a labelmap over your region of interest. VolumeMath Module: Modules  Measurement  VolumeMath

35. MaskStat Button in VolumeMath We use the MaskStat button, which: 1) uses our labelmap as a “mask” over the FA volume 2) calculates “stats” on the region contained under the labelmap First, however, we have to “cast” our FA volume as a different file type. (*note: this is an extra step that will be resolved in the near future, but for now it is necessary!)

36. “Cast” FA Volume The FA volume must be cast as a different file type (“short”) for the computation to work 1) click Cast button 2) Volume to Cast: FractionalAnisotropy 3) Cast Output: FractionalAnisotropy 4) Output Type: Short 5) click Run

37. MaskStat 1) click MaskStat button 2) Volume to Mask: FractionalAnisotropy 3) LabelMap: Working 4) Masked Output: Create New 5) make sure Mask color (e.g., 2) is the same as your labelmap 6) optional: choose a directory to place the output text file 7) click Run

38. MaskStat Result result in Slicer result in output text file

39. Do Some DTI!