1. Surgical Planning Laboratory http://www.slicer.org -1- Brigham and Women’s Hospital Slicer Tutorial 4 Module: DTMRI Data: Sample Slicer DTI Sonia Pujol, Ph.D. Tina Kapur, Ph.D. Randy Gollub, M.D., Ph.D

2. Surgical Planning Laboratory http://www.slicer.org -2- Brigham and Women’s Hospital Acknowledgments National Alliance for Medical Imaging NIH U54EB005149 Neuroimage Analysis Center NIH P41RR013218 Laboratory of Mathematics in Imaging, Brigham and Women’s Hospital Thanks to Carl-Fredrik Westin, Lauren O’Donnell, Raul San Jose Estepar, Carlos Isorna, Maxime Boucher,Matthan Caan.

3. Surgical Planning Laboratory http://www.slicer.org -3- Brigham and Women’s Hospital Disclaimer It is the responsibility of the user of 3DSlicer to comply with both the terms of the license and with the applicable laws, regulations and rules.

4. Surgical Planning Laboratory http://www.slicer.org -4- Brigham and Women’s Hospital Material Slicer 2.5 http://www.na-mic.org/Wiki/index.php/Slicer:Slicer2.5_Getting_Started DTI Sample Data Set SlicerSampleDTI.zip http://www.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101

5. Surgical Planning Laboratory http://www.slicer.org -5- Brigham and Women’s Hospital Goal of this tutorial Guiding you step-by-step through the process of Tractography within DTI data Final result of the tutorial

6. Surgical Planning Laboratory http://www.slicer.org -6- Brigham and Women’s Hospital Prerequisites Slicer Training Slicer Training 1: Loading and Viewing Data Slicer Advanced Modules Slicer Training 2: Manual Segmentation http://www.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101

7. Surgical Planning Laboratory http://www.slicer.org -7- Brigham and Women’s Hospital Slicer DT-MRI Module

8. Surgical Planning Laboratory http://www.slicer.org -8- Brigham and Women’s Hospital Overview of Training 4 Part 1: Loading and Converting DTI Data Part 2: Computing Fractional Anisotropy Part 3: Manual Tractography Part 4: Automatic Tractography Part 5: Use Case

9. Surgical Planning Laboratory http://www.slicer.org -9- Brigham and Women’s Hospital Loading DTI Data Slicer can load DWI Volumes ……………………. Tensors…………………………… Tracts……………………………… DTI Scenes ……………………….

10. Surgical Planning Laboratory http://www.slicer.org -10- Brigham and Women’s Hospital Loading Slicer Sample DTI data Use the Basic Reader Click File Browse Pick the first file D.001 Select ImageHeader: Auto Click Apply Select the Volumes Module Select the Props Panel

11. Surgical Planning Laboratory http://www.slicer.org -11- Brigham and Women’s Hospital The DWI images appear in the Viewer Loading Slicer Sample DTI data

12. Surgical Planning Laboratory http://www.slicer.org -12- Brigham and Women’s Hospital Observe the axial slices using the slider Loading Slicer Sample DTI data

13. Surgical Planning Laboratory http://www.slicer.org -13- Brigham and Women’s Hospital Loading Slicer Sample DTI data The white strips correspond to an oblique acquisition.

14. Surgical Planning Laboratory http://www.slicer.org -14- Brigham and Women’s Hospital Acquisition protocol The Slicer DTI Sample Data were acquired at Brigham and Women’s Hospital with the protocol BWH_6g.1bSlice corresponding to: n=6 gradients Gradients directions = {0.707107 0.707107 0}, {0 0.707107 0.707107 }, {0.707107 0 0.707107 }, {0 0.707107 -0.707107 }, {0.707107 -0.707107 0}, {-0.707107 0 0.707107} Gradient order: Slice interleaved b=1 baseline B-value = 750

15. Surgical Planning Laboratory http://www.slicer.org -15- Brigham and Women’s Hospital Left click on Axial and select AxiSlice in the Menu Loading Original DTI data

16. Surgical Planning Laboratory http://www.slicer.org -16- Brigham and Women’s Hospital The original Axial slice appears in the Viewer. Loading Original DTI data

17. Surgical Planning Laboratory http://www.slicer.org -17- Brigham and Women’s Hospital Browse the original axial slices corresponding to the baseline. Loading Original DTI data Example: display the slice 111

18. Surgical Planning Laboratory http://www.slicer.org -18- Brigham and Women’s Hospital Loading Original DTI data Observe the baseline

19. Surgical Planning Laboratory http://www.slicer.org -19- Brigham and Women’s Hospital Browse the original axial slices corresponding to the gradients Loading Original DTI data Example: display the slices 112 to 117

20. Surgical Planning Laboratory http://www.slicer.org -20- Brigham and Women’s Hospital The 6 gradients appear in the viewer. Loading Original DTI data

21. Surgical Planning Laboratory http://www.slicer.org -21- Brigham and Women’s Hospital Left click on Sagittal, select SagSlice Left click on Coronal, select CorSlice Loading Original DTI data

22. Surgical Planning Laboratory http://www.slicer.org -22- Brigham and Women’s Hospital Observe the original data in the Sagittal and Coronal viewers Loading Original DTI data

23. Surgical Planning Laboratory http://www.slicer.org -23- Brigham and Women’s Hospital DT-MRI Module Select Modules in the Main Menu Select Visualization  DTMRI

24. Surgical Planning Laboratory http://www.slicer.org -24- Brigham and Women’s Hospital DT-MRI Module Select the Convert Panel The interface of the DTMRI module appears

25. Surgical Planning Laboratory http://www.slicer.org -25- Brigham and Women’s Hospital Convert To Tensors Select InputVolume D Click on Convert Volume Select Protocol BWH_6g.1bSlice Click on Prop. to display the parameters of the acquisition protocol

26. Surgical Planning Laboratory http://www.slicer.org -26- Brigham and Women’s Hospital Convert to Tensors Resulting viewer window

27. Surgical Planning Laboratory http://www.slicer.org -27- Brigham and Women’s Hospital Adjust Image Window Level Select the Volumes module Adjust Window and Level Select the D_AvGradient volume

28. Surgical Planning Laboratory http://www.slicer.org -28- Brigham and Women’s Hospital Adjust Image Window Level Resulting viewer window

29. Surgical Planning Laboratory http://www.slicer.org -29- Brigham and Women’s Hospital Overview of Training 4 Part 1: Loading and Converting DTI Data Part 2: Computing Fractional Anisotropy Part 3: Manual Tractography Part 4: Automatic Tractography Part 5: Use Case

30. Surgical Planning Laboratory http://www.slicer.org -30- Brigham and Women’s Hospital Computing Fractional Anisotropy Left-click on DTMRI to come back to the DTI Module Click on More to naviguate in the different panels

31. Surgical Planning Laboratory http://www.slicer.org -31- Brigham and Women’s Hospital Computing Fractional Anisotropy Select the panel Scalars Select Fractional Anisotropy in the Create Volume Menu Click on Apply

32. Surgical Planning Laboratory http://www.slicer.org -32- Brigham and Women’s Hospital Computing Fractional Anisotropy The Viewer displays the FA volume.

33. Surgical Planning Laboratory http://www.slicer.org -33- Brigham and Women’s Hospital Overview of Training 4 Part 1: Loading and Converting DTI Data Part 2: Computing Fractional Anisotropy Part 3: Manual Tractography Part 4: Automatic Tractography Part 5: Use Case

34. Surgical Planning Laboratory http://www.slicer.org -34- Brigham and Women’s Hospital Tractography Panel Click on the More Panel inside the DTMRI module

35. Surgical Planning Laboratory http://www.slicer.org -35- Brigham and Women’s Hospital Tractography Panel Select the Display Panel Select the Tractography Menu

36. Surgical Planning Laboratory http://www.slicer.org -36- Brigham and Women’s Hospital Tracts Color Display Left-click on Color A Color selection panel appears Double click on a new color

37. Surgical Planning Laboratory http://www.slicer.org -37- Brigham and Women’s Hospital Create a single tract Position the mouse on a point inside the corpus callosum, and hit the s key.

38. Surgical Planning Laboratory http://www.slicer.org -38- Brigham and Women’s Hospital Create a single tract A tract appears in the 3D Viewer. Drag right mouse button down in the 3D Viewer to zoom in.

39. Surgical Planning Laboratory http://www.slicer.org -39- Brigham and Women’s Hospital Create a single tract Click on the V buttons The 3D window shows a closer view of the tract.

40. Surgical Planning Laboratory http://www.slicer.org -40- Brigham and Women’s Hospital Create a single tract Slicer displays the slices in the 3D window. Drag left mouse button in the 3D Viewer to rotate the volume, Drag right mouse button to zoom in, until you get to a convenient view.

41. Surgical Planning Laboratory http://www.slicer.org -41- Brigham and Women’s Hospital Generate Multiple Tracts Position the mouse on different points in the corpus callosum and hit the s key.

42. Surgical Planning Laboratory http://www.slicer.org -42- Brigham and Women’s Hospital Generate Multiple Tracts The tracts that correspond to the visited points appear in the 3D Viewer.

43. Surgical Planning Laboratory http://www.slicer.org -43- Brigham and Women’s Hospital Generate Multiple Tracts Hold the s key down and drag the mouse in the corpus callosum

44. Surgical Planning Laboratory http://www.slicer.org -44- Brigham and Women’s Hospital Generate Multiple Tracts Multiple tracts are generated for each point visited by the mouse.

45. Surgical Planning Laboratory http://www.slicer.org -45- Brigham and Women’s Hospital Overview of Training 4 Part 1: Loading and Converting DTI Data Part 2: Computing Fractional Anisotropy Part 3: Manual Tractography Part 4: Automatic Tractography Part 5: Use Case

46. Surgical Planning Laboratory http://www.slicer.org -46- Brigham and Women’s Hospital AutoTracts Select AutoTracts in the Visualization Menu The DT-MRI module provides a a functionality for automatic generation of tracts from a segmented region of interest.

47. Surgical Planning Laboratory http://www.slicer.org -47- Brigham and Women’s Hospital AutoTracts Select the Editor module in the main Menu. Select the Effects panel. Left click on Draw in the Effects Menu.

48. Surgical Planning Laboratory http://www.slicer.org -48- Brigham and Women’s Hospital AutoTracts Left click on Output and select a new color for the region of interest

49. Surgical Planning Laboratory http://www.slicer.org -49- Brigham and Women’s Hospital AutoTracts Draw the contour of the corpus callosum in the sagittal slice, and click Apply

50. Surgical Planning Laboratory http://www.slicer.org -50- Brigham and Women’s Hospital Come back to the DTMRI module Click on the ROI Labelmap menu and select the ROI Working Click on Seed ‘Tracts’ in ROI AutoTracts

51. Surgical Planning Laboratory http://www.slicer.org -51- Brigham and Women’s Hospital The resulting Tracts appear in 3D view. AutoTracts

52. Surgical Planning Laboratory http://www.slicer.org -52- Brigham and Women’s Hospital Zoom and rotate the 3D view by dragging right and left mouse buttons. AutoTracts

53. Surgical Planning Laboratory http://www.slicer.org -53- Brigham and Women’s Hospital Save Tracts Select SaveTracts in the Visualization Menu Save your tracts as SampleDTITracts Select SaveTracts in model file(s)

54. Surgical Planning Laboratory http://www.slicer.org -54- Brigham and Women’s Hospital Overview of Training 4 Part 1: Loading and Converting DTI Data Part 2: Computing Fractional Anisotropy Part 3: Manual Tractography Part 4: Automatic Tractography Part 5: Use Case

55. Surgical Planning Laboratory http://www.slicer.org -55- Brigham and Women’s Hospital Goal Measure Fractional Anisotropy Statistics in a Region of Interest Use Case Tool VolumeMath Module

56. Surgical Planning Laboratory http://www.slicer.org -56- Brigham and Women’s Hospital Measure FA Statistics in ROI Select Measurement  VolumeMath in the Modules Section of the Main Menu

57. Surgical Planning Laboratory http://www.slicer.org -57- Brigham and Women’s Hospital MaskStat functionality The MaskStat functionality uses the labelmap as a mask over the FA volume, and calculates “ stats ” on the region contained under the labelmap.

58. Surgical Planning Laboratory http://www.slicer.org -58- Brigham and Women’s Hospital MaskStat functionality Use the Cast functionality to convert the FA volume to a different file type: Set Volume to Cast to FractionalAnisotropy_D_Tensor Set Cast Output to FractionalAnisotropy_D_Tensor Set Output Type to Short Click on Run

59. Surgical Planning Laboratory http://www.slicer.org -59- Brigham and Women’s Hospital MaskStat Click MaskStat button Set Volume to Mask to FractionalAnisotropy_D_Tensor Set LabelMap to Working Set Masked Output to Create New Set the Mask color to the same color as your Labelmap Optional: Choose a directory to place the output text file Click Run

60. Surgical Planning Laboratory http://www.slicer.org -60- Brigham and Women’s Hospital MaskStat Result A window shows the results, and Slicer writes the values in a file.

61. Surgical Planning Laboratory http://www.slicer.org -61- Brigham and Women’s Hospital Conclusion Intuitive interface for manual and automatic tracts generation Enhanced visualization of the anatomy by fusion of tracts and DTI images Open-source environment