1. Sonia Pujol, PhD -1- National Alliance for Medical Image Computing Neuroimage Analysis Center Diffusion Tensor Imaging tutorial Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School

2. Sonia Pujol, PhD -2- National Alliance for Medical Image Computing Neuroimage Analysis Center DTI tutorial This tutorial is an introduction to the advanced Diffusion MR capabilities of the Slicer3 software for medical image analysis.

3. Sonia Pujol, PhD -3- National Alliance for Medical Image Computing Neuroimage Analysis Center The Slicer3 software An end-user application for image analysis An open-source environment for software development A software platform that is both easy to use for clinical researchers and easy to extend for programmers

4. Sonia Pujol, PhD -4- National Alliance for Medical Image Computing Neuroimage Analysis Center Download the material Slicer3 is a multi-platform software running on Windows, Linux, and Mac OSX. Download and install the Slicer3.4 software from the Slicer web site http://www.slicer.org/pages/Special:SlicerDownloads 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.

5. Sonia Pujol, PhD -5- National Alliance for Medical Image Computing Neuroimage Analysis Center Download Slicer3.4 Select the type of download ‘Stable Releases’

6. Sonia Pujol, PhD -6- National Alliance for Medical Image Computing Neuroimage Analysis Center Download Slicer3.4 Select the Operating System appropriate for your computer.

7. Sonia Pujol, PhD -7- National Alliance for Medical Image Computing Neuroimage Analysis Center Outline This tutorial guides you through the process of loading diffusion MR data, estimating diffusion tensors, and performing tractography of white matter bundles. The processing pipeline uses 8 image analysis modules of the Slicer3.4 software.

8. Sonia Pujol, PhD -8- National Alliance for Medical Image Computing Neuroimage Analysis Center Tutorial Dataset The Diffusion MR tutorial dataset is composed of a Diffusion Weighted MR scan of the brain acquired with 12 gradient directions and 2 baseline. Diffusion Sensitizing Gradients Diffusion Weighted Images

9. Sonia Pujol, PhD -9- National Alliance for Medical Image Computing Neuroimage Analysis Center Start Slicer3 Linux/Mac users Launch the Slicer3 executable located in the Slicer3.4 directory Windows users Select Start  All Programs  Slicer3 3.4 2009-05-21  Slicer3

10. Sonia Pujol, PhD -10- National Alliance for Medical Image Computing Neuroimage Analysis Center Slicer Welcome The SlicerWelcome module is the module displayed by default. This module gives an overview of the GUI of Slicer3, and data loading & saving functionalities.

11. Sonia Pujol, PhD -11- National Alliance for Medical Image Computing Neuroimage Analysis Center Part 1: Diffusion data loading and tensor estimation

12. Sonia Pujol, PhD -12- National Alliance for Medical Image Computing Neuroimage Analysis Center Loading the DWI volume Select File  Add Volume from the File menu

13. Sonia Pujol, PhD -13- National Alliance for Medical Image Computing Neuroimage Analysis Center Loading the DWI volume Browse to the location of the Diffusion tutorial dataset directory and select the file dwiDataset.nhdr Click on Apply to load the volume

14. Sonia Pujol, PhD -14- National Alliance for Medical Image Computing Neuroimage Analysis Center Loading the DWI volume Slicer displays the anatomical views of the baseline volume of the diffusion dataset in the 2D Slice Viewer.

15. Sonia Pujol, PhD -15- National Alliance for Medical Image Computing Neuroimage Analysis Center Tensor Estimation Left click on the menu Modules and select All Modules to display the list of 95 modules available for image analysis and 3D visualization. Select the module Diffusion Tensor Estimation.

16. Sonia Pujol, PhD -16- National Alliance for Medical Image Computing Neuroimage Analysis Center Tensor Estimation Select the Input DWI Volume dwiDataset Left click on OutputDTIVolume and select ‘Create New Diffusion Tensor Volume’ Left click on Output Baseline Volume and select ‘Create New Volume’ Left click on Otsu Threshold Mask and select ‘Create New Volume’

17. Sonia Pujol, PhD -17- National Alliance for Medical Image Computing Neuroimage Analysis Center Tensor Estimation Select the Tensor Estimation Algorithm LS ( Least Squares), and click on Apply to estimate the tensors.

18. Sonia Pujol, PhD -18- National Alliance for Medical Image Computing Neuroimage Analysis Center Tensor Estimation Left click on Diffusion Tensor Volume 1 to display the list of volumes that have been computed by Slicer

19. Sonia Pujol, PhD -19- National Alliance for Medical Image Computing Neuroimage Analysis Center Tensor Estimation Diffusion Tensor Estimation Volume is the volume of estimated tensors Diffusion Tensor Estimation Volume 1 is the Baseline volume Diffusion Tensor Estimation Volume 2 is the tensor mask (blue)

20. Sonia Pujol, PhD -20- National Alliance for Medical Image Computing Neuroimage Analysis Center Tensor Estimation Click on the link icon, left click on Diffusion Tensor Volume 2 and select None

21. Sonia Pujol, PhD -21- National Alliance for Medical Image Computing Neuroimage Analysis Center Tensor Estimation Select the module Volumes in the modules’ toolbar

22. Sonia Pujol, PhD -22- National Alliance for Medical Image Computing Neuroimage Analysis Center Tensor Estimation Select the Active Volume ‘Diffusion Tensor Estimation 1’ and click on the tab Display

23. Sonia Pujol, PhD -23- National Alliance for Medical Image Computing Neuroimage Analysis Center Tensor Estimation Adjust the Window/Level parameters of the baseline volume using the slider

24. Sonia Pujol, PhD -24- National Alliance for Medical Image Computing Neuroimage Analysis Center Tensor Estimation Browse through the baseline images, which correspond to the volumes that have been acquired without a gradient.

25. Sonia Pujol, PhD -25- National Alliance for Medical Image Computing Neuroimage Analysis Center Part2: Scalar Measurements

26. Sonia Pujol, PhD -26- National Alliance for Medical Image Computing Neuroimage Analysis Center Scalar Measurements Select the category Diffusion from the list of modules, and left click on the Diffusion Tensor Scalar Measurement module.

27. Sonia Pujol, PhD -27- National Alliance for Medical Image Computing Neuroimage Analysis Center Scalar Measurements Select the Input DTI Volume Diffusion Tensor Estimation Volume Select the Output Scalar Volume ‘Create New Volume’ Select the Operation Fractional Anisotropy, and click on Apply

28. Sonia Pujol, PhD -28- National Alliance for Medical Image Computing Neuroimage Analysis Center Fractional Anisotropy Volume Left click on the Slicer Viewer Menu icon, and select Show label volume outlines

29. Sonia Pujol, PhD -29- National Alliance for Medical Image Computing Neuroimage Analysis Center Slicer displays the outline of the tensor mask overlaid on the Fractional Anisotropy volume Fractional Anisotropy Volume

30. Sonia Pujol, PhD -30- National Alliance for Medical Image Computing Neuroimage Analysis Center Move the mouse over the Fractional Anisotropy map to explore the FA values which range from 0 to 1, and are displayed in the bottom corner of the active (Bg) window. Fractional Anisotropy Volume

31. Sonia Pujol, PhD -31- National Alliance for Medical Image Computing Neuroimage Analysis Center Part 3: Region of Interest based Tractography

32. Sonia Pujol, PhD -32- National Alliance for Medical Image Computing Neuroimage Analysis Center LabelMap Generation Select the module Editor in the modules’ menu. Select the Source Volume Diffusion Tensor Scalar Measurements Volume Select the label map volume Working and click on Create Label Map

33. Sonia Pujol, PhD -33- National Alliance for Medical Image Computing Neuroimage Analysis Center LabelMap Generation Left click on the Slicer Viewer Menu icon, and select Don’t Show label volume outlines

34. Sonia Pujol, PhD -34- National Alliance for Medical Image Computing Neuroimage Analysis Center LabelMap Generation Select the label 2 (pink), click on the icon Paint, set the radius to 2 and draw a region of interest within the corpus callosum in the sagittal view

35. Sonia Pujol, PhD -35- National Alliance for Medical Image Computing Neuroimage Analysis Center LabelMap Seeding Select the module Labelmap Seeding from the Modules’ menu

36. Sonia Pujol, PhD -36- National Alliance for Medical Image Computing Neuroimage Analysis Center LabelMap Seeding Select the Input DTI volume ‘Diffusion Tensor Estimation Volume’ Select the Input Label Map ‘Working’ Select Output Fiber Bundle ‘Create New Fiber Bundle’

37. Sonia Pujol, PhD -37- National Alliance for Medical Image Computing Neuroimage Analysis Center LabelMap Seeding Set the Seed Spacing to 2 mm and select the Stopping Mode Fractional Anisotropy Use the default parameters for the minimum and maximum tract length, stopping value and stopping track curvature. Set Seeding label to label 2, and click on Apply

38. Sonia Pujol, PhD -38- National Alliance for Medical Image Computing Neuroimage Analysis Center LabelMap Seeding The tracts generated within the corpus callosum region appear in the 3DViewer. The color map used represent the FA values along the tracts.

39. Sonia Pujol, PhD -39- National Alliance for Medical Image Computing Neuroimage Analysis Center LabelMap Seeding Select the module FiberBundles, and click on the tab Tube in the Display panel Check the Visibility box.

40. Sonia Pujol, PhD -40- National Alliance for Medical Image Computing Neuroimage Analysis Center LabelMap Seeding Slicer displays the computed tracts as tubes colored with FA values.

41. Sonia Pujol, PhD -41- National Alliance for Medical Image Computing Neuroimage Analysis Center Part 4: Tractography on-the-fly

42. Sonia Pujol, PhD -42- National Alliance for Medical Image Computing Neuroimage Analysis Center Fiducial Seeding Select the module Fiducials

43. Sonia Pujol, PhD -43- National Alliance for Medical Image Computing Neuroimage Analysis Center Fiducial Seeding Set Fiducial List to Create New FiducialList

44. Sonia Pujol, PhD -44- National Alliance for Medical Image Computing Neuroimage Analysis Center Fiducial Seeding Left click on FiducialList and select Rename

45. Sonia Pujol, PhD -45- National Alliance for Medical Image Computing Neuroimage Analysis Center Fiducial Seeding Enter the new name Seed and click on Apply

46. Sonia Pujol, PhD -46- National Alliance for Medical Image Computing Neuroimage Analysis Center Fiducial Seeding Click on the cross icon to add a fiducial to the list Seed

47. Sonia Pujol, PhD -47- National Alliance for Medical Image Computing Neuroimage Analysis Center Fiducial Seeding The fiducial Seed-P1 appears in the 3D Viewer

48. Sonia Pujol, PhD -48- National Alliance for Medical Image Computing Neuroimage Analysis Center Fiducial Seeding Position the fiducial in the cingulum region located above the corpus callosum

49. Sonia Pujol, PhD -49- National Alliance for Medical Image Computing Neuroimage Analysis Center Fiducial Seeding Select the Seed-P1 fiducial: we will use this fiducial to drive the tractography

50. Sonia Pujol, PhD -50- National Alliance for Medical Image Computing Neuroimage Analysis Center Fiducial Seeding Select the module Fiducial Seeding

51. Sonia Pujol, PhD -51- National Alliance for Medical Image Computing Neuroimage Analysis Center Fiducial Seeding Set the DTI Volume to Diffusion Tensor Estimation Volume Select the Fiducial List Seed Set the Output FiberBundleNode to Create New FiberBundle

52. Sonia Pujol, PhD -52- National Alliance for Medical Image Computing Neuroimage Analysis Center Fiducial Seeding Set the Stopping Mode to Fractional Anisotropy and set the tractography parameters to the values that we used for the corpus callosum: Stopping Value: 0.1 Stopping Track Curvature: 0.8 Step Length: 0.8 mm Minimum Length: 0.1 mm Fiducial Stepping Size: 1.5 mm

53. Sonia Pujol, PhD -53- National Alliance for Medical Image Computing Neuroimage Analysis Center Fiducial Seeding Slicer displays the tracts seeded from the Fiducial Seed-P1. The tracts correspond to the region of the cingulum located above the corpus callosum.

54. Sonia Pujol, PhD -54- National Alliance for Medical Image Computing Neuroimage Analysis Center Fiducial Seeding Move the fiducial Seed-P1 from the left cingulum to the corresponding region in the right cingulum in the coronal slice.

55. Sonia Pujol, PhD -55- National Alliance for Medical Image Computing Neuroimage Analysis Center Fiducial Seeding Slicer displays the right cingulum tracts which are seeded from the new position of the fiducial Seed-P1

56. Sonia Pujol, PhD -56- National Alliance for Medical Image Computing Neuroimage Analysis Center Part 5: Saving a DTI Scene

57. Sonia Pujol, PhD -57- National Alliance for Medical Image Computing Neuroimage Analysis Center DTI Scene Select the module Data Slicer displays the list of volumes and models generated in this tutorial

58. Sonia Pujol, PhD -58- National Alliance for Medical Image Computing Neuroimage Analysis Center Saving a DTI Scene Select File  Save from the main menu

59. Sonia Pujol, PhD -59- National Alliance for Medical Image Computing Neuroimage Analysis Center Saving a DTI Scene Browse to the directory SlicerData to save the data and click on Save Selected

60. Sonia Pujol, PhD -60- National Alliance for Medical Image Computing Neuroimage Analysis Center Saving a DTI Scene Select File  Close Scene to close the current DTI Scene

61. Sonia Pujol, PhD -61- National Alliance for Medical Image Computing Neuroimage Analysis Center Loading a DTI Scene Select File  Load Scene and browse to the location where you saved the scene SlicerScene1.mrml

62. Sonia Pujol, PhD -62- National Alliance for Medical Image Computing Neuroimage Analysis Center Loading a DTI Scene Select the scene SlicerScene1.mrml and click on Open

63. Sonia Pujol, PhD -63- National Alliance for Medical Image Computing Neuroimage Analysis Center Loading a DTI Scene Select the module Data

64. Sonia Pujol, PhD -64- National Alliance for Medical Image Computing Neuroimage Analysis Center Loading a DTI Scene Slicer loads all the elements of the DTI Scene that were previously computed.

65. Sonia Pujol, PhD -65- National Alliance for Medical Image Computing Neuroimage Analysis Center Conclusion This tutorial guided you through some of the Diffusion MR capabilities of the Slicer3 software. For more tutorials and teaching events, please visit spujol@bwh.harvard.edu www.slicer.org www.na-mic.org/Wiki/index.php/Events

66. Sonia Pujol, PhD -66- National Alliance for Medical Image Computing Neuroimage Analysis Center Acknowledgments National Alliance for Medical Image Computing NIH U54EB005149 Neuroimage Analysis Center NIH P41RR013218