Session 4 Diffusion Tensor Imaging

1. National Alliance for Medical Image Computing NA-MIC Training Workshop NCBC AHM Session 4 Diffusion Tensor Imaging Sonia Pujol, Ph.D. Randy Gollub, M.D., Ph.D.

2. Acknowledgments National Alliance for Medical ImageComputing 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. Material • Slicer 2.6 http://www.na-mic.org/Wiki/index.php/Slicer:Slicer2.6_Getting_Started • DTI Sample Data Set Dwi-dicom.zip SlicerSampleDTI.zip http://www.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101

4. Goal of this tutorial Guiding you step-by-step through the DWI data analysis capabilities of Slicer, including generation of tensors, calculation of scalar metrics and tractography tools. Final result of the tutorial

5. Slicer DT-MRI Module

6. Overview • Part 1: Loading and Converting DTI Data • Part 2: Computing Fractional Anisotropy • Part 3: Generating Fiber Tracts • Part 4: Selective Seeding • Part 5: Clustering

7. Diffusion Weighted Imaging (DWI) Diffusion Weighted Images Diffusion Sensitizing Gradients

8. Diffusion Weighted Imaging (DWI) Example: Correlation between the orientation of the 11th gradient and the signal intensity in the Splenium of the Corpus Callosum

9. Loading DTI Data Slicer can load • DWI Volumes ……………………. • Tensors…………………………… • Tracts……………………………… • DTI Scenes ……………………….

10. DWI Training Dataset 1 • 2 Baselines and 12 Gradients

11. DWI Training Dataset 2 • 1 Baseline and 6 Gradients

12. Loading the DWI Training Dataset 1 Click on Add Volume to load the Dicom-DWI training dataset

13. Loading DWI data The Props Panel of the module Volumes appears. Select Nrrd Reader in the Properties field

14. Loading DWI data Click on Browse and load the file namic01-dwi.nhdr in the directory Dwi-dicom Check that the path to the file is correct. If needed, manually enter it Click on Apply

15. Loading DWI data Slicer loads the Nrrd DWI dataset

16. Loading DWI data Left-click on the button Or, and select the orientation Slices

17. Loading DWI data The anatomical slices are now aligned with the sampling grid

18. Loading DWI data Change the FOV to 2000

19. Loading DWI data The sagittal and coronal viewers display the 14 MR volumes: 2 baselines and 12 diffusion weighted volumes

20. Loading DWI data Left-Click on the V button to display the axial and sagittal slices inside the viewer. Use the axial slider to slice trough the baselines and diffusion weighted MR volumes.

21. DT-MRI Module Select Modules in the Main Menu Select VisualisationDTMRI

22. DT-MRI Module The panel Input of the DTMRI module appears Click on the tab Conv

23. DT-MRI Module The panel Conv of the DTMRI module appears

24. Converting DWI data to tensors Select the Input Volume namic01-dwi.nhdr and click on ConvertVolume

25. D D D xx xy xz D D D yx yy yz D D D zx zy zz Converting DWI data to tensors {Si} represent the signal intensities in presence of the gradients gi (Stejskal and Tanner 1965, Basser 1994 ) Slicer computes the symmetric 3x3 tensor matrix D for each voxel

26. Converting DWI data to tensors • At the end of the calculation, Slicer displays the average of all diffusion weighted images (_AvGradient) and the baseline volume (_Baseline). • The tensors volume is available from the DTMRI module for additional calculations.

27. Converting DWI data to tensors Slicer displays the anatomical views of the average of all 12 diffusion weighted images (average over all gradient directions)

28. Adjusting Window Level Click on the Module Volumes and select the tab Display

29. Adjusting Window Level Select the Active Volume namic01-dwi-nhdr_AvGradient Use the sliders Win and Lev to adjust the Window level

30. Adjusting Window Level Slicer displays the anatomical views of the average of all 12 diffusion weighted images (average over all gradient directions) Inspect the anatomy using the axial, sagittal and coronal sliders.

31. Converting DWI data to tensors Left-click on Bg and select the volume namic01-dwi nhdr_Baseline

32. Converting DWI data to tensors Slicer displays the baseline (T2) images. Browse the baseline images to check if the anatomy is correct

33. Converting DWI data to tensors Click on the module Data Slicer displays the list of DTI volumes

34. Converting DWI data to tensors Select File Close in the Main Menu to clear the scene

35. Loading the DWI Training Dataset 2 Click on Add Volume

36. Loading Slicer Sample DWI data Select the Props Panel Use the Basic Reader Click on Browse Navigate to the folder containing the tutorial data Select the first file D.001 Click Open Select ImageHeaders: Auto Click Apply

37. Loading Slicer Sample DWI data The DWI images appear in the Viewer

38. Loading Slicer Sample DWI data Observe the axial slices using the slider

39. Loading Slicer Sample DWI data A sequence of white stripes appears in the diffusion weighted images. They correspond to intersections with the baseline images in Slicer Axial/Sagittal/Coronal (AxiSagCor) slice mode.

40. Loading Slicer Sample DWI data Superior In Axial/Sagittal/Coronal mode the slices planes, which are aligned with the RAS coordinates, are cutting through the DWI volume Inferior

41. Loading Slicer Sample DWI data Left click onOr and select the orientation Slices in the Menu

42. Loading Slicer Sample DWI data The original slices appear in the Viewer

43. Loading Slicer Sample DWI data Superior In AxiSlice/SagiSlice/CorSlice mode the slices are aligned with the DWI volume Inferior

44. Loading Slicer Sample DWI data Notice that the viewer displays the stack of S0 and diffusion weighted images {Si}

45. Loading Slicer Sample DWI data Browse the original axial slices corresponding to the baseline (S0) image. Example: display the slice 209

46. Loading Slicer Sample DWI data Adjust the window level and observe the baseline image (S0)

47. Adjusting Image Window Level Select the Volumes module Select the Display panel Select the volume D Adjust Window and Level

48. Loading Slicer Sample DWI data Observe the baseline image (S0)

49. Loading Slicer Sample DWI data Notice that the image intensity for each of the six gradient orientations is much lower than the S0 image.

50. DT-MRI Module Select Modules in the Main Menu Select VisualizationDTMRI