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Slicer Tutorial 4 Module: DTMRI Data: Sample Slicer DTI

Slicer Tutorial 4 Module: DTMRI Data: Sample Slicer DTI. Sonia Pujol, Ph.D. Tina Kapur, Ph.D. Randy Gollub, M.D., Ph.D. Acknowledgments. National Alliance for Medical Imaging NIH U54EB005149 Neuroimage Analysis Center NIH P41RR013218 Laboratory of Mathematics in Imaging,

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Slicer Tutorial 4 Module: DTMRI Data: Sample Slicer DTI

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  1. Slicer Tutorial 4Module: DTMRIData: Sample Slicer DTI Sonia Pujol, Ph.D. Tina Kapur, Ph.D. Randy Gollub, M.D., Ph.D

  2. 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. 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. 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. Goal of this tutorial Guiding you step-by-step through the process of Tractography within DTI data Final result of the tutorial

  6. 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. Slicer DT-MRI Module

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

  10. Loading Slicer Sample DTI data Select the Volumes Module Select the Props Panel Use the Basic Reader Click File Browse Pick the first file D.001 Select ImageHeader: Auto Click Apply

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

  12. Loading Slicer Sample DTI data Observe the axial slices using the slider

  13. Loading Slicer Sample DTI data The white strips correspond to an oblique acquisition.

  14. 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. Loading Original DTI data Left click onAxialand select AxiSlice in the Menu

  16. Loading Original DTI data The original Axial slice appears in the Viewer.

  17. Loading Original DTI data Browse the original axial slices corresponding to the baseline. Example: display the slice 111

  18. Loading Original DTI data Observe the baseline

  19. Loading Original DTI data Browse the original axial slices corresponding to the gradients Example: display the slices 112 to 117

  20. Loading Original DTI data The 6 gradients appear in the viewer.

  21. Loading Original DTI data Left click onSagittal,select SagSlice Left click on Coronal,select CorSlice

  22. Loading Original DTI data Observe the original data in the Sagittal and Coronal viewers

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

  24. DT-MRI Module The interface of the DTMRI module appears Select the Convert Panel

  25. Convert To Tensors Select InputVolume D Select Protocol BWH_6g.1bSlice Click on Prop. to display the parameters of the acquisition protocol Click on Convert Volume

  26. Convert to Tensors Resulting viewer window

  27. Adjust Image Window Level Select the Volumes module Select the D_AvGradient volume Adjust Window and Level

  28. Adjust Image Window Level Resulting viewer window

  29. 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. Computing Fractional Anisotropy Left-click on DTMRI to come back to the DTI Module Click on More to naviguate in the different panels

  31. Computing Fractional Anisotropy Select the panel Scalars Select Fractional Anisotropy in the Create Volume Menu Click on Apply

  32. Computing Fractional Anisotropy The Viewer displays the FA volume.

  33. 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. Tractography Panel Click on the More Panel inside the DTMRI module

  35. Tractography Panel Select the Display Panel Select the Tractography Menu

  36. Tracts Color Display Left-click on Color A Color selection panel appears Double click on a new color

  37. Create a single tract Position the mouse on a point inside the corpus callosum, and hit the s key.

  38. Create a single tract A tract appears in the 3D Viewer. Drag right mouse button down in the 3D Viewer to zoom in.

  39. Create a single tract The 3D window shows a closer view of the tract. Click on the V buttons

  40. 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. Generate Multiple Tracts Position the mouse on different points in the corpus callosum and hit the s key.

  42. Generate Multiple Tracts The tracts that correspond to the visited points appear in the 3D Viewer.

  43. Generate Multiple Tracts Hold the s key down and drag the mouse in the corpus callosum

  44. Generate Multiple Tracts Multiple tracts are generated for each point visited by the mouse.

  45. 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. 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. AutoTracts Select the Editor module in the main Menu. Select the Effects panel. Left click on Draw in the Effects Menu.

  48. AutoTracts Left click on Output and select a new color for the region of interest

  49. AutoTracts Draw the contour of the corpus callosum in the sagittal slice, and click Apply

  50. AutoTracts Come back to the DTMRI module Click on the ROI Labelmap menu and select the ROI Working Click on Seed ‘Tracts’ in ROI

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