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Hands-on Diffusion Tensor Imaging Training

Hands-on Diffusion Tensor Imaging Training. Sonia Pujol, Ph.D. Brigham and Women’s Hospital Harvard Medical School. Randy Gollub, M.D, Ph.D. Massachusetts General Hospital Harvard Medical School. 13 th Annual Meeting of the Organization for Human Brain Mapping – OHBM 2007.

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Hands-on Diffusion Tensor Imaging Training

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  1. Hands-on Diffusion Tensor Imaging Training Sonia Pujol, Ph.D. Brigham and Women’s Hospital Harvard Medical School Randy Gollub, M.D, Ph.D. Massachusetts General Hospital Harvard Medical School 13th Annual Meeting of the Organization for Human Brain Mapping – OHBM 2007

  2. Acknowledgments National Alliance for Medical Image Computing NIH U54EB005149 Neuroimage Analysis Center NIH P41RR013218 Laboratory of Mathematics in Imaging, Brigham and Women’s Hospital

  3. NA-MIC Kit • End User Application: 3D Slicer, FiberViewer • Software and methodologies for Medical Image Computing • ITK, VTK, KWidgets, CMake, Dart, CTest, CPack

  4. OHBM 2007 Workshop Guiding you step-by-step through a complete DTI analysis of the corpus callosum which includes the generation of tensors, calculation of scalar metrics and tractography tools.

  5. 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://wiki.na-mic.org/Wiki/index.php/Training:OHBM2007_Training_Workshop

  6. 3D Slicer • Open-source application available for Windows, Linux, Solaris and Mac

  7. 3D Slicer • Open-source application available for Windows, Linux, Solaris and Mac • 447,233 lines of code

  8. 3D Slicer • Open-source application available for Windows, Linux, Solaris and Mac • 447,233 lines of code • Neuroscience and Image-guided therapy

  9. 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.

  10. DTI Analysis with Slicer Slicer can load • DWI Volumes ……………………. • Tensors…………………………… • Tracts……………………………… • DTI Scenes ……………………….

  11. Slicer Interface Menu Viewer Tk window Slicer101 Compendium: SlicerTraining 1: Loading and Viewing Data

  12. DWI Exemplar Dataset 1 • 2 Baselines and 12 Gradients • Volume interleaved

  13. DWI Exemplar Dataset 2 • 1 Baseline and 6 Gradients • Volume interleaved • Slice interleaved

  14. Hands-on Session Overview • Session 1: Data Loading and Visualization • Session 2: From DWI to DTI • Session 3: Scalar maps calculation • Session 4: Fiber Tract 3D Visualization

  15. National Alliance for Medical Image Computing NA-MIC Training Workshop OHBM 2007 Session 1Data Loading and Visualization

  16. DWI Exemplar Dataset 1 • 2 Baselines and 12 Gradients • Volume interleaved

  17. Loading the DWI Training Dataset 1 Click on Add Volume to load the Dwi-dicom training dataset

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

  19. 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

  20. Loading the DWI training dataset 1 Slicer loads the Nrrd DWI dataset

  21. Loading the DWI training dataset 1 Left-click on the button Or, and select the orientation Slices

  22. Loading the DWI training dataset 1 The anatomical slices are now aligned with the sampling grid

  23. Loading the DWI training dataset 1 Change the FOV to 2000

  24. Loading the DWI training dataset 1 The sagittal and coronal viewers display the 14 MR volumes: 2 baselines and 12 diffusion weighted volumes. This corresponds to a volume-interleaved dataset.

  25. Interacting with 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.

  26. Interacting with DWI data • Position the mouse inside the 3D Viewer. • Window/Linux users: • Left-click and move the mouse to the left (right): • Mac users: • Move the mouse button to the left •  the volume moves to the left (right).

  27. Interacting with DWI data • Position the mouse inside the 3D Viewer. • Window/Linux users: • Left-click and move the mouse up (down): • Mac users: • Move the mouse button up (down): •  the volume moves up (down).

  28. Hands-on Session Overview • Session 1: Data Loading and Visualization • Session 2: From DWI to DTI • Session 3: Scalar maps calculation • Session 4: Fiber Tract 3D Visualization

  29. National Alliance for Medical Image Computing NA-MIC Training Workshop OHBM 2007 Session 2From Diffusion Weighted Imaging to Diffusion Tensor Imaging

  30. 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

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

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

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

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

  35. 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 DT-MRI module for additional calculations.

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

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

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

  39. Adjusting Window Level Inspect the anatomy using the axial, sagittal and coronal sliders.

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

  41. Converting DWI data to tensors Slicer displays the baseline images. Browse the baseline images to check if the anatomy is correct

  42. Converting DWI data to tensors Click on the module Data • Slicer displays the list of available volumes: • DWI dataset • Tensor volume • Average Gradient volume • Average Gradient mask • Baseline volume

  43. Glyphs Visualization Click on the DTMRI module and select the panel Glyphs

  44. Glyphs Visualization Select the Active DTMRI volume namic01-dwi-nhdr_Tensor Select Glyphs on Slice for the axial (red) view Set Display Glyphs On

  45. Glyphs Visualization Slicer displays the orientation of the glyphs in the Axial view.

  46. Glyphs Visualization Right-click and move the mouse down The 3D Viewer gets closer to the volume.

  47. Glyphs Visualization Observe the orientation of the glyphs in the Corpus Callosum

  48. Glyphs Visualization Click on Off to leave the glyphs visualization mode.

  49. Closing the scene Click on the module Data and select File Close in the Main Menu to clear the scene For details on the Nrrd file format, see Slicer 101 Compendium: Training 8: Nrrd File Format

  50. DWI Exemplar Dataset 2 • 1 Baseline and 6 Gradients • Volume interleaved • Slice interleaved

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