1. NA-MIC National Alliance for Medical Image Computing http://na-mic.org Hands-on Diffusion Tensor Imaging Training Randy Gollub, M.D, Ph.D. Massachusetts General Hospital Harvard Medical School Sonia Pujol, Ph.D. Brigham and Women’s Hospital Harvard Medical School 13 th Annual Meeting of the Organization for Human Brain Mapping – OHBM 2007

2. Pujol S., Gollub R. National Alliance for Medical Image Computing 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. Pujol S., Gollub R. National Alliance for Medical Image Computing NA-MIC Kit End User Application: 3D Slicer, FiberViewer Software and methodologies for Medical Image Computing ITK, VTK, KWidgets, CMake, Dart, CTest, CPack

4. Pujol S., Gollub R. National Alliance for Medical Image Computing 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. Pujol S., Gollub R. National Alliance for Medical Image Computing 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. Pujol S., Gollub R. National Alliance for Medical Image Computing 3D Slicer Open-source application available for Windows, Linux, Solaris and Mac

7. Pujol S., Gollub R. National Alliance for Medical Image Computing 3D Slicer Open-source application available for Windows, Linux, Solaris and Mac 447,233 lines of code

8. Pujol S., Gollub R. National Alliance for Medical Image Computing 3D Slicer Open-source application available for Windows, Linux, Solaris and Mac 447,233 lines of code Neuroscience and Image- guided therapy

9. Pujol S., Gollub R. National Alliance for Medical Image Computing 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. Pujol S., Gollub R. National Alliance for Medical Image Computing DTI Analysis with Slicer Slicer can load DWI Volumes ……………………. Tensors…………………………… Tracts……………………………… DTI Scenes ……………………….

11. Pujol S., Gollub R. National Alliance for Medical Image Computing Slicer Interface ViewerMenu Tk window Slicer101 Compendium: SlicerTraining 1: Loading and Viewing Data

12. Pujol S., Gollub R. National Alliance for Medical Image Computing DWI Exemplar Dataset 1 2 Baselines and 12 Gradients Volume interleaved

13. Pujol S., Gollub R. National Alliance for Medical Image Computing DWI Exemplar Dataset 2 1 Baseline and 6 Gradients Volume interleaved Slice interleaved

14. Pujol S., Gollub R. National Alliance for Medical Image Computing 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. NA-MIC National Alliance for Medical Image Computing http://na-mic.org Session 1 Data Loading and Visualization National Alliance for Medical Image Computing NA-MIC Training Workshop OHBM 2007

16. Pujol S., Gollub R. National Alliance for Medical Image Computing DWI Exemplar Dataset 1 2 Baselines and 12 Gradients Volume interleaved

17. Pujol S., Gollub R. National Alliance for Medical Image Computing Loading the DWI Training Dataset 1 Click on Add Volume to load the Dwi-dicom training dataset

18. Pujol S., Gollub R. National Alliance for Medical Image Computing Loading DWI data Select Nrrd Reader in the Properties field The Props Panel of the module Volumes appears.

19. Pujol S., Gollub R. National Alliance for Medical Image Computing Loading DWI data Click on Apply 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

20. Pujol S., Gollub R. National Alliance for Medical Image Computing Loading the DWI training dataset 1 Slicer loads the Nrrd DWI dataset

21. Pujol S., Gollub R. National Alliance for Medical Image Computing Left-click on the button Or, and select the orientation Slices Loading the DWI training dataset 1

22. Pujol S., Gollub R. National Alliance for Medical Image Computing The anatomical slices are now aligned with the sampling grid Loading the DWI training dataset 1

23. Pujol S., Gollub R. National Alliance for Medical Image Computing Change the FOV to 2000 Loading the DWI training dataset 1

24. Pujol S., Gollub R. National Alliance for Medical Image Computing The sagittal and coronal viewers display the 14 MR volumes: 2 baselines and 12 diffusion weighted volumes. This corresponds to a volume-interleaved dataset. Loading the DWI training dataset 1

25. Pujol S., Gollub R. National Alliance for Medical Image Computing 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. Pujol S., Gollub R. National Alliance for Medical Image Computing 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. Pujol S., Gollub R. National Alliance for Medical Image Computing 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. Pujol S., Gollub R. National Alliance for Medical Image Computing 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. NA-MIC National Alliance for Medical Image Computing http://na-mic.org Session 2 From Diffusion Weighted Imaging to Diffusion Tensor Imaging National Alliance for Medical Image Computing NA-MIC Training Workshop OHBM 2007

30. Pujol S., Gollub R. National Alliance for Medical Image Computing Converting DWI data to tensors zzzyzx yzyyyx xzxyxx DDD DDD DDD (Stejskal and Tanner 1965, Basser 1994 ) {Si} represent the signal intensities in presence of the gradients gi Slicer computes the symmetric 3x3 tensor matrix D for each voxel

31. Pujol S., Gollub R. National Alliance for Medical Image Computing DT-MRI Module Select Modules in the Main Menu Select Visualization  DTMRI

32. Pujol S., Gollub R. National Alliance for Medical Image Computing DT-MRI Module The panel Input of the DTMRI module appears Click on the tab Conv

33. Pujol S., Gollub R. National Alliance for Medical Image Computing DT-MRI Module The panel Conv of the DTMRI module appears

34. Pujol S., Gollub R. National Alliance for Medical Image Computing Converting DWI data to tensors Select the Input Volume namic01-dwi.nhdr and click on ConvertVolume

35. Pujol S., Gollub R. National Alliance for Medical Image Computing 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. Converting DWI data to tensors

36. Pujol S., Gollub R. National Alliance for Medical Image Computing 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. Pujol S., Gollub R. National Alliance for Medical Image Computing Adjusting Window Level Click on the Module Volumes and select the tab Display

38. Pujol S., Gollub R. National Alliance for Medical Image Computing Adjusting Window Level Select the Active Volume namic01-dwi-nhdr_AvGradient Use the sliders Win and Lev to adjust the Window level

39. Pujol S., Gollub R. National Alliance for Medical Image Computing Adjusting Window Level Inspect the anatomy using the axial, sagittal and coronal sliders.

40. Pujol S., Gollub R. National Alliance for Medical Image Computing Left-click on Bg and select the volume namic01-dwi nhdr_Baseline Converting DWI data to tensors

41. Pujol S., Gollub R. National Alliance for Medical Image Computing Browse the baseline images to check if the anatomy is correct Converting DWI data to tensors Slicer displays the baseline images.

42. Pujol S., Gollub R. National Alliance for Medical Image Computing 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. Pujol S., Gollub R. National Alliance for Medical Image Computing Glyphs Visualization Click on the DTMRI module and select the panel Glyphs

44. Pujol S., Gollub R. National Alliance for Medical Image Computing 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. Pujol S., Gollub R. National Alliance for Medical Image Computing Glyphs Visualization Slicer displays the orientation of the glyphs in the Axial view.

46. Pujol S., Gollub R. National Alliance for Medical Image Computing Glyphs Visualization Right-click and move the mouse down The 3D Viewer gets closer to the volume.

47. Pujol S., Gollub R. National Alliance for Medical Image Computing Glyphs Visualization Observe the orientation of the glyphs in the Corpus Callosum

48. Pujol S., Gollub R. National Alliance for Medical Image Computing Glyphs Visualization Click on Off to leave the glyphs visualization mode.

49. Pujol S., Gollub R. National Alliance for Medical Image Computing 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. Pujol S., Gollub R. National Alliance for Medical Image Computing DWI Exemplar Dataset 2 1 Baseline and 6 Gradients Volume interleaved Slice interleaved

51. Pujol S., Gollub R. National Alliance for Medical Image Computing Loading the DWI Training Dataset 2 Click on Add Volume to load the SlicerSampleDTI training dataset

52. Pujol S., Gollub R. National Alliance for Medical Image Computing Loading the DWI Training Dataset 2 Select ImageHeaders: Auto Click Apply Select the Props Panel Use the Basic Reader and click on Browse Navigate to the folder containing the tutorial data Select the first file D.001 Click Open

53. Pujol S., Gollub R. National Alliance for Medical Image Computing Loading the DWI Training Dataset 2 The DWI images appear in the Viewer

54. Pujol S., Gollub R. National Alliance for Medical Image Computing Observe the axial slices using the slider DWI Training Dataset 2

55. Pujol S., Gollub R. National Alliance for Medical Image Computing 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. DWI Training Dataset 2

56. Pujol S., Gollub R. National Alliance for Medical Image Computing Inferior Superior In Axial/Sagittal/Coronal mode the slices planes, which are aligned with the RAS coordinates, are cutting through the DWI volume DWI Training Dataset 2 Baseline Gradient

57. Pujol S., Gollub R. National Alliance for Medical Image Computing Slices mode Inferior Superior

58. Pujol S., Gollub R. National Alliance for Medical Image Computing Left click on Or and select the orientation Slices in the Menu DWI Training Dataset 2

59. Pujol S., Gollub R. National Alliance for Medical Image Computing The original slices appear in the Viewer DWI Training Dataset 2

60. Pujol S., Gollub R. National Alliance for Medical Image Computing Inferior Superior In AxiSlice/SagiSlice/CorSlice mode the slices are aligned with the DWI volume Loading the DWI Training Dataset 2

61. Pujol S., Gollub R. National Alliance for Medical Image Computing Loading the DWI Training Dataset 2 Notice that the viewer displays the stack of S 0 and diffusion weighted images {Si}: this corresponds to a slice-interleaved dataset.

62. Pujol S., Gollub R. National Alliance for Medical Image Computing Browse the original axial slices corresponding to the baseline (S 0 ) image. Loading the DWI Training Dataset 2 Example: display the slice 209

63. Pujol S., Gollub R. National Alliance for Medical Image Computing Loading the DWI Training Dataset 2 Adjust the window level and observe the baseline image (S 0 )

64. Pujol S., Gollub R. National Alliance for Medical Image Computing Adjusting Image Window Level Select the Volumes module Adjust Window and Level Select the volume D Select the Display panel

65. Pujol S., Gollub R. National Alliance for Medical Image Computing Loading the DWI Training Dataset 2 Observe the baseline image (S 0 )

66. Pujol S., Gollub R. National Alliance for Medical Image Computing Notice that the image intensity for each of the six gradient orientations is much lower than the S 0 image. Loading the DWI Training Dataset 2

67. Pujol S., Gollub R. National Alliance for Medical Image Computing Converting DWI data to tensors Select Modules in the Main Menu Select Visualization  DT MRI

68. Pujol S., Gollub R. National Alliance for Medical Image Computing Converting DWI data to tensors Select the Conversion Panel: Conv

69. Pujol S., Gollub R. National Alliance for Medical Image Computing Acquisition protocol Acquisition parameters are essential for tensor calculation, and further DTI analysis. Parameters such as gradient directions might not be included in the header of the image files. In this example, the datasets were acquired with a known protocol BWH_6g1bSlice.

70. Pujol S., Gollub R. National Alliance for Medical Image Computing Converting DWI data to tensors Select InputVolume D Select Protocol BWH_6g.1bSlice Click on Prop to display the parameters of the acquisition protocol

71. Pujol S., Gollub R. National Alliance for Medical Image Computing Acquisition protocol The parameters of the acquisition protocol used to acquire the DTI Sample Data BWH_6g.1bSlice at Brigham and Women’s Hospital correspond to: n=6 gradients Gradient 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 and B-value = 1000

72. Pujol S., Gollub R. National Alliance for Medical Image Computing Converting DWI data to tensors Click on Convert Volume

73. Pujol S., Gollub R. National Alliance for Medical Image Computing Converting DWI data to tensors Slicer displays the anatomical views of the average of all 6 diffusion weighted images

74. Pujol S., Gollub R. National Alliance for Medical Image Computing Converting DWI data to tensors Left Click on the button Bg and select the volume D_Baseline

75. Pujol S., Gollub R. National Alliance for Medical Image Computing Converting DWI data to tensors Observe the volume D_Baseline

76. Pujol S., Gollub R. National Alliance for Medical Image Computing 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

77. NA-MIC National Alliance for Medical Image Computing http://na-mic.org Session 3 Scalar Maps Processing National Alliance for Medical Image Computing NA-MIC Training Workshop OHBM 2007

78. Pujol S., Gollub R. National Alliance for Medical Image Computing Scalar maps The tensors derived from diffusion tensor imaging describe complex diffusion in tissues. Scalar measures that map the three- dimensional eigenvalues of the diffusion tensor into scalar values provide efficient solutions for extracting desired aspects of the tensors. In the following section, we’ll compute exemplar scalar maps: the Relative Anisotropy map and the Fractional Anisotropy map.

79. Pujol S., Gollub R. National Alliance for Medical Image Computing Computing Relative Anisotropy The Relative Anisotropy (RA) represents the ratio of the anisotropic part of D to its isotropic part: where

80. Pujol S., Gollub R. National Alliance for Medical Image Computing Computing Relative Anisotropy Select the panel Scalars Browse the menu Create Volume to see the list of calculations that Slicer can perform on the D_Tensor dataset. Select Relative Anisotropy

81. Pujol S., Gollub R. National Alliance for Medical Image Computing Computing Relative Anisotropy Click on Apply Select the Region of Interest ROI:Mask The Scale Factor is set by default to 1000, because the standard range of RA values (0.0 to 1.0) is not compatible with Slicer The Relative Anisotropy Panel appears

82. Pujol S., Gollub R. National Alliance for Medical Image Computing Computing Relative Anisotropy The Viewer displays the RA volume. Move the mouse in the slices to see RA values for each voxel. Observe High RA values in the Corpus Callosum and low RA values in Grey matter areas

83. Pujol S., Gollub R. National Alliance for Medical Image Computing The Fractional Anisotropy (FA) is a measure of the diffusion anisotropy that can be calculated without explicitly computing any eigenvalue: where |D| and trace(D) are the norm and trace of the Diffusion Tensor. Computing Fractional Anisotropy

84. Pujol S., Gollub R. National Alliance for Medical Image Computing Computing Fractional Anisotropy Select the panel Scalars Browse the menu Create Volume to see the list of calculations that Slicer can perform on the D_Tensor dataset. Select Fractional Anisotropy

85. Pujol S., Gollub R. National Alliance for Medical Image Computing Computing Fractional Anisotropy Click on Apply Select the Region of Interest ROI:Mask The Scale Factor is set by default to 1000, because the standard range of FA values (0.0 to 1.0) is not compatible with Slicer The Fractional Anisotropy Panel appears

86. Pujol S., Gollub R. National Alliance for Medical Image Computing Computing Fractional Anisotropy The Viewer displays the FA volume. Move the mouse in the slices to see FA values for each voxel.

87. Pujol S., Gollub R. National Alliance for Medical Image Computing Computing Fractional Anisotropy Note high FA values over large tracts such as the corpus callosum Note low FA values over gray matter

88. Pujol S., Gollub R. National Alliance for Medical Image Computing ROI Drawing Select the Editor module in the main Menu. Select the Volumes panel. Select the Original Grayscale FractionalAnisotropy_D Select the Working Labelmap NEW and keep the Default Descriptive Name Working. Click on Start Editing

89. Pujol S., Gollub R. National Alliance for Medical Image Computing ROI Drawing Select the Effects panel Left click on Draw in the Effects Menu

90. Pujol S., Gollub R. National Alliance for Medical Image Computing ROI Drawing The Draw Panel of the Editor Module appears Left-click on Output, and select the color label #2 (pink)

91. Pujol S., Gollub R. National Alliance for Medical Image Computing ROI Drawing Draw the contour of the Corpus Callosum with the mouse in the sagittal slice

92. Pujol S., Gollub R. National Alliance for Medical Image Computing Statistical analysis Select Modules  Measurement  VolumeMath in the Main Menu

93. Pujol S., Gollub R. National Alliance for Medical Image Computing Statistical analysis Select MaskStat The MaskStat functionality uses the labelmap as a mask over the FA volume, and calculates statistical values on the region contained under the labelmap.

94. Pujol S., Gollub R. National Alliance for Medical Image Computing Statistical analysis Set Volume to Mask to FractionalAnisotropy_D_Tensor Set LabelMap to Working Set Masked Output to Create New

95. Pujol S., Gollub R. National Alliance for Medical Image Computing Statistical analysis Click on Run Click on Mask, select the same color as your labelmap (Label 2, pink)

96. Pujol S., Gollub R. National Alliance for Medical Image Computing Statistical Analysis A pop-up window shows statistical values (multiplied by the Scale Factor) of the Fractional Anisotropy in the Corpus Callosum. The results have been saved in the file FractionalAnisotrop y_D_Tensor_hist.txt written on the disk.

97. Pujol S., Gollub R. National Alliance for Medical Image Computing 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

98. NA-MIC National Alliance for Medical Image Computing http://na-mic.org Session 4 Fiber Tracts 3D Visualization National Alliance for Medical Image Computing NA-MIC Training Workshop OHBM 2007

99. Pujol S., Gollub R. National Alliance for Medical Image Computing Motivations for DTI visualization Clinical drivers applications for nerve fiber tract visualization, tract measurements and tract clustering include –neurosurgical planning for tumor resections –study of fiber tract abnormality in schizophrenia –white matter disruption in multiple sclerosis

100. Pujol S., Gollub R. National Alliance for Medical Image Computing Fiber tract visualization DTI data contain useful information related to the anatomy of nerve fiber tracts. In the following section, visualize white matter fiber tract trajectories in the Corpus Callosum.

101. Pujol S., Gollub R. National Alliance for Medical Image Computing Tractography Panel Select the DTMRI module and click on the Panel More Select the Panel Tract inside the DTMRI module

102. Pujol S., Gollub R. National Alliance for Medical Image Computing Tractography Panel Select the Tab Settings Left-click on Color

103. Pujol S., Gollub R. National Alliance for Medical Image Computing Tractography Panel A Color selection panel appears Select a new color for the tracts

104. Pujol S., Gollub R. National Alliance for Medical Image Computing Create a single tract Position the mouse on a point inside the Corpus Callosum, and hit the s key.

105. Pujol S., Gollub R. National Alliance for Medical Image Computing Create a single tract A tract appears in the 3D Viewer. ZOOM IN: Position the mouse on the images inside the Viewer Right-click and move the mouse down Press the apple button, click and move the mouse button down Linux/Unix/Windows Mac users

106. Pujol S., Gollub R. National Alliance for Medical Image Computing Create a single tract Click on the V buttons to display the anatomical slices in the Viewer. The 3D window shows a closer view of the tract.

107. Pujol S., Gollub R. National Alliance for Medical Image Computing Create a single tract Position the mouse on different points in the corpus callosum and hit the s key. The tracts that correspond to the visited points appear in the 3D Viewer.

108. Pujol S., Gollub R. National Alliance for Medical Image Computing Generate Multiple Tracts Hold down the s key and move the mouse in the corpus callosum

109. Pujol S., Gollub R. National Alliance for Medical Image Computing Generate Multiple Tracts Multiple tracts are generated for each point visited by the mouse.

110. Pujol S., Gollub R. National Alliance for Medical Image Computing Generate Multiple Tracts The viewer moves away from the model Zoom Out Position the mouse on the images inside the Viewer Right-click and move the mouse up Press the apple button, click and move the mouse button up Linux/Unix/Windows Mac users

111. Pujol S., Gollub R. National Alliance for Medical Image Computing Region of Interest Seeding Slicer has functionalities to generate tracts automatically from a pre-defined Region Of Interest (ROI). In the previous section, we manually segmented the corpus callosum from the Fractional Anisotropy Map. This defines our working region of interest

112. Pujol S., Gollub R. National Alliance for Medical Image Computing ROI Seeding Go back to the DT-MRI module and select Seed in the Tracts Panel

113. Pujol S., Gollub R. National Alliance for Medical Image Computing ROI Seeding Select the ROI Working Click on Seed Tracts Select the color label of the ROI (#2) A warning message appears, Click Yes if you are ready to process the data.

114. Pujol S., Gollub R. National Alliance for Medical Image Computing Corpus Callosum Tracts Slicer displays the fiber tracts of the corpus callosum overlaid on the FA map.

115. Pujol S., Gollub R. National Alliance for Medical Image Computing Corpus Callosum Tracts Click on Spin to visualize the tracts from different angles.

116. Pujol S., Gollub R. National Alliance for Medical Image Computing Corpus Callosum Tracts The fiber tracts overlaid on the FA map start spinning inside the Viewer Panel, providing dynamic visualization.

117. Pujol S., Gollub R. National Alliance for Medical Image Computing Corpus Callosum Tracts For details on the DT-MRI advanced functionalities, including selective seeding and tract clustering, see Slicer 101 Compendium: Slicer Training4:DT-MRI module

118. Pujol S., Gollub R. National Alliance for Medical Image Computing Conclusion Intuitive interface for manual and automatic tracts generation Enhanced visualization of the anatomy by fusion of tracts and DWI images Open-source environment

119. Pujol S., Gollub R. National Alliance for Medical Image Computing Slicer Compendium A series of courses have been developed to facilitate the use of advanced image analysis techniques available into Slicer to clinicians and scientists. Our compendium is available at: http://www.namic.org/Wiki/index.php/Slicer:Workshops: User_Training_101

120. Pujol S., Gollub R. National Alliance for Medical Image Computing Slicer Compendium

121. Pujol S., Gollub R. National Alliance for Medical Image Computing Appendix

122. Pujol S., Gollub R. National Alliance for Medical Image Computing Color By Orientation Click on Display and Select Display Tracts Off

123. Pujol S., Gollub R. National Alliance for Medical Image Computing Color By Orientation Select the DT-MRI module and click on the Tab Scalars. Select ColorByOrientation

124. Pujol S., Gollub R. National Alliance for Medical Image Computing Color By Orientation Browse through the volume to observe the orientation of major fiber bundles

125. Pujol S., Gollub R. National Alliance for Medical Image Computing ROI Drawing Go back to the Editor module in the main Menu. Select the Volumes panel. Select the Original Grayscale FractionalAnisotropy _ D_Tensor Select the Working Labelmap NEW and keep the Default Descriptive Name Working2. Click on Start Editing

126. Pujol S., Gollub R. National Alliance for Medical Image Computing ROI Drawing Select the Effects panel Left click on Draw in the Effects Menu

127. Pujol S., Gollub R. National Alliance for Medical Image Computing ROI Drawing Left-click on Bg and display the Fractional Anisotropy map in background.

128. Pujol S., Gollub R. National Alliance for Medical Image Computing ROI Drawing Left-click on Output, and select the color label #7 (blue-green)

129. Pujol S., Gollub R. National Alliance for Medical Image Computing ROI Drawing Draw the contour of the cingulum with the mouse.

130. Pujol S., Gollub R. National Alliance for Medical Image Computing ROI Seeding Go back to the DT-MRI module and select Seed in the Tracts Panel

131. Pujol S., Gollub R. National Alliance for Medical Image Computing ROI Seeding Select the ROI Working2 Click on Seed Tracts Select the color label of the ROI (#7) A warning message appears, Click Yes if you are ready to process the data.

132. Pujol S., Gollub R. National Alliance for Medical Image Computing Tracts visualization Observe the spatial orientation of fibers tracts in the Corpus Callosum and in the Cingulum